The Evolutionary Biology of Extinct and Extant Organisms [1 ed.] 0128226552, 9780128226551

Table of contents :
Front-Matter_2021_The-Evolutionary-Biology-of-Extinct-and-Extant-Organisms
The Evolutionary Biology of Extinct and Extant Organisms
Copyright_2021_The-Evolutionary-Biology-of-Extinct-and-Extant-Organisms
Copyright
Preface_2021_The-Evolutionary-Biology-of-Extinct-and-Extant-Organisms
Preface
Acknowledgments_2021_The-Evolutionary-Biology-of-Extinct-and-Extant-Organism
Acknowledgments
Introduction--Missing-link--When-an--outmoded-te_2021_The-Evolutionary-Biolo
. Introduction: Missing link: When an “outmoded term” holds “in-between features” between the ancestors and its descendants
Chapter-1---The-transitional-features-of--missin_2021_The-Evolutionary-Biolo
1. The transitional features of “missing link” illuminate the molecular nuts and bolts of biological evolution
Chapter-2---If-and-when-evolution-is-the-ultimate-e_2021_The-Evolutionary-Bi
2. If and when evolution is the ultimate essence of life: what is the evolutionary identity of the missing link (resembling Ar ...
Chapter-3---Walking-with-Cynodont-to-explore-the-_2021_The-Evolutionary-Biol
3. Walking with Cynodont to explore the uncharted evolutionary trail of mammalian lineage diverged out of reptilian
Chapter-4---One-small-step-for-amphibious-fis_2021_The-Evolutionary-Biology-
4. One small step for amphibious fish, one evolutionary leap for moving tetrapods on Earth
Chapter-5---Evolutionary-origin-of-amniotic-egg--_2021_The-Evolutionary-Biol
5. Evolutionary origin of amniotic egg: the transitional form between amphibians and reptiles in the doubt clear session
Chapter-6---When-contemporary-discoveries-pushes-the-_2021_The-Evolutionary-
6. When contemporary discoveries pushes the bony fish to ancestral or evolutionary back seat and discreetly pushes cartilagino ...
Chapter-7---Hemichordates--the-bilaterians-lineage-_2021_The-Evolutionary-Bi
7. Hemichordates: the bilaterians lineage (also known as phylum- Deuterostome) in the evolutionary crossroads of developmental ...
Chapter-8---Cambrian-evolution-of-Onychophorans-_2021_The-Evolutionary-Biolo
8. Cambrian evolution of Onychophorans: in the evolutionary labyrinth of Arthropods, Annelids, and Molluscs
Chapter-9---The-extent-of-Ctenophore-uniqueness-_2021_The-Evolutionary-Biolo
9. The extent of Ctenophore uniqueness—distinctly recognized to be “quasi-Cnidarians” or “stunted Bilaterians”
Chapter-10---The-Protistan-link-in-transition--do_2021_The-Evolutionary-Biol
10. The Protistan link in transition: down the evolutionary trail from unicellular Protozoa to multicellular Metazoa
Chapter-11---Evolutionary-mysticism-of-Euglen_2021_The-Evolutionary-Biology-
11. Evolutionary mysticism of Euglena: a sagacious soul of a plant in the body of an animal
Chapter-12---Virus--a-stepping-stone-in-transition-_2021_The-Evolutionary-Bi
12. Virus: a stepping stone in transition in the course of evolutionary journey from the world of “nonliving” to the world of “ ...
Chapter-13---Once-there-was-an-ancestor-between_2021_The-Evolutionary-Biolog
13. Once there was an ancestor between humans and apes: in the quest for the enigmatic missing link
Chapter-14---Mitochondrial-Eve-and-Y-chromosomal-Ada_2021_The-Evolutionary-B
14. Mitochondrial Eve and Y-chromosomal Adam on planet Earth: Humanity’s metaphoric missing-link between prehistoric past and c ...
Conclusion--Missing-link--In-search-of-our-dista_2021_The-Evolutionary-Biolo
Conclusion: Missing link: In search of our distant cousins footprints, a quest for our evolutionary journey to the past
Conclusion
References_2021_The-Evolutionary-Biology-of-Extinct-and-Extant-Organisms
References
Further reading
Index_2021_The-Evolutionary-Biology-of-Extinct-and-Extant-Organisms
Index
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Citation preview

The Evolutionary Biology of Extinct and Extant Organisms Subir Ranjan Kundu Edited by

Sofia Naznim

Academic Press is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1650, San Diego, CA 92101, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom Copyright © 2021 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein).

Notices

Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-0-12-822655-1 For information on all Academic Press publications visit our website at https://www.elsevier.com/books-and-journals

Publisher: Charlotte Cockle Acquisitions Editor: Anna Valutkevich Editorial Project Manager: Devlin Person Production Project Manager: Maria Bernard Cover Designer: Miles Hitchen Typeset by TNQ Technologies

Preface This book is the creation of a dedicated and determined effort by a single and experienced author on the topic of evolutionary links of living things. It primarily emphasizes the biological evolution of major groups of organisms in the backdrop of a diverse array of hypothetical examples to match with a distinct biological set of evidence that testifies to our understanding of major evolutionary developmental transitions, specifically over the last four decades. This book is an earnest attempt to present the critically reviewed unique progress of biological evolution via the advancement of genomics/molecular footprints that have made significant contributions in the past two decades and continue to play a key role in our better understanding of evolutionary progress in the current environmental scenario. The work of the author will advance our knowledge and provide a source of valuable information. I have no doubt that this is a significant contribution to research in the field that would be of substantial interest and relevance to a large proportion of the readership. I had the opportunity to read the book written by Subir Ranjan Kundu with a great deal of interest. In the first part of the book, the author has critically reviewed and exclusively synthesized data with supporting shreds of evidence on the lack of information and how the recent significant fossil finds have also added greatly to our understanding of several major clades and transitions. At the end of this book, an earnest endeavor has been made to depict the evolutionary journey of microscopic organisms by highlighting the important points as a strong set of evidence, though key occurrences of evolutionary transition are still puzzling. Readers would surely be enthralled to enjoy the remaining chapters in the middle, as those chapters would be equally interesting to hold their attention and walk them through the trail of evolutionary transitions. This book is for all (graduate and postgraduate students, researchers, and inquisitive heterogeneous readers) who are interested in biological evolution, and I do believe that it might serve as a sourcebook for review and for understanding the scientific concepts of biological evolution in transition in a simplified manner for curious learners even from nonscientific communities. The book is written to help clearly understand and access either parts of or much of the whole of evolutionary theory as required by the reader. I hope this book will give us the opportunity to address important knowledge gaps and research. I also believe that it will definitely provide evolutionary biologists with an alternative way to explore and decipher evolutionary mysteries of

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large macroscopic, tiny microscopic, and transitional forms of prehistoric organisms in between with fascinating structural formation by undertaking phylogenomic investigations. Dr. Sundar, S. Scientist S.S.Research Foundation 130/123 Veerappa Puram Street Kallidaikurichi, Tamil Nadu PIN-627416 India Tel: 04634-252369 E-mail: [email protected]

Acknowledgments I express my deep sense of gratitude and indebtedness to Dr. Rafal Kuczewski, Deputy Director, National Park of Wielkopolska, Mosina, Poland; Dr. Mohaned Shebl, Faculty of Agriculture, Suez Canal University, Ismailia, Egypt; Dr. Nikunj Bhatt, Associate Professor in Zoology, VP & RPTP Science College, Gujarat, India; Mr. Bipul Chakrabarty, Director, Tata Steel Zoological Society, Jamshedpur, and Former Scientific Officer, Central Zoo Authority, Ministry of Environment, Forests and Climate Change, and the Government of India for their suggestions and guidance in this present writing. I am especially pleased to acknowledge Dr. Pradipta Kumar Sarangi, Lecturer, Department of Zoology, Indira Gandhi Memorial College, Odisha, India; Mr. Rogier van Rossem, Board of Directors, Projects and Programs Coordinator, King Cobra Conservancy, USA; Mr. Patrick Comins, Executive Director, the Connecticut Audubon Society, Fairfield, USA; and Mr. Anirban Roy, Senior Scientific Officer, SAFE-South Asian Forum for Environment, Kolkata, India, who helped me in drafting the different parts of the manuscript that required reviewing consultations of literature, library consultations, discussions, etc. I am thankful to Susan Zadek and Sung-Min Han, Albert Campbell Library, and Eva Lew, Bloor Gladstone Library, Toronto Public Library Network, Toronto, Canada, for extending library facilities and providing necessary help in locating literature required for this project to be completed. I am also thankful to Ms. Sashi Sinha and Mr. Goutam Saha, freelance graphics artists from Kolkata, India, for preparing the graphical presentation of this book. I express my gratitude and thank all academicians, editors, publishers of books and journals, and colleagues for sharing the printed and digital materials, providing valuable suggestions, tendering necessary clarifications during the past few years, and for selflessly helping me out to complete this task.

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Introduction: Missing link: When an “outmoded term” holds “in-between features” between the ancestors and its descendants Man appears to be the missing link Between anthropoid apes and human beings dKonrad Lorenz

The sudden shouting of my fellow passengers woke me up from my half-asleep state on the day I got stranded in the Hong Kong International Airport, as the flight operations had been put on hold for an indefinite period of time due to the emergency situation immediately after the devastating fallout of the earthquake and the scary aftermath of tsunamis on the Christmas of 2004. I still recognize that natural disaster as the worst, most dreadful experience in my life, as I did not have much choice but to witness an insurmountable human misery and mass losses of human life in the tsunami-affected countries across South and Southeast Asia. When I got stranded in the transit lounge of Hong Kong for almost 17 hours, after traveling from Toronto for more than 15 hours of nonstop flight, I was exhausted due to jet lag. I was anxiously looking for the information about the departure schedule of the connecting flight to Calcutta to meet my ailing father. I did not remember precisely how long I waited in the transit lounge for the connecting flight to reach Calcutta, which was only around a 4-hour flight from Hong Kong. I only remembered that I started my journey in the late afternoon of Christmas 2004, and I reached Calcutta, my parental home, between the end of December 28 and the beginning of December 29, 2004, after an exhausting, prolonged journey and the dreadful episode that was difficult for anyone to ever forget. People from the northern hemisphere would definitely understand how difficult it is to secure an airplane ticket in Europe and North America during Christmas time. Most of the office establishments and travel agencies remained closed, and hardly anyone could get in touch with any friends and acquaintances during this time of the year. Either they are away from their working places or on a planned vacation to spend time with family and friends. On my way back home from my workplace,

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I got a telegram (which is apparently a missing link in the arena of conventional communication in India since 2014 and gradually made obsolete in different parts of North America a little earlier than 2014), which clearly mentioned four words “Father ill, come home,” dated December 24, 2004. After going through the telegraphic message, it seemed to be an impossible task for me to secure a flight ticket on the next day. But I kept on trying with different travel agencies across Toronto and the Greater Toronto area from west-end Kipling to east-end Scarborough to secure a confirmed airplane ticket to see my father, who had suffered from a severe brain hemorrhage. Eventually, one of the travel agents finally informed me of the booking confirmation from Toronto to Calcutta via Hong Kong just 7 hours before traveling, which I considered to be an experience like winning a jackpot after I had gone through an intensive period of anxiousness. I did not know at that time I would face such a difficult moment in my life, full of dreadful memories. After traversing around 7,802 miles from Toronto to Hong Kong in a nonstop 15-and-half-hour flight, I tried to lie on a cozy seat at the Hong Kong Airport to stretch out my legs and arms and wait for connecting flights to Calcutta. As most of the passengers on the flight I traveled with were of Chinese origin, Hong Kong was the final destination for most of them, whereas the rest of the passengers were taking connecting flights to different parts of China or its neighboring countries of East Asia and far East, Singapore, Indonesia, Laos, Japan, Mongolia, etc. I still remember the devastating news I received after getting into the transit lounge, which still gives me goosebumps to this day, that a severe earthquake (a magnitude of around 9.1 on Richter scale) had triggered in the epicenter of Indonesia and extended Sumatra to Andaman in the Indian Ocean region, leading to a series of tsunamis that hit and washed away a vast array of sea-coastal regions of 14 countries around the Indian Ocean. The occurrence of such an unexpected natural disaster created an almost warlike emergency situation, resulting in the cancellation and further delaying of most of the flights that were scheduled to be flown out of the Hong Kong International Airport till the situation became stable for flight operations. Having to wait for an indefinite period of time, I did not have many options and there were only a few things to do. I kept on drinking the same black coffee and helplessly watched the news on the giant-sized LCD screens telecasted by different news channels including BBC, CNN, and ATN and witnessed the worst part of the human loss caused by the cascading effect of natural calamities, the unforgettable earthquake, and series of tsunamis which took around 230,000 lives in 2004. I waited impatiently for the connecting flight and checked the display boards with the arrival and departure schedule of all flights every half hour. As the information desk was closed, the stranded passengers like me kept asking the same questions and vented their frustration to a few airport personnel at the information desk. I remembered that while I waited for the connecting flight I was trying to explore the metaphoric resemblance between me and Viktor Navorski, the main character of the

Introduction: Missing link: When an “outmoded term”

movie The Terminal, who gets stranded in the Terminal 1 of an airport for an indefinite period of time. I still remember the movie vividly, as I watched it when it was released earlier that year. The movie was directed by one of my favorite directors Steven Spielberg, partly inspired by a real-life incident of an Iranian citizen, Mehran Karimi Nasseri, who got stranded in the Terminal 1 of Charle de Gaulle, Paris, France, for 18 years. In reality, my situation was not as bad as in the movie, as I was only stranded for 17 hours. But I realized that on a journey, any biological entity has to be stranded in transit for an indefinite period of time. Like any other accident, the earthquake and tsunamis created a situation where most people would not define their journey as progressing toward their destinations in terms of change of their life journey progress in spatiotemporal scale. As the clock “tick-tocked” and remained working, an apparent movement of the life had remained standstill during the post-tsunami disaster regime. Hence, it is difficult sometimes to narrate this phase of the journey of life in the backdrop of spatiotemporal changes, driven by an unexpected and unleashed vortex of the natural disaster. My journey during Christmas time in 2004 and the experience of being stranded in the transit lounge for connecting link was a metaphoric journey of life experiencing devastation in the middle of desolate, deserted, war-torn battlefields, where the mode of the voluntary journey of life has unexpectedly been changed to the mode of involuntary journey amid the chaotic ambiance of devastation, helplessness, tears, and death. Apparently, the gravity of those natural calamities left me dumbstruck to lie on a chair in the transit lounge where time ticked on through the X-axis, but no spatial movement was found to be in a functional state in the Y- axis, and my fatigued brain could not properly figure out whether I was really waiting for a “connecting link” or if state as a mere instance of “entity with missing link” left me stuck helplessly in the labyrinth of emotional upheaval. However, to elucidate the concept of “missing link” and “connecting link” in real life and to provide a better understanding of its integration to the journey of evolution, let us consider a socioeconomic example, an effort to establish the missing link between two distinct segments in human society: “poor” and “rich” people. According to the contemporary Western concept, money is the missing link between these two socioeconomic segments of society, as money could make our present life wealthy and ensure our prosperous future; this money seems to be the ultimate wealth that could make our life happy. Apparently, it seems that there is a linear relationship between the missing links of “wealth” and “happiness.” Is that kind of relationship found to be linear always in real life? Let us find out whether rich people are always happier than poorer ones or otherwise. From the psychological perspectives, the two famous psychologists Ed Diener and Robert Biswas-Diener (2008) have mentioned in their book entitled Happiness: Unlocking the Mysteries of Psychological Wealth, that “It seems natural to assume

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that the rich people will be happier than others,” further stating that “money is only one part of psychological wealth, so the picture is complicated.” The authors agreed that there is apparently no doubt that rich people and developed nations are happier than poor people and developing nations, but they have contemplated that money as financial capital is not strong or powerful enough to secure happiness. From the psychological perspective, they considered that fulfillment of the prime necessities of life by availability of food, clothing, and dwelling place would make people happy in a way that enhancement of the “disposable income” would hardly impact “the sense of well-being” of the people. As an example, the family income of a fourmember family in Canada can be considered poor in terms of the financial scale if the net annual earnings of that family were $44,266 or less in the financial year of 2018-19. Consequently, a supplementary grant of $6,000 would really bring a sense of happiness among the family members living below the poverty line. On the other hand, the same grant for the family of the same size with a net annual income of $150,000 has little impact on their enhancement of well-being. J.D. Roth (2010), one of the famous financial analysts and eminent economists of North America, has mentioned in his book entitled Your Money: the Missing Manual that the life-changing potential of money is found to be a one-sided story, as the unlimited influx of money to any needy person might be proven to have a substantially negative impact if the concerned person could not maintain a balance between earning and spending or did not maintain a sustainable living between too much wealth and too little wealth. Seemingly, more spending eased our life, as we could achieve our dream of living by spending money. But then, is that true in real life? In a recent personal finance publication, entitled Your Money or Your Life, Vicky Robins and Dominguez (2008) have contemplated that the relationship between a spending spree and happiness is found to be nonlinear. That means that spending money on impulsive buying would make us a little more unhappy than our earlier state and that overspending without setting any well-adapted social goal could drag anyone into the debt-strapped condition and a more unhappy state. To be happy, a sense of freedom needs to be nurtured, which could be ensured by exploring and culminating social values, social relationships, proper utilization of wealth to achieve social goals, and achieving sustainability and development in the socioeconomic arena. The missing link between unhappy and happy people in society is found to be related to the utilization of these abstract forms of values, apparently invisible, which are popularly considered as “social capital.” Hence, the recognition of “financial capital” might be apparently considered a valid currency, the transcending of which from one end to the other would transform social status from poor to rich or vice versa, But the ultimate missing link, “social capital,” rather than “financial capital” needs to be recognized as it has unbound potential in driving the social and socioeconomic evolution in our society.

Introduction: Missing link: When an “outmoded term”

The term “missing link” is a media-friendly term that has frequently been used in contemporary scientific literature (mainly in literature related to physical anthropology) as an effort to build an evolutionary bridge between the lower group of primates and apes and between apes and modern human species. In a number of situations in the scientific world, particularly in the world of biology, this terminology has been used without understanding its deep-rooted ramifications. Technically, the term “missing link” explicates the transitional morphologies or forms of the paleontological evidence discovered, which possess a number of common features that evolutionists and evolutionary biologists would scientifically establish as an evolutionary relationship between the extinct form of organisms and its likelihood-derived living successor, the extant form of the organism. Therefore the missing link shows the possession of a set of features “in transition” of the ancestral organism, evolved with a set of derived traits found in its descendants that are supposedly evolved from those erstwhile predecessors. Apparently, the term “missing link” was not an unusual or unknown term to Charles Darwin, the father of biological evolution, as his mentor, Charles Lyell, used this term in 1851 whenever he had been engaged in paleontological studies, in particular studying transitional fossil specimens to establish evolutionary relationships between extinct and extant. Yet, Darwin had put aside this terminology and did not use it in his work. On November 24, 1859, after the publication of The Origin of Species by Means of Natural Selection, the bible of biological evolution, Charles Darwin was invariably convinced that his monolithic doctrine on biological evolution must be effectively substantiated by the future discoveries of paleontological evidence in transition (i.e., transitional fossil evidence between two distinct forms of species) between small primates and modern human species. But the terminology “missing link” is surprisingly missing from his bible of biological evolution. In 1861, Alfred Wagner discovered a transitional fossil between reptiles and avians, called Archaeopteryx (which means ancient wing), from the limestone deposit of Solnhofen, Germany, which evolved around 150e40 million years ago (MYA) in the Jurassic Period (Howells, 2011). It was quite surprising that such an important observation was missing from Darwin’s work; nevertheless, he received a scientific communication, dated January 3, 1863, from a renowned paleontologist, Hugh Falconer, who studied meticulously the fossil of Archaeopteryx of the Jurassic era, which had composite features of birds and reptiles: possession of feathers, claws, teeth, and bony tails (Black, 2018). When the presence of feathers encouraged a group of scientists to consider Archaeopteryx as a Jurassic bird, the presence of Saurian traits (dinosaurs) made another group of scientists consider it of reptilian origin. Nowadays, the world of science still recognizes “Archaeopteryx” as a “missing link” between birds and dinosaurs, though a detailed molecular investigation needs to be done to substantiate the paleontological evidence. According to Nicholas Pyenson, the current curator of marine mammal fossils, the “Smithsonian

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Museum of Natural History” has argued that most likely Darwin has tried not to use the term “missing link” consciously in his doctrine of evolution, and Nicholas Pyenson has further argued that “Life is a tree, not a chain” (Black, 2018). Technically, it is clear that missing link is the transitional form of the fossilized remnant of any organism that helps to build an evolutionary bridge between a phylogenetically related extinct organism and its extant descendants; for example, Archaeopteryx acts like a missing link between the extinct group of reptiles, the dinosaurs, and the modern-day extant group of birds. From a logical perspective of evolution, there is no difference between missing link and connecting link, as connecting link plays the same cardinal role as a missing link, establishing an evolutionary bridge between the organisms belonging to the two distinct taxonomic groups, which are phylogenetically adjacent to each other. Although both forms of evolutionary bridges have played the same role to elucidate the evolutionary succession of evolutionary tracking from its ancestral form to the contemporary descendants when missing links represent the transitional extinct forms or fossils of any organism, the connecting links are the living ones, sometimes alternately recognized as “living fossils.” For example, the duck-billed platypus or Ornithorhynchus is found to be the transitional living form between reptiles and mammals. Let us review the interpretation of Briana Pobiner, the paleoanthropologist in charge of the “Smithsonian Human Origins Program,” who has defined missing link as: “To me, the idea of a ‘missing link’ implies a template of ‘family chain’, a unidirectional linear chain of one species evolving into another, evolving into another, and so on” (Black, 2018). Briana Pobiner has further clarified that biological evolution does not fit into the stereotypical perception of “missing link,” as she defined biological evolution as a metaphoric “family-tree” that “produces a diverging treelike branch with multiple descendants of an ancestor species existing at the same time, and sometimes even alongside that ancestor species” (Black, 2018). It has further been clarified by paleoanthropologists that the linear chain-like model of evolutionary interpretation has an obsolete perception as evolutionary progress has followed the path of the reticulate pattern of advancement in terms of spatiotemporal divergence and mode of diversification from ancestral lineage to emerge in a derived form after traversing down the long evolutionary trail. This results in the logical emergence of paleontological evidence or fossil evidence that has difficulties being assigned to a certain category or form, which could directly indicate its phylogenetic success, where the emergence of the extant member supposedly descended from its erstwhile ancestor. As a matter of fact, the history of biological evolution has gone through an evolutionary meshwork of a spatiotemporal trail, where the species did not have any other choice but to adapt to the dynamic changes of environment and tune in on its process of diversification and migration to survive in a favorable environment. On its way to the evolutionary journey, a number of species with their ancestral traits have

Introduction: Missing link: When an “outmoded term”

been pushed into extinction by their descendants or have become extinct when they were not flexible enough to cope with a changing environment. So, it is apparently reasonable that the long trail of biological evolution of any organism must have innumerable patches of “missing links,” the unavailability of which poses a serious challenge to paleontologists, evolutionists, and evolutionary biologists who wish to sketch out an undisputed, unanimous blueprint of evolution, without being involved in scientific bickering and counter-bickering of observations, interpretations, and explanations to solve the puzzle of evolution. In this regard, the theoretical perception of the missing link of the eminent paleoanthropologist, John Hawks, at the University of Wisconsin, Madison, USA, needs to be shared. He firmly stated: “Missing link is an outmoded term in biology, which I have to say most of us think it should be forgotten and never used,” and he further said: “On the one hand, it’s a truism we can never recover every individual that contributed genetically to today’s species, so we should expect ‘links’ to be missing. On the other hand, it implies total ignorance, where we usually know quite a lot about transitional forms” (Melina, 2010). In support of further elucidation of the reticulate pattern of evolution, rather than the linear, straight-line one, John Hawks stated: “Probably the most important thing is that most of the fossils we find aren’t actually links” (Melina, 2010). He further stated: “The number of extinct sidebranches is much larger than the number of true genealogical connections in the fossil record, and so when we find a fossil, we don’t assume it’s an ancestor of anything, we interpret it as a sister group of somethings” (Melina, 2010). Ian Tattersall, one of the well-known academic and famous North American paleoanthropologists, and curator of the American Museum of Natural History, New York, USA, is found to be less critical about using the term “missing link” as he believes that the term “missing link” itself is a bewildering terminology in terms of improper interpretation of a biological “term.” In support of his explanation on this particular term, Ian Tattersall stated: “The notion of the ‘missing link’ dates from the early 20th century when it was thought that human ancestors formed a sort of singlechain receding into the remotest past,” and he further stated with firm affirmation: “We now know that the picture was much more complex than that, with a lot of nowextinct species jostling for ecological space and evolutionary success” (Melina, 2010). With respect to its application, there is no technical difference between the terms “missing links” and “connecting links,” and both apparently seem to be two sides of the same coin as they are both used to elucidate the establishments of phylogenetic relationships between two taxonomically or phylogenetically distinct evolutionary groups. There is a clear visual distinction that missing links represent the transitional fossils (without life) on the ancient type, whereas connecting links represent the living fossils (extant entities but possessing erstwhile ancestral traits) that follow the cascade of a life cycle. Perceptually, there is a subtle difference between missing

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links and connecting links: the difference between the Aristotelian interpretation of potentiality and actuality. When paleontologists work together with interdisciplinary scientists to decipher the phylogenetic encryption of extinct forms of paleontological evidence to get closer to its ancients and establish its phylogenetic relationships with its descendants, scientists need to go through a reticulate meshwork of interpolation and extrapolations. In studying the missing link evidence, there was a minor problem that paleontologists and evolutionary biologists often used to face because they would not have the opportunity to study the entire life cycle of the concerned organism (as the fossil is normally found to be available in a particular form of life in a certain point of time of the life cycle of the organism). Sometimes, phylogenetic interpretations that are solely based on paleontological studies would not go above and beyond biased observation and/or interpretation of observation to refer to the missing link as a “metaphoric cousin” of a particular organism, which belonged to an evolutionary group, when it could have been interpreted as “a metaphoric parent” of the concerned organism, or might have been phylogenetically distant in relation. Hence, the phylogenetic interpretation of the missing link seems to be more tenable to interpret when exploring the uncharted territory as well as a “potential”-guided expedition process, where the personal level of observation and interpretation of observation could alter the final inference of the progress of the evolution of any organism. While the connecting link is much more an “actual”driven exploration, where scientists have a chance to study the physiological/ morphological changes of the connecting link (the living fossil) to correlate it to the two phylogenetically distinct, extant, evolutionary groups, the chances of biased observation and interpretations are less likely. The imposition of pseudoscientific acquisition of using the term “missing link” has been stigmatized with random usage or portrayal of an imaginary picture of apes in biology textbooks, which has some visible resemblance to chimpanzees on the one hand and resembles part of some features found predominantly in modern human species on the other hand. Presentation of such a picture a the textbook as a missing link creates a buzz among creationists and antievolutionists who may raise their voice and try to influence students even at secondary level to disbelieve and accept the scientific evolutionary interpretation of origin and evolution of modern human species in the course of time (which took millions of years). However, contemporary elucidation of the history of the origin and evolution of modern human species by anthropologists, paleontologists, evolutionary biologists, and genomicists revealed that the chimpanzee, one of our evolutionary close relatives, diverged out of the ancestral anthropogenic rootstock around 3.6 MYA and we, the modern human species, phylogenetically split out of the hominid rootstock around 6 MYA (Black, 2018). If it is one side of reality that our genome is the “evolutionary holy grail” of our origin and evolution, the other side of the reality of narrating the history of origin and evolution of modern human species would remain incomplete without extensive studies of the vast array of collections of our transitional fossils (comprising fossils

Introduction: Missing link: When an “outmoded term”

of hominoids and hominids), and this prompts us to use the term, which most of us dislike to use, “missing link.” Well, it is not necessary to utter a term that sounds “pseudoscientific” or scientifically incorrect, but there is nothing wrong in accepting reality by referring to it as “transitional form” or “intermediate form.” Without acknowledging the evolutionary importance of those links in transition (whether be recognized as connective links or evolutionary links), any scientific effort to dig out the mystery of origin and evolution of modern human species on Earth would have remained incomplete. Instead of using a controversial term like missing link or connecting link, it is better to consider the entire transitional forms of entity, either extinct or extant as “connective link” as the paleoanthropologists recognized the “transitional form” or “intermediate form” as either extinct or extant entails the “ever-changing continuum” journey of evolution of the biological organisms (those are phylogenetically related) in species level (Black, 2018). And without integrating the existence and its predictive phylogenetic interpretation of the transitional forms of connective links that form bridging the extinct and extant, as well as its gross absence (rather considered as missing) in the story of biological evolution of any specific organism or as a whole, a further narration of the evolutionary biology as well as the progress of life would have been poorly defined or would never be defined ever. It is a matter of fact that in this digital era, there has been tremendous progress in molecular biology and the exorbitant advent of biotechnology has lifted molecular phylogenetics to that level; apparently, it would supposedly elucidate the journey of evolution in this biosphere, specifically in the animal kingdom of Earth. But two plus two does not always equal four in the biological world. In one of his best books in the contemporary literature of popular science, entitled Spying on Whales: The past, present, and future of earth’s most awesome creature, Nick Pyenson clearly stated: “If we only had DNA to go on and no fossil record, we’d still be scratching our head as to where whales come from.” He also clarified in his book that there is immense importance in the transitional fossils collected and studied by different scientists since 1970s in the National Museum of Natural History, Smithsonian Institute, Washington, USA (Black, 2018). A rigorous and time-consuming study on the vast collections of transitional fossils of different species of whale in the Smithsonian Institute by Pyenson helped him to define the transmigration of amphibian whales to the deep oceans around 10 MYA, with the substantial transformation of their hand and leg bones and spines to flippers, paddles, and the undulating tail-end of the shape of the body of fishes, for getting used to in aquatic adaptations (Pyenson, 2018). After intensive research into connective linking evidence, Pyenson shared his evolutionary narration on this largest of aquatic mammals by stating: “Whales don’t look anything like their nearest relatives” (Pyenson, 2018). The academic elucidation of divergent evolution along with the anatomical review of the forelimbs of whales humans bats and cats proved that though they look morphologically different, having a different type of adaptation and occupying distinct niches of this biosphere with the possibility of interbreeding less likely, they

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all diverged from a unique ancestral rootstock (Scoville, 2019). Pyenson (2018) further strongly supported the importance of the studies of “connective links” to decipher the phylogenetic relationship of the whale with other mammals, and stated, “Fossils tell us about these :connections” (Pyenson, 2018). Thus it is a proven fact that “connective links” have played their cardinal role in defining and redefining the evolutionary journey of any organism in particular or biological evolution as a whole of our biosphere. So, it makes more sense to use the term “evo-links” rather than “connective links” to understand and narrate the metaphoric journey of biological evolution transcending from extinct to extant.

CHAPTER

The transitional features of “missing link” illuminate the molecular nuts and bolts of biological evolution

1

“Missing link is an outmoded term in biology, which I have to say most of us think should be forgotten and never used . On the one hand, it’s a truism we can never recover every individual that contributed genetically to today’s species, so we should expect ’links’ to be missing. On the other, it implies total ignorance, where we usually know quite a lot about transitional forms.” -John Hawks.

For a formal lodging a complaint about a missing person to seek help from the missing squad/police station to track them down, it is a quite similar experience that we have gone through in our life who have the dreadful experience, failed to get back/trace out their beloved friends, family, and acquaintances and moved to the nearby police stations to lodge a “missing diary” and the missing investigation has normally started with the name of the missing person’s social identity and a recent photographs that gave an idea about the missing person’s outlook that would help out the missing person’s squad to find out the missing person. We considered someone as missing when that person has mysteriously disappeared. So we do not consider that person as missing one if that person has been reported to visit far away may be other parts of the globe. So the literary meaning of the term “missing link” is a misnomer to some extent. As the fossilization process is a random process most of the living organisms would have gone through the favorable cascade of fossilization to leave their imprint or remnants left behind for the paleontologists so the future generation could have a glimpse of their ancestral lineages through the viewfinder/magic-eye of evolution. But happened in some rare situation whenever the recent photograph of some person has found to be missing then it is a cumbersome process that the investigating agency has to go through as they need to prepare a composite sketch by a portrait artist according to the accessibility of the person’s outlook and that made the task of the police investigators more difficult. So, it is convincible to undertake any identical situation to track down the archaic predecessor of any biological identity, who had supposedly lost in the matrix of the fourth dimension of prehistoric time as the evolutionary biologists and the molecular anthropologists do not have any clue about the outlook of such extinct predecessor of any extant biological entity, which has been disappeared down the trail The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00018-0 Copyright © 2021 Elsevier Inc. All rights reserved.

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of biological evolution. Though it is a convincible analogy to track down a missing person by police personnel and the meticulous effort of a molecular biologist or molecular phylogeneticist to track down the missing link (of any biological entity either extinct or extant) having the key transitional features in between the archaic evolutionary features of the prehistoric predecessors and the derived features of its extant descendants. It just reminds about a popular commercial of globally famous paint in the late 1980s, as it displays a big pair of leaps on massive billboards with bright magenta color lipstick on it with an intriguing caption, of the big font size and sticking out 3-D caption “When you think of color, think of us.” From the phylogenetic exploration perspective of any extant biological entity, the primary objective of any molecular phylogeneticist is to nurture a metaphoric quest when he or she looks for the missing link (that maintain a transitional link between the past and present) of that extant biological entity to get in the process of evolutionary backtracking to identify and establish the true identity of the archaic predecessor of that extant biological entity, supposedly roaming around in our biosphere around few million years ago. It is a matter of fact that successful narration of the history of biological evolution has ultimately got in touch with one or more missing links in the cross-roads or evolutionary transits of past and present when any species has passed through a reticulate labyrinth of the evolutionary trail. In course of its evolutionary journey, a species has to go through a series of adaptation cascades in its environment it belonged to. Eventually, it had gradually been replaced by its descendants, evolved in these processes of evolution, unless it has been pushed into extinction. So, the next concern is how justified it is to acknowledge the term “missing link” or to refer to any biological identity with transitional features in between two terminal ends of the archaic or extinct form Banfield/entity in the past and derived form of entity or extant in the present as most of the time we are not very much aware of the true identity of the concerned organism having transitional features. Technically, the term “missing link” is a phylogenetically outmoded state as the molecular geneticists do not have the potential to resurrect or recover any individual with archaic or ancestral characteristics, but they played a cardinal role in the evolution of newly formed species with derived characteristics. As the metaphoric voyage of evolution usually burnt down the key evolutionary transits of its evolutionary trail, it just stalled the process of going back from its contemporary derived state to its erstwhile ancestral state so, the phylogenetic perspective of the evolutionists have strongly admitted that “links are missing” (Remy, 2010). The review of the scientific literature has ascertained that it is Charles Lyell, one of the famous naturalists and evolutionists in the 18th century, and he was Charles Darwin’s mentor as well and has used this term “Missing Link” for the first time to describe some samples of the fossils. In 1859, when Charles Darwin has published “On the origin of species,” the epic on the biological evolution of species has reportedly used this terminology but most of the people and protagonists of Darwinian doctrine has strongly believed that Darwin had never used it during narrating the principles of natural selection (Black, 2018). Yet, the protagonists of Darwinian

The Evolutionary Biology of Extinct and Extant Organisms

doctrine have contemplated that he might have avoided using this particular term consciously in his book but he was sure that this unique perception of missing like which has silently omitted in Darwin’s literature of biological evolution utilizing natural selection would be very helpful in upholding the paleontological evidence of a species (characterized by the transitional features between the archaic ancestral lineages and its likelihood extant descendants or derived successors) down the trail of the evolutionary journey. In Chapter 10 of the “Origin of Species,” Darwin has discussed the geological evidence that directly or indirectly supports his principle of biological evolution and he admitted at that time that lack of availability of the transitional fossils would be a real challenge for flawless depicting the long journey of biological evolution as he commented, “. we have no right to expect to find in our geological formations, an infinite number of those fine transitional forms . we ought only to look for a few links, some more closely, some more distantly related to each other .. ”(Westmoreland, 2018). The supporters of Darwinian principles of evolution has claimed that just a couple of years after the publication of his “Origin of Species” in January 3, 1863, Darwin had received a letter from Hugh Falconer, his friend and one of the eminent paleoanthropologist, who discovered a piece of paleontological evidence from Solenhofen, Germany, recognized in the name of Archaeopteryx, a unique feathery fossil of a big bird along with the key reptilian features of reptiles like the presence of bony tail, sharp claws and presence of teeth in the mouth cavity and the presence of overlapping characteristics of birds and reptiles of this unique creature in the Jurassic Period (Black, 2018). In his letter of communication, Hugh Falconer did not try to hush up his delight as he said “Had the Solenhofen quarries been commissioned-by august command-to turn out a strange being ‘a la Darwin’ .. it could not have executed the behest more handsomelydthan in Archaeopteryx” (Black, 2018). It has proved the hunch of Darwin about the existence of transitional biological entities that narrowed down the evolutionary bridge between two distinct forms of biological entities like birds and reptiles and it naturally promotes the ideas of the existence of “Missing Links” to narrate the brief history of evolution from its erstwhile archaic, prehistoric beginning of past to its derived contemporary present. The evolutionary biologists have considered that it requires to check some check-boxes of transitional traits possessed by an organism before acknowledged it to be a tantalizing evolutionary link between two well distinct categories of an organism. In this regard, John Hawks, the eminent paleoanthropologists, affiliated to the University of Wisconsin, Macedon, USA has contended that “Probably the most important thing is that most of the fossil we find aren’t actually links” and he has observed furthermore “The number of extinct side branches is much large than the number of true genealogical connections in the fossil record, and so when we find a fossil, we don’t assume it’s an ancestor of anything we interpret it as a sister group of somethings” (Remy, 2010). Briana Pobiner, the Smithsonian Human Origins Program Anthropologist, has acknowledged this part of the evolutionary journey as she said “To me, the idea of a ‘missing link’ implies a linear chain of one species evolving into another, evolving into another, and so on . [evolution] produces a tree-like branching with

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multiple descendants of an ancestor species existing at the same time, and sometimes even alongside that ancestor species” (Black, 2018). The functional analogy of “Missing Link” to a chain-like evolutionary function appears to be like a straightlinear, back-tracking evolutionary liaison maintenance from a theoretical perspective; in reality, the evolutionary functionalities of “missing link” is found to be digressive. The misconception of the linear evolutionary progress of life has typically been moved through the hierarchy from low to high and which has been discarded, rather the scientists have embraced the model like a “branching bush with numerous lineages splitting apart and coexisting simultaneously” (Prothero, 2008). Even we could ascertain the authenticity of the branching bush model and discarding the linear “great chain of being” by citing the contemporary reference on molecular phylogenetics where apes and humans split out of a common phylogenetic stock around 6e7 MYA and both of the lineages have found to be coexisting together instead of following the linear evolutionary model of “great chain of being”; where the ending of the evolutionary journey of apes would supposedly be initiated with beginning of the evolutionary journey of the anatomically modern human species (Prothero, 2008). Even the paleontologists try to do it meticulously, every fossil representative had found to be difficult to be phylogenetically related to the extant organism as the extinct or archaic representative. In his article “Charles Darwin and human evolution,” Tattersall (2009) has tried to promote the idea of links (whether it is missing or not) has a deep-rooted connection to its previous concepts of the “Great Chain of Being” an idea that would like to promote the ideas of the sequential arrangement of the organisms in a hierarchy begin from the lowest level to end up in highest level (from simple to complex form of life). According to Tattersall (2009), Darwin was not in favor of such ideas of “Great Chain of Being.” As human being has been placed in the most advanced evolutionary slot as par the concept of “Great Chain of Being,” it is convincible that this promulgation has found to be quite intriguing to most the members to the scientific communities. The paleontologists and the supporters of this “Great Chain of Being” have contended “Humans view the tree of life from the vantage point of our own tiny twig. We trace the hominid branch back in timeepassing long-lost relatives along the way (our Neanderthal cousins, great Aunt Lucy .)duntil we reach the ancestor linking us with other primates and marvel at how far we have come” (Thanukos, 2009). In the article, entitled “Missing links in the evolution of language,” the author H.S. Terrance (2011) has clearly mentioned that “evolution of language is an intractable problem” when it is assumed that emergence of language has supposedly taken place around 6,000,00 years ago and it had been taken place during the divergence of hominid had supposedly split out of Chimpanzee, the nearest cousin of human species. The scientists have considered it intractable as its antecedent, nonverbal nature of conversation, an intricate human phenomenon, that did not recognize the role played by the evolution of verbal conversation. To recognize the functionality of evolution of conversation, we need to comprehend the behavioral evolutionary transition (from knuckle walking to bipedalism) of divergence of hominids out of the ancestral lineage of hominoids. The anthropologists and

The Evolutionary Biology of Extinct and Extant Organisms

evolutionary biologists have contemplated that the emergence of bipedalism has taken place as a result of the reduction in the size of the pelvis, along with the reduction in the size of the birth canal; as the reduced sized birth canal would not accommodate an infant having a carinal cavity of the less than 1000 cc (Terrace, 2011). So, it is convincible that why the size of the infant of the anatomically modern human species born with a considerably smaller brain and skeletal system than their counterparts of nonhuman/apes primates. The primatologists have also noticed that human infant requires a longer period to be inside mother’s body before it was born than their counterparts (i.e., the offsprings of apes) born out of apes/nonhuman primates (Terrace, 2011). Naturally, human infants have got a better chance to spent “face-to-face” contacts and direct eye contacts, which rendered them to be better attribution of nonverbal communication. So the neuroscientists and primatologists have hypothesized that such interactions have rendered the infant to be better perceived with nonverbal communication for getting better opportunities to understand the mindset of their mother. Hence, it has also been perceived by the scientists that such better opportunity for nonverbal communication and another advanced level of behavioral traits (like the advanced level of cognitive aptitude), the better orientation of brain cells (that induced the human infants to think and communicate better way), advanced level of anatomical traits (like the development of vocal cords, tongue, glottis, epiglottis, presence of pinna, eardrum, etc.) would render the human infants to be capable in effective verbal communications, the divergence of language has been evolved from such evolutionary advancement of hominids in course of time. In a meticulous research publication, Douglas M. Banda, the renowned postdoctoral research fellow and a group of researchers from the University of California Davis, University of California Berkeley, and Lawrence Berkeley National Laboratory have shared their discoveries on the missing link of a biomolecule and plant enzyme, called Rubisco, that helped to trace back the evolutionary history of photosynthesis and carbon fixation, the molecular nature of the missing link, evolved around 2.4 MYA (Banda et al., 2020). Rubisco, the ancient carbon-fixing enzyme, is one of the prevalent enzyme natural enzymes found to be possessed by some green and a diverse group of photosynthesizing plants, cyanobacteria, or blue-green algae. Regarding the defining the functionalities of this prevalent, ancient nature of enzyme on earth, Doug Banda, the postdoctoral research fellow in the department of plant biology in the University of California, Davis, one of the key researchers in the team of Patrick Shih, the assistant Professor of this department of UC Davis, has said “it’s the primary driver for producing food, so it can take CO2 from the atmosphere and fix that onto sugar for plants and other photosynthetic organisms to use. It’s the primary driving enzyme for feeding carbon into the life that way” (Banda et al., 2020). The molecular biologists and evolutionary biologists have observed that “I rubisco” has most likely to be evolved over 2.4 BYA. Before the “Great Oxygenation” event, supposedly at the time of Cyanobacteria started generating oxygen employing photosynthesis (Banda et al., 2020). A diverse array of rubisco (some of them are devoid of small subunits) is traced out in a diverse group of

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microorganisms recognized as Archaea. Hence, its role at the beginning of the evolutionary journey of life has drawn the attention of scientists. The molecular geneticists and genomicists have been able to successfully sequence rubisco genes and synthesize the “form I-prime rubisco,” in the laboratory environment. The structural alterations of “form I-prime rubisco” to the formation of “form I-rubisco” would give an insight into its functional role of this enzyme that changed the planet’s biosphere from oxygen-deficient ambiance to the oxygen-rich ambiance as it played a key role in the fixation of atmospheric carbon on earth (Banda et al., 2020). Dr. Patric Shih of UC Davis has tried to give an idea about the functional footprint of “form I-rubisco,” the small, biomolecular, missing link on the earth as he said, “Something intrinsic to understanding how to form I Rubisco evolved is knowing how the small subunit evolved . it’s the only form of rubisco, that we know of, that makes this kind of octameric assembly of large submits” (Banda et al., 2020). Professor Jill Banfield, of the department of planetary science, UC Berkley one of the key members of the research team of Banda, who had expertise in metagenomics analysis on the groundwater samples of rubisco has examined the genes and genetic sequence of the rubisco, without culturing the microbes producing it and he said: “We know almost nothing about what sort of microbial life exists in the world around us, and so the vast majority of diversity has been invisible” (Banda et al., 2020). Banda and his research colleagues have been found to be successful in coordinating gene expression of Form I-prime Rubisco and studied further its molecular configuration that has been examined in the laboratory condition, extracted from Escherichia coli. The molecular biologists have observed that form I rubisco has been built from eight large subunits with eight small subunits perched top and bottom and form I-prime rubisco has been built from the eight large subunits of form I rubisco and each unit is important for photosynthesis and carbon fixation (fixing atmospheric inorganic carbon to plant biomass). Regarding the evolutionary origin and functional aspects of the octameric rubisco, Banda had wondered “The discovery of octameric rubisco that forms without small subunits allows us to ask evolutionary questions about what life would’ve looked like without the functionality imparted by small subunits . specifically, we found form I-prime enzymes had to evolve fortified interactions in the absence of small subunits, which enabled structural stability in a time when Earth’s atmosphere was rapidly changing” (Banda et al., 2020). From a biotechnological perspective, digging out of the evolutionary history and mode of function of such molecular missing link like “form I-rubisco” has inspired the molecular biologists to understand the biomolecular identity of the natural enzymes those evolved around billions of years ago and understanding of its functional potential in better photosynthesizing capability in better production of crops, etc. However, as a phrase, “missing link” is not a favored one to the paleontologists as they felt that uttering this terminology would not help to depict the true functionality of the evolutionary changes. Nicholas Pyenson, the curator of the Section of fossil marine mammals at Smithsonian National Museum of Natural History, USA, has echoed the contemporary perception of the major part of the paleontologists as

The Evolutionary Biology of Extinct and Extant Organisms

he said “Life is a tree, not a chain” (Black, 2018). However, the majority of the paleontologists have preferred to use the term “intermediate form” or “transitional form” instead of “missing link” as the biological concept of species promotes not to recognize the species as an end product of an evolutionary journey that supposed to have a stable status (from taxonomic perspective, the species has been recognized as a ranked hierarchy where the newer and recent ones come to occupy the slot of old ones by pushing them to the backseat), rather it acknowledged it as a “part-of everchanging continuum” (Black, 2018). In support of her observation about the proper consideration of using the phrase “missing link,” Briana Pobiner further said “In some sense, every species is a transitional form from its ancestor because it retains many ancestral traits to be a separate species . paleontologists often use this the term when talking about larger anatomical or ecological shifts that occurred the history of life” (Black, 2018). So, as terminology, “missing link” has a literary analogy with a language interpreter, where interpersonal efficiency/skill of that interpreter helps to interpret or translate a word or sentence or content convincible from one language to another language. So, flawless, feasible interfacing of two unique contents to stream in or presenting in a unique convincible way or translating or interpreting the potential of an interpreter depends upon the reach vocabulary and choice of correct words. Often, the essence of translation or interpretation of any content lost in translation due to choosing improper words of that interpreter that often end-up introducing the “evolutionary cousin” as “evolutionary ancestor” utilizing unwanted mistakes (Black, 2018). So, it rendered Charles Darwin to express his skepticism about consciously using this phrase in defining evolutionary back-tracking the phylogenetic relationship between the ancestors and their likelihood descendants (as the branching out of the descendants happens in so fast pace and overlapping manner, that made it difficult to keep track the complete fossil histories to make the evolutionary functions convincible for a particular group of an organism) as he said “I look at the natural geological record . as a history of the world imperfectly kept . [the literature on the history of evolution] Of this volume only here and there a short chapter has home been preserved; and of each page, only here and there are few lines” (Black, 2018). Yet, Darwin spent two chapters of his maiden publication and apologized for the fossil records to backtrack the phylogenetic relations of the descendants to its ancestral lineages but he was sure that his predictions would support his evolutionary doctrine in the future. Most often the antievolution or procreationist groups have tried to establish an alternative meaning of the phrase “missing link” as they have claimed that missing links are grossly missing information that desperately denies the functionalities of biological evolution. At the initial stage, Darwin was not so comfortable with the unavailability of transitional fossils as he was contemplated to refer the intermediate morphological and anatomical features to stretch out the dotted phylogenetic linkages between two distinct groups of organisms. These transitional fossils are considered to be “missing links” in the “great chain of being” from lowly corals through higher organisms such as birds and mammals to humans (and ultimately to God) (Prothero, 2008). The molecular phylogeneticists have argued that as the phrase “missing link” is confusing as they argued that any

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transitional form does not need to be a linking entity exactly halfway between two distinct groups of organisms rather keep a book-keeping record that the evolutionary changes an evolutionary lineage went through during its phylogenetic split from another or archaic lineage. So an extrapolation of such a missing link analogy between two distinct forms of evolutionary entities has not necessarily to be the fossil specimen, it might be identified as a living extant lineage with transitional features (Prothero, 2008). About this perception, scientists have tendered the example of the existence of corals and sponges instead of being vanished from the Earth, whereas the advanced, derived group of organisms like worms have split out of this simple, extant group of organisms around 600 MYA (Prothero, 2008). Since the maiden publication of Darwin’s “On the Origin of Species” in 1859, the concepts of evolution have been started changing with the enhanced level of interactive bits of knowledge of paleontological data, geological and biological info. Since the days of maiden advocation of the Darwinian doctrine of biological evolution, the explanation of the evolutionary principles and the evolutionary continuity of any biological organism has heavily relied on the availability of fossil records, the examination and classification of such available fossil records have found to be related to the ideas of “missing links.” From the perspective of taxonomic classification, the transitional entities, as well as the missing links, have broadly been categorized in two hierarchies: either in the infraspecies-species or at the supraspecies level. The taxonomists have a deal with all transitions in and among the different groups of metazoans and metaphytes have carefully been made according to the available “evidence of origins of groups in the fossil record” (Olson, 1981). The evolutionists have contended that the “problem of existence of linkages and phylogenies at the species and generic level has been much reduced during the last one hundred and twenty years” and such a drastic level of changes had influenced the changes of evolutionary theories by altering the level of knowledge and interpretation of the brief history of the evolution of life on Earth. Such altered (mainly reduced level) level of interpretation of palaeontological evidence is referred by different groups of evolutionists either to upheld or deny the Darwinian principle of “phyletic gradualism.” The scientists have observed that at the suprafamilial and higher level, an effort of establishing the links between different categories was found not to be so successful, and such a negative trend prevails in suprafamilial ranks (Olson, 1981). However, it has also been observed that the transitional links (either morphological or fossil records) between the hierarchy of classes and subclasses have found to be existing to some extent but it is missing in the phyla and above categories. The scientists have contended that mega-evolutionary change is a controversial matter that requires an orientation to be familiar with critical, unique perceptions and understanding to comprehend the challenging conceptions and grasping abstract evidence. The “missing link” arguments have considered being such an abstract form of challenge that fosters the critical thinking of the disciples standing behind the Darwinian doctrine of biological evolution, engaged in reviewing the

The Evolutionary Biology of Extinct and Extant Organisms

principles of evolutionary biology. In this point, the weakness of the perceptional comprehension of the phrase “missing link” has fostered a wide-open rift between the creationists and evolutionists as the creationists have primarily armored with the key impediment, lack of availability of enough “transitional fossils” that rendered the ultimate weakness of the functionality of evolutionary progress as it has been argued (Westmoreland, 2018): a. The journey of evolution has gone through an intermittent lineage of organisms, initiated from the first living cell of life on earth, and exists to the diverse array of life. b. The lack of availability of a diverse array of transitional fossils would be failed to support continuous lineage. So the creationists have tried to make an oversimplified observation that fossil evidence has hardly supported the functional progress of biological evolution. Hence, straight-forward oversimplified arguments have been made by the creationists when it said “the geologic record should . be riddled with thousands of transitional forms that show a slow and gradual progression, as well as the many dead ends in the evolutionary story. The absence of these transitional forms and the abrupt appearance of any complex life forms is evidence that these groups were created by God and then later buried in the global Flood of Noah’s day” (Patterson, 2006). If we would initiate a logical counter-argument, how logical it would be to consider that the main weakness of the “missing link” argument lies in the available, incomplete record of the fossil histories between two distinct categories of an organism as the availability of the fossil records depends upon the proper execution of fossilization process that involves the presence of hard (e.g., calcified) tissues, the right temperature, congenial level of sedimentation, length of time that the specimen stayed over in that fossil site that would be enough to complete the process, etc. (Scott, 2005; Prothero, 2007). So the availability of fossils depends on some composite factors that would influence its completion of the fossilization process when an organism has gone through the cascade of this complicated process. Hence, a few organisms would have gone through this process of fossilization with the distinct, untampered parts of the body preserved as fossils. So the evolutionary biologists would not expect that most of the “intervening steps of an evolutionary transition (e.g., from ancestral arthropod to modern butterfly) would not likely be captured in fossil evidence (Thanukos, 2008). Even the scientists have noticed that as long as the diversity of plants and fossils are concerned, there are around 1.5 million plants and animals found to report on Earth but the availability of the fossils found to be around 250,000 (which is around 15% or lesser in reality) (Prothero and Singer, 1999). So, if the observation of the creationists were found to be justified about the availability of the fossil species that supposedly represent the extant biological entities, then each extant species should have a fossil record but that is not a matter of fact. Everything, the paleontologists know about geological processes and biological interactions that indicate that the expectation of depicting a brief history of life on

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earth would never be deciphered from the fossil records as the availability of the fossil record is mainly incomplete that would not highlight any consistent evolutionary history. If a plenty number of transitional fossils were available to paleontologists and evolutionary scientists, then it would help them to shed light on the evolutionary history of some phylogenetic lineages. But the lack of availability of such transitional fossils would not ascertain that those lineages did never evolve likewise in the same way if we look at the sky at night time we would not say that the sun did not exist. However, the paleontologists are found to be interested in major transitions in tracking down the history of life and they prefer to use the term “transitional feature” to “missing link” for some technical reasons: a. Are the “missing links” are missing in action, possibly not. b. The different features of a derived organism may have evolved more than one time in the backdrop of a wide geological timescale in the evolutionary life history of that organism. The term “missing link” refers to a fossil under consideration that represents an ancestral lineage of the contemporary descendant, particularly refers to a genealogical chain of a link between ancestor and its descendant. It is a matter of fact that paleontologists study the evolutionary transitions mostly represents the close allies of the concerned ancestors, not the ancestors themselves (Thanukos, 2009). The paleontologist has observed that direct exploration of the ancestors is found to be almost impossible mainly due to the incomplete process of fossilization and the random process of extinction in the biological world. Scientists have observed that around 99 of the species, lived on the Earth, have been pushed into extinction so the fossils have been discovered by scientists from time to time representing the short evolutionary lineages. However, the ancient relatives are considered to be very important to evolutionary science as mostly they display the identical transitional features that the ancestors have supposedly possessed once. So, all these transitional stepping stones elucidate the evolutionary journey that had gone through the crossroads of the long evolutionary trail extended from a few thousand to a few million years. Naturally, the functional aspects of those newly acquired traits, their emergence among descendants, and their mode of functions have been elucidated by the paleontologists. The maiden discovery of a 375 MYA old archaic paleontological evidence of a fish referred to as “large Shallow-water fish” alias Tiktaalik roseae has been reported from Ellesmere island of Canadian Arctic on April 6, 2006 in the renowned journal “Nature” and the elder members of the aboriginal communities at Nunavut in the North West Territories of Canada have chosen to suggest the name “Tikataalikis” (Daeschler et al., 2006). The most intriguing features of this transitional fossiliferous archaic fish are that it has shared part of the ancestral features of fishes (like the presence of fins, gills, scales, and archaic jaw) and part of the features of the land-dwelling tetrapods (the animals have four legs, stiffy scales, stout skeletons, functional wrist, etc.), its discovery has jokingly been cracked by its discoverers as “fishapod” (Shipman, 2006). Farish Jenkins Jr., one of the members of the

The Evolutionary Biology of Extinct and Extant Organisms

discoverer of Tiktaalik, has observed that the front fins of this “fishapod” have surprisingly evolved with a couple of sturdy locomotory organ of this creature that supposedly helps this creature to move in shallow water habitat or the land with low elevation. In this regard, the paleontologists have referred that in the evolutionary history of transmigration of tetrapods from water to land it involved the accumulation of many adaptive features encompassing from adaptive changes of locomotory organs to adaptive change of sense organs to adaptive changes of breathing organs to reproductive adaptations and production of a big number of populations in the newly acquired, dry terrestrial habitat, etc. (Thanukos, 2009). Ted Daeschler of the Academy of Natural Sciences, one of the members of its discovery team has rejoiced with comments “We were surprised at the features of the specimens . That is one of the beauties of this material. We knew the endpointsdfish at the beginning and tetrapods at the end ebut we could not have predicted the sequence in which those anatomical changes occurred” (Shipman, 2006). The change in habitat from water to land for any animal whose ancestors lived in aquatic habitat and its descendants managed to survive in the terrestrial habitat supposedly gone through a series of structural in the course of adaptive changes like the appearance of stout limbs found to be in its terrestrial descendants in the place of its flexible fins, possessed by its ancestral members. Usually, the big-sized predatory fishes (4e9 feet long) caught the aquatic prey in the water and passed the extra water through its gills so the identical mechanism has been assumed for this archaic fish Tiktaalik but lack of presence of the gill cover and long crocodile-like snout has indicated its change of food habit from aquatic food resources to terrestrial insects along with a tentative adaptation like the possibility of having lungs instead of gills (Shipman, 2006). So, Tiktaalik is an ideal example of microevolutionary changes as it shows how did the adaptive transition take place in parallel to the transmigration of any organism from water to land. As land and water is an oversimplistic dichotomy for any ecosystems as there are some transitional habitats between these two extremes like water-flooded plains, bogs, dry wetlands, plant-chocked streams, etc. that an organism requires a diverse range of adaptations to ensure its survival in those ecosystems. So the evolutionists have contended that the transitional fossil of Tiktaalik ascertained: that the transition was not an “all-or-nothing affair” (Shipman, 2006). The Tiktaalik’s discovery has exposed the transitional adaptive changes from water to land and at the same time, the revere transitional adaptive changes from land to water has been evidenced during the discovery of fossil whales specifically with the discovery of Pakicetus, a 50 million-year-old animal with whale-like teeth and skull but without deep-diving potential and underwater hearing potential, proved that Pakicetus have surviving potential in both shallow and deep water aquatic environment (Shipman, 2006). The fossiliferous pelvis of Pakicetus has shown typical aquatic adaptations but its limbs and feet had been adapted typically for aquatic or terrestrial habitat we do not know. Whereas the evolutionists have noticed that Rodhocetus had been found to be well adapted in an aquatic habitat, as its hind feet were adapted for swimming but its ankles and front feet with hooves had structural similarity with terrestrial animals. So whatever it is both transitions either. Tiktaalik, either moved

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from water to land or from land to water whatever it was being occurred in a “mosaic fashion” that rendered Tiktaalik to be adapted in a diverse range of habitat between land and water to be believed. The evolutionary scientists observed that around 45 MYA, the fossil whale Dorudon’s front legs had been modified to flippers, the hind legs were vestigial in nature and the powerful tail had been used for footpropelled swimming. However, these three species: Pakicetus, Rodhocetus, and Dorudon had been referred by the evolutionary biologists to be cited as the archaic land species that evolved to be settled in water in course of transmigration from land to the waterbodies. However, successful exploration of any missing link is considered to be a lifetime experience for any ambitious paleoanthropologist though it’s a matter of luck but hard work and travel to remote corners of the world. If exploration of missing link involves the celebration of joy as one link would have been found but it also involves the creation of two more new links the first ones are supposed to be the recognition of “immediate ancestor” and the next one would have been recognized as “immediate descendant” of the newly recognized missing link. The fossils are solid paleontological evidence that we could see and feel in our hand so it is not like an abstract form of evidence that would be considered as unobservable, transitional life forms. So meticulous study of any paleontologists on any fossil specimen the anatomical and morphological characteristics would be studied and a lucid observation could be made on its evolutionary adaptations. The meticulous narratives on the evolutionary adaptations on Tiktaalik, the archaic, prehistoric fish debrief a brief story of mosaic changes of “Peacemeal adaptation” to its diverse range of transitional niches on its pilgrimage of transmigration from water to land (Shipman, 2006). Although the creationists and the supporters of the intellectual designs have criticized such observation of the evolutionists and the observation of the supporter of the intellectual designs, Stephen Meyer, the director of the Center for Science and culture of the Discovery Institute, commented “the transitional life forms that ostensibly occupy the nodes of Darwin’s branching tree of life are unobservable . ” (Shipman, 2006). There is a colloquial saying that a swallow does not make a summer, likewise the isolated story of an exploration of a “missing link” would not present the successful completion of an evolutionary journey of life, that would go through the nodes of adaptive changes. Rather, the evolutionists have contended “It joins myriad other ‘founder links’ that document transitions from one type of creature to another or from one habit to another. Together these found links form a stony edifice in support of evolutionary theory” (Shipman, 2006). Recently, Robert Root-Bernstein, Department of Physiology, Michigan State University along with Meredith Root-Bernstein the eminent molecular biologists have tried to recognize “The ribosome as a missing link in prebiotic evolution III” as they have proposed that ribosomal RNA (rRNA) has supposedly formed the basis of maiden cellular genomes, evidenced from the review of the literature and proteogenomic investigations (Root-Bernstien and Root-Bernstein, 2019). In their studies, the scientists’ duo has contemplated Ribosome as the maiden, vestigial, selfreplicating, biomolecular missing link of life, where rRNA (ribosomal RNA) has

The Evolutionary Biology of Extinct and Extant Organisms

acted as an early form of genes, that has been transcribed in mRNA (messenger RNA) and encoded by mRNAs; in the last lap of it tRNAs (transfer RNAs) carried out translation of ribosomal proteins. Being self-replicating bodies, rRNAs have managed their replication, encoded by the polymerase. In their experimental model, Root-Bernstein and Root-Bernstein (2019) have hypothesized with the “ribosomefirst” theory, where they have considered the ribosomal genome has laid the basis of a maiden cellular genome or first cellular, self-replicating body in a cellular matrix. The molecular biologists have contended that rRNA, tRNA, and ribosomal proteins in a cellular entity have made up most of the macromolecules in most of the living, macrocellular organisms (According to the “ribosome first” theory), the contemporary genome among the descendant entities, there supposed to be a huge reserve of t-RNA and rRNA modules, procured from the reading frames of sense and antisense RNA so it supposedly encodes a diverse array of ribosomal and nonribosomal proteins responsible for major cellular functions (Oritz et al., 2006; Scott et al., 2010). Hence, the scientists have considered that regular or surged levels of synthesis of ribosomal proteins should be considered in the structural and functional evolution of cellular entity and that would supposedly justify the alleviated-level of ribosomal functions. The theoretical considerations of this “ribosomal first” hypothesis, promulgated by Root-Bernstein and Bernstein (2018) have primarily been supported by the literature review. By analyzing the higher frequencies of mRNA duplications (beyond the level of predictions) in course of ribosomal protein synthesis, scientists have come to the functional efficacy of the “ribosome first” hypothesis triggered the structural and functional evolutionary diversification of cellular entities. The molecular biologists have observed that the origins and evolution of life have broadly been categorized under three hypothesis (Bowman et al., 2015; RootBernstein and Root-Bernstein, 2015): a. RNA or genome first theories: According to the RNA or genome first theory, the ribosome appeared to be a late addition of a functional, preexisting genome, which evolved out of RNA or RNAeDNA world. So, the preexisting genome formed the basis of the cellular genome that initiated the early version of protein metabolism, and the genes possessed by ribosomes likely to carry out the genomic functions. The molecular biologists have contemplated that the evolution of extraribosomal functions of tRNA, rRNA, and ribosomal proteins have hardly been taken place as rRNAs do not contain any gene of its own. The scientists have contemplated that random evolution of genetic sequences is the basis for the formation of the erstwhile genome followed by a selection of basic functionality from the selection of diversity of genetic sequences. b. Protein or metabolism first theories: According to this hypothesis, protein has supposedly evolved before the formation of genome or ribosome, with preadapted proteinaceous substances followed by the formation of the genome with encoding potential of these proteins employing RNA or DNA genes. The scientists have contemplated that ribosome has played an inconsequent role in

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protein translation mechanism so rRNA does not have to possess any genetic information of its own. It has further been construed that rRNA and ribosomal proteins have hardly evolved any extrachromosomal functions. However, predominance of protein-encoding genes has been found in this genome throughout. c. Coevolution theories: According to this theory, the ribosome is the first selfreplicating organism and considered to be the first genome in which protein, genome, and metabolism occur at the same time. Hence, the evolution of the metabolism of proteins and the emergence of the core genome supposedly evolved before the emergence of cellular entities. According to the observation of several molecular biologists, “Ribosome first” theory of cellular evolution is a version of coevolution theory where it promotes RNA genome encoding that rendered functional ribosome to carry out ribosomal protein synthesis like replication, transcription, and translation (Root-Bernstein and Root-Bernstein, 2015). According to this theory, the ribosome-like genes are over dominated in cellular genomes, and rRNA, tRNA, and ribosomal proteins are pleiofunctional. Furthermore, the scientists have contemplated the overdominance of the macromolecules like tRNA, mRNA and ribosomal proteins in the rest of the genome and its removal from rRNA based genome during ribosomal proteins/enzymes (including polymerases, ligases, amino acid transferases, phosphatases, etc.) translation would validate the “ribosome first” hypothesis as well as indicating that evolution of ribosome has taken place as a self-replicating body, supposedly rendered evolution of cellular organisms. Root-Bernstein and Root-Bernstein (2015, 2016) have contended that rRNA encodes two sets of tRNAs to translate its sequence to its unique ribosomal proteins/enzymes; occasionally rRNAs retained the function of mRNAs, encoding proteins, translated in modern organisms. It has also been observed that modern ribosome-binding proteins, autologously regulating its synthesis by binding its mRNA. So the scientists have advocated the attribution of the autologous control of the evolution of ribosome as a self-replicating network, that does not admit ribosomal function as a “specialized molecular machine” to promote “RNA World hypothesis” as it recognized ribosome as a vestigial organelle of a prebiotic self-replicating cellular entity, most likely appeared to be a primitive nature of the cell, containing few genes and limited potential of metabolism (Root-Bernstein and Root-Bernstein, 2015). In a series of meticulous experiments, Mauro and Edelman (1997) have observed that a diverse array of mRNA sequences are there in a large number of cellular, eukaryotic genomes as they have contended “Many eukaryotic mRNAs contain sequences that resemble segments of 28S and 18S rRNAs, and these rRNA-like sequences are present in both the sense and antisense orientations. Some are similar to highly conserved regions of the rRNAs, whereas others have sequence similarities to expansion segments. In particular, four 18S rRNA-like sequences are found in several hundred different genes, and the location of these four sequences within

The Evolutionary Biology of Extinct and Extant Organisms

the various genes is not random. One of these rRNA-like sequences are preferentially located within protein-coding regions immediately upstream of the termination codon of a number of genes . We consider the hypotheses that rRNA-like sequences may have spread throughout eukaryotic genomes and that their presence in primary transcripts may differentially affect gene expression.” From intensive genome-wide sequencing investigation, the molecular biologists have observed that the complementary gene sequences to RNA genes have found to be large numbers in cellular genomes, those are supposedly incorporating transcription products of rRNA in the cellular genomes. There are a number of examples include the complementary sequence of ferritin H mRNA and 28s ribosomal RNA (Jain et al., 1985); between eukaryotic 28s ribosomal RNA (Dooley et al., 1992) and avian myeloblastosis oncogene and between a wide range of mRNAs and murine 18s rRNA (Matveena and Shabalina, 1993). The molecular geneticists have strongly affirmed that such occurrence of complementary sequences is unlikely to comply with either “genome-first,” or “metabolism first” or “cellular evolution” hypothesis but it has found to be in total compliance of “ribosome efirst theory” in which all of the six reading frames are found to be utilized for encoding entire ribosomal and extraribosomal protein sequences (Root-Bernstein and Root-Bernstein, 2019). The contemporary works of molecular geneticists and genomicists on the genome biology of prokaryotes and eukaryotes have noticed that a fairly large number of rRNA sequences have been transcribed into polyadenylated mRNAs and eventually translated into functional proteins and it has also been observed that rRNAs and tRNAs like transposons (jumping genes) have occupied a large segment of genomes, that might trigger a transitional mechanism of structural and functional optimization of ribosome-related genes, got functionally ready to be part of cellular genomes (Root-Bernstein and Root-Bernstein, 2019). Furthermore, the scientists have observed that rRNAs and tRNAs and their breakaway parts have given functional proxy of extraribosomal entities and regulate the activity of transcription and translation, act as mRNAs to coordinate cell signaling functions and carry out the synthesis of nonribosomal proteins. The scientist has also noticed that almost all ribosomal proteins have carried out a range of extraribosomal actions ranging from autologous regulation of their mRNAs (by adhering to them); regulating the extent of replication, transcription, translation; taking part in polyphosphate synthesis and metabolism and regulating a chain of enzymatic functions, ranging from energy metabolism, RNA editing to the synthesis of amino acids. Hence, the molecular biologist has contemplated further that their “ribosomal-first theory of cellular evolution has indicated that ribosome-related molecules are found to be most proactive biomolecules to carry out the cellular functions flawlessly. The meticulous investigations on the genome biology of E.coli by Root-Bernstein and Root-Bernstein (2019) have ascertained that the genome of E. coli has substantially constituted with the fairly large volume of rRNA sequences and it indicated that the genomes of E. coli have likely to be emerged either from random sequences of RNA or directly diverged from protein-encoding genes. The meticulous investigations of

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Root-Bernstein and Root-Bernstein (2019) have ascertained further than 100 orthologous genes, those are conserved among a diverse range of species, forming the “Universal Gene Set of Life” or UGSL are ribosome-related genes (Harris et al., 2003; Koonin, 2003; Charlebois and Doolitle, 2004). To review the validity of the “genome first theory”, the genomicists and the molecular geneticists have observed that translation is integrated to cellular functions after an RNA-world has evolved autonomously, independent of protein-world interaction and it does not fit to the multiple ribosomal molecule function. The scientists have tried to predict that if the evolution of ribosomes took place separately either from RNA or DNA-based genetic world, then ribosomal genes would have little functions none but encoding rRNA, which is a lack of any genetic information. The consideration of the validity of “metabolism first theory” integrated to the evolution of the cell, that would likely be rendered little confusion as rRNAs, tRNAs, and ribosomal proteins, evolved separately for nontranslational functions and leading to an inherent contradiction that the evolution of cellular life took place without production of proteins need to make it happen in reality. So, the “metabolism first” theory has promoted the predictions of the emergence of ribosomal proteins would be involved in nonribosomal functions but the divergence of the ribosome in the first place has marred the “metabolism first” theory over the “gene model” and the experimental evidence, referred by Root-Bernstein and Root-Bernstein (2019) have further ascertained that the “protein-first model of genome evolution” is considered to be substantially better than the theory of “random origin of genome sequences.” The molecular geneticists and evolutionary biologists have contemplated that “ribosome first theory” has unique constancy to define the prebiotic evolution of an RNAprotein world hypothesis (Liberman and Wedekind, 2011; Brandman et al., 2012; Altman, 2013; Bowman et al., 2015; Wong et al., 2016) by a thematic amalgamation of “RNA World” hypothesis (Steitz and Moore, 2003; Cech, 2012; Carter, 2015) and “protein World” hypothesis (Ikehara, 2014; Sharov, 2016) and it has in compliance with the coevolution of genetic information and translation function from outset. The “ribosome-first theory” has found to comply with several studies on molecular taxonomic analysis as it recognizes that the origin of all functional ribosomes happens before the divergence of LUCA (Last Universal Common Ancestor) so it is supposed to have emerged before the inception of cellular life on Earth (Lecompte et al., 2002; Fox, 2010; Kovak et al., 2017). However, it rendered the molecular biologists to construe that if the inception of any cellular entity happened on Earth in the conjecture with preexisting ribosomal entities, the cellular entity would have been endowed in a homeostatic environment with a basic supply of energy, then incorporation of the sequences of the ribosomal RNA to the cellular genome in multiple copies and multiple reading frames are considered to be a possibility in tracking down the evolutionary footprints of life. As ribosomal RNAs have the potential to act as tiny genomes encoding the ribosomes, its tRNAs, and proteins, so its integration with cellular entities and the emergence of cellular genomes would attribute the organisms better living and functional stability, metabolic efficiency and to have emerged as a genetically unique

The Evolutionary Biology of Extinct and Extant Organisms

biological entity that would able to cope in any environmental alterations in its ambiance. The molecular geneticists have observed that the unique genetic information (stored in ribosomal genes), packed in the considerably less-stable rRNA, has been transferred and unpacked in cellular genomes, being edited by the promoter and repressor sequences and further stored in the stable form of DNA genes. Since the inception of DNA as an encoding genetic material, the evolution of life has primarily investigated on its genetic origin. The contemporary world of molecular genetics have recognized genes as the structural and functional engine of life as the successful interactive transmission of genes from one biological entity to another one has been contemplated as the journey of biological evolution that either make one biological entity to fit it in its ever-changing ambiance or pushed it to the way of extinction. So, in the language of Richard Dawkins, the great author of “The Selfish Gene,” one of the great evolutionary biologist of Oxford University, UK, cellular evolutions and divergence of distinct organisms happened to be as an act of protecting packages that ensured the protection and transmission of genes in intra and intercellular level. If we look into the intracellular structure, we would see that there are three key intracellular structures, present in the cell except for chromosome (that contain genes) and those are (Root-Bernstein and RootBernstein, 2015): i. Ribosomes: translating genetic information to proteins. ii. Cell membrane: controlling the gateway of cells to regulate materials get in and out and iii. Acidocalcisomes: storing and regulating ions that control biochemical reactions of life. In their online article, entitled “Never mind the Selfish gene-ribosomes are the missing link,” Root-Bernstein and Root-Bernstein (2015) have challenged the concept of “Selfish gene” as they contended “. if a cellular component is “selfish” it must be ribosomes. Cells e and DNA itselfdevolved, we argue, to optimize the functioning of ribosomes. That upends everything we think we know about the evolution of cellular life and ribosomes themselves.” In a straightforward question, the molecular geneticists have tried to get the answer about the functions of DNA, and the most common answer from the perspective of molecular biology, DNA would like to replicate itself. On the other hand, the chemists have contemplated that like other bio-molecules, DNA would prefer to be in its lowest energy confrontation and it has resembled the movement of people, as they moved through many positions but they return to a resting state. If we would consider the resting position of the DNA molecule (which has resembled the energetic molecule), we would visualize the DNA, “tightly curled up with its genes inaccessible” and the scientists observed that the resting DNA are stable enough to protect its integrity of gene for more than 10,000 years (e.g., scientists extracted DNA from a frozen mammoth, got extinct in the last ice age) (Root-Bernstein and Root-Bernstein, 2015). It made the scientists define the cellular functions at the molecular level that would like to replicate genes followed by transcription and translation of proteins that trigger the ribosomes to

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regulate cellular functions. So, in the resting state, the ribosome is ready to translate DNA to protein biomolecules. So, it made the molecular biologists construe that “ribosomes ‘want’ to convert genes to working molecules” to keep the journey of cellular evolution uninterrupted (Root-Bernstein and Root-Bernstein, 2015). Henceforth, the critical observation of the scientists duo on the functionality of DNA as a stable genetic material Root-Bernstein and Root-Bernstein (2019) have proclaimed “The evolution of DNA-encoded genes may have provided a high degree of stability to a previously highly varying ecology of self-replicating ribosome-like entities, and selection for stabilization of the translation function of these ribosome-like entities at the expense of their evolvability.” However, the molecular biologists have realized that the early form of molecular foot-prints of life or the genes, those have been contained and functionally processed by the erstwhile, precellular ribosomal entity ha come across a long trail of molecular evolution to traverse through the transitional threshold of RNA-World to anchor in the DNA world in course of cellular evolution and it’s appeared like completion of a full cycle of the journey of biological evolution. So, it rendered Root-Bernstein and Root-Bernstein (2019) to give a feasible impression of the missing link of the molecular footprint of life that has likely to be started in the prehistoric time with the origin and evolution of “ribosome” precellular entities to came across a long way to the door-step of cellular evolution of “DNA-World” as they have said furthermore “Evolutionary processes would have replicated and produced divergences in the DNA-encoded genetic sequences and recombined these sequences with genetic material from other sources to yield molecular novelties so that the various reading frames of the rRNAs would have found novel uses throughout the new cellular genome.”

CHAPTER

If and when evolution is the ultimate essence of life: what is the evolutionary identity of the missing link (resembling Archaeopteryx)

2

The most extraordinary thing about trying to piece together the missing links in the evolutionary story is that when you do find a missing link and put it in the story, you suddenly need all these other missing links to connect to the new discovery. The gaps and questions actually increase - it’s extraordinary David Attenborough.

The progress of science has always traversed through the trail of trial and error that helped the scientific community to testify the efficacy of hypothesis to pass through the paradigm shift from lifting the status of hypothesis to the status of theory. A journey of biological evolution is no exception. To interpret and prove “Missing Link” as an “unscientific jargon” that is hardly interpreted and defined the progress of biological evolution or evolutionary function of life, the monolithic work, entitled “On the Origin of Species by means of Natural Selection,” which has been written by Sir Charles Darwin in 1859, has been referred by a number of contemporary paleoanthropological proceedings, where “Missing Link” has been considered as “abominable” and “pseudoscientific” terminology seems to be untouchable to define or redefine sacred journey of evolution. Nonetheless, the community of science should have a clear conscience to make an unbiased inference of a judgment. The contemporary observation of the paleoanthropologists tried to give an interpretation that tried to present that Charles Darwin had a well-assumed premonition that he did not use this abominable term “Missing Link” in his theory of natural selection. However, the matter of fact is that in 1859, during the publication of the Darwinian doctrine of evolution “On the Origin of Species by means of natural selection,” paleoanthropologists did not have enough chance to study enough fossil evidence, which could help to define the progress of evolutionary changes. When the availability of fossil evidence is the key issue to define evolutionary functions, is it feasible to understand and elucidate the evolutionary progress of life? Possibly it is The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00007-6 Copyright © 2021 Elsevier Inc. All rights reserved.

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difficult as molecular footprints solely could not resolve all mysteries. When the missing link is directly integrated into the availability of enough transitional fossil evidence, the fragmented patches of the evolutionary jigsaw puzzle remained unresolved for an indefinite period of time. The nonavailability of ample fossil evidence specifically the transitional fossil evidence is the key impediment for such investigations. This is the main issue to interpret evolutionary changes, yet in such a limited situation, Darwin has spent two chapters to narrate the progress of evolution in the backdrop of fossil evidence and expressed optimism that the discovery of plenty paleontological evidence in the future would help the community of science to understand his theory of evolution in a better way (Prothero, 2008). Supposedly, Darwin was concerned about the poor collection of “transitional fossils,” which would help the scientists to make a structural and anatomical comparison of the characteristic features between two closely related taxonomic organisms or two organisms belonging to two evolutionary groups. Although the battle between creationists and evolutionists has ever been settled on Earth, there was a faint line of philosophical connection, represented by those less number of collections of transitional fossils and which are considered to be “Missing Link” or “great chain of being” from a lower group of organisms sea corals to the higher group of organisms birds or humans extended up to “God” in the first half of the 19th century (Prothero, 2008). From the confident level of discussion, as argued earlier, it seems that conventional “Missing Link” is an absolutely right interpretation of Charles Lyell in 1951, which define the linear progress of biological evolution initiating from a lower group of the organism to end up in the emergence of a higher group of organisms. According to the contemporary perception of biological evolution, chiefly based on the composite studies of the ultrastructure of fossil evidence and examining the molecular footprints of the closely related organisms of two evolutionary groups (which is technically recognized as DNA sequencing), such linear progression of biological evolution from lower strata of life to reach higher strata and so-called end of a less advanced organism to emergence of a more advanced organism has found to be absolutely wrong interpretation of progress of evolution. Rather, contemporary, the advancement of phylogenetic studies in the molecular level since the 1990s ensured that the journey of evolution is a random movement, rather than considered to be a progressive (moved from lower hierarchy to higher, bottom-up journey) or regressive (moved through the higher hierarchy to lower one, topdown journey) as the dynamism of evolution absolutely depends upon the fitness of adaptation of that organism in the changing ambiance and which is the key factor to drive-up evolution in the backdrop of space and time. Thus, it seems that “Missing Link” is absolutely a hoax, which failed to interpret the evolutionary function and misguiding the community of science to understand the evolutionary progress of life on Earth. The recent investigations of the interdisciplinary scientists in the field of evolutionary biology, paleontology, paleoanthropology, molecular phylogenetics, and genetic engineering revealed that progress of life forms a thematic branching pattern,

The Evolutionary Biology of Extinct and Extant Organisms

giving an analogy of a bottle-brush, comprising multisplit lineages, coexisted in the main branch (Prothero, 2008). Most interestingly it has not been witnessed that the end of the journey of simple organisms belonging to the lower group in the hierarchy level does not necessarily begin the evolutionary journey of a higher group of an organism as it is noticed that existence of sea corals, which has been emerged around 600 million years has not been found as an extinct group of an organism with the emergence of the modern human species, the most advanced mammals on the earth, which has supposedly been emerged from the prehistoric apes around 7e6 million years ago and both groups of organisms coexisted in this biosphere in their own niche (Prothero, 2008). Hence, the literary usage of “Missing Link” as a scientific term might be considered as an erroneous measure to define the progress of evolution in the wrong way. Nevertheless, that does not necessarily mean that there is no importance of these connecting or evolutionary links or the transitional links in defining the progress of evolution. Any effort to recognize the pseudoscientific term like “Missing Link” or a scientifically correct term like “transitional link” or “Evo-link” as the half-way entity between two distinct forms of evolutionary groups of organisms as the representational state of transition (whether its extinct or fossil form or in extant or in the form of living fossil) could represent any point of the evolutionary journey when one phylogenetic line would split out of another evolutionary line at any point of evolutionary divergence, in the dynamic background of a reticulate mode of the evolutionary progress of life. Using the term “Missing Link” is absolutely wrong but ignoring the importance of terms like “transitional links” or “Evo-links” either extinct or extant form seems to be ignoring the principles of biological evolution and giving a thematic “walkover” to the creationists, which is the absolute instance of compromise to accept and uphold the scientific principles, absolutely unacceptable to the community of science. Since the journey of biological evolution of Darwin’s “On the Origin of Species by means of Natural Selection” started in 1859, the prime acquisitions of the creationists against the evolutionists were the paucity of fossils, mainly the transitional fossils that would stall the impediments on the evolutionary investigations on the intermediate species to establish a link between the past to the present. But the matter of fact is that lack of collection of transitional fossils does not necessarily indicate that it does not exist, as an undergrad student could explain that fossil formation and its preservation and discovery of which is not necessarily defined in terms of its nonexistence. Rather, as being a rational supporter of the Darwinian doctrine of evolution or even the supporter of contemporary Neo-Darwinism, the perception of “transitional fossil” needs to be considered to the next level by using terms like “Connective links” or “Evo-links” to understand and narrate the evolutionary progress of life. The new shift of paradigm would definitely help us to understand that as long as any organism, which is not getting a tag “Extinct,” has not been found in its terminal end of evolution, the perception of Connective-link is valid. Therefore, in terms of evolutionary progress, all living organisms are somewhere in-between the two terminal ends of evolution, and biologically we, all living organisms should be

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recognized as extant connecting links or extant Evo-links. Technically, if we did not reach the dead-end down the evolutionary trail, acknowledging the evolutionary changes of the “Evo-links” is necessary to understand the evolutionary progress of a particular organism and the evolutionary progress of life as a whole. Scientific authenticity has been made on the basis of testing the predictions and falsifying the hypothesis. Although there was not enough collection of fossil evidence whenever Darwin created his theory of evolution, he proposed the availability of fossils and further paleontological studies would help to understand his theory in the future (thelogicofscience, 2015). Subsequently, the logical clarification ascertains that availability of the huge collection of fossils in the 1990s, particularly the transitional ones, would support the predictions as well as upholding the principles of evolution, whereas the nonavailability of it in some group of organisms even in the passage of time and space, would fail to falsify the evolutionary hypotheses, logically (thelogicofscience, 2015). If we look at the other side of the story, creationism does not have any obligation to test predictions and/or falsify hypothesis as it depicts the creation of a distinct form of organisms originated by means of special creation and hence it is not necessary to look or recognize the transitional links to define the evolutionary progress of life in the backdrop of spatiotemporal matrix of life in this biosphere. Let us proceed to the core part of the debate that would help to understand the importance of evo-links to define the progress of evolution. Let us start with some hypothetical scenarios like a lady from a remote Oceanian Island (who has been considered as the most evolved mammals) gave birth to a composite baby girl, the front part of that miracle baby a human being but at the end of her body, it looks like a mermaid that has a big fin, a big fish species. Technically, that baby girl who is appeared like a little mermaid should be recognized as the transitional “evo-link” between mammal and fish, two distinct organisms belonging to two separate evolutionary groups. Realistically, the mermaid has been a good topic of discussion in fairy-tale storybooks, but anyone from the community of science has not witnessed any mermaid in real life so far; hence, the evo-links between fish and mammal still remained as an enigmatic concern. Then, we read the fairy-tale stories of the massive-sized bird of paradise called “Dragon Birds” with sharp claws, a long snout with teeth, the whole body covered with feathers and have a long bony-tail, apparently, appeared (under the assistance of 3D virtual imaging restoration computer graphics of its fossil remnant) to be a big flying animal between bird and reptiles. The discovery of paleontological evidence and its intensive studies by the scientists drag it down from the book of fairy-tale to the world of science and introduced it further to the community of science as “Archaeopteryx” (Hecht, 2008). The prehistoric existence of Evo-link established the preliminary link of evolution between reptiles and birds. Any scientific concept that is not above and beyond the clouds of skepticism so the critics of evolutionary principle might deliberately ignore such existence of “evo-links” in the past. Nonetheless, the gradual discovery of a number of Evo-links between dinosaurs and birds: Confuciusornis, Jeholornis, Sinornis, Xiaotingia, etc. proved that the transitional

The Evolutionary Biology of Extinct and Extant Organisms

existence of evo-links (Howells, 2011; Wang et al., 2016). It is proven that there is no clear gap between two distinct evolutionary groups of organisms, rather the existence of multiple intermediate forms of species or transitional evo-links, ascertained that journey of evolution of life through the reticulate and complex meshwork of evolutionary transition is very much existing in the world of science. In this regard, the credit of discovery of ancient fossil bird, Archaeopteryx, needs to be dedicated to Andres Wagner, who discovered this transitional fossil of 150e140 million years old from the Jurassic deposit of Solnhofen in erstwhile Bavaria (now in Germany) in 1861 but he named it as “Gyphosaurus” as he considered this fossil as a newly discovered, extinct species of dinosaur (Bhatnagar and Bansal, 2008; Howells, 2011). After critical review, The German paleontologist, Hermann von Meyer has redefined the erstwhile “Gyphosaurus” as an intermediate form of organism between dinosaur and birds and he renamed it as Archaeopteryx lithographica in 1861 (Howells, 2011). After 16 years of its discovery, in the year of 1877, a complete fossil has been discovered from a nearby location of Solnhofen, which has been identified as Archaeomis siemensi, having transitional features inbetween reptiles and birds (Bhatnagar and Bansal, 2008). Later, the eminent paleobotanists like T.J. Parker, W.A. Haswell, and De Beer observed their meticulous studies that both paleontological specimens (those appeared to be distinct due to different appearance of their age, sex, size, etc.) belong to the same species that is Archaeopteryx (Bhatnagar and Bansal, 2008). The diagrammatic sketch of the Archaeopteryx is presented herewith Fig. 2.1. The geologists, paleontologists, and paleo-climatologists have studied the fossil specimen of Archaeopteryx along with in-depth studies (extensive data analysis to make a tentative prediction about the organism, evolved in a particular time in a particular place and its ecological interaction with biotic and abiotic factors) of its palaeoclimatic environmental conditions and other fossils, found in the petrified from the same fossil site, to have an idea of the ecological conditions of this unique transitional link between reptiles and birds. The scientists revealed that this unique evolutionary link supposedly evolved in the shallow, tropical lagoon, contained with ammonites, starfishes, shrimps, horseshoe crabs, etc. (Wellnhofer, 2009; Howells, 2011). The terrestrial habitat of Archaeopteryx has poorly represented with the fossil representatives of arthropods like dragonflies and the dinosaurs Compsognathus, found in the fossil site of this ancient bird (Wellnhofer, 2009; Howells, 2011). Let us review the status of transitional links from the perspective of creationism. Creationism did not recognize any intermediate or transitional forms of organisms and according to the stereotype perception of it, each organism is a distinct “Kind.” Hence, the doctrine of Creationism would recognize well-demarked gaps between distinct “Kinds” and disagree with any possibility of the existence of gradual transitions between the two distinct “Kinds” of organisms. In contrary to such theoretical doctrine, the evolutionary perceptions have more flexibility to narrate the characteristic features, critical reviewing those characteristic features would help further to get closer to a certain evolutionary group. Finally, after the scientific review of available characteristics (possession of a number of intermediate

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FIGURE 2.1 The diagrammatic sketch of Archaeopteryx. Courtesy Sashi Sinha.

features in that organism, found to be available in other organisms, belonging to more than one evolutionary groups) of the concerned organism, if the evolutionary judgments failed to assign the concerned organism to a certain evolutionary group, the transitional state needs to be recognized and evolutionary biology and molecular biology of such state have strived to establish the phylogenetic relationships between such preexisting evolutionary nodes, witnessed by the concerned evo-links. If we tried to visualize a prehistoric, massive reptile in our mind, the pictures of the massive sized body of which the surface covered with stiff scales and those entities roamed in the gymnosperm forests in the Jurassic age (whoever watched the movie “Jurassic Park”, would easily be able to visualize such animated dinosaurs as well as prehistoric, extinct reptiles) like Triceratops or Stegosaurus come in our minds that have predominantly terrestrial adaptation. Even a student in biological science would hardly refer to any members of “Theropods” in his or her first choice as an example of dinosaurs. Any expert in paleontology, paleoherpetology, or evolutionary biology could hardly criticize any such student for his or her preferential choice of examples of dinosaurs as the presence of unique anatomical, physiological, and biobehavioural features have rendered them to do so. Although birds and reptiles both distinct organisms are oviparous (reproduce by laying eggs), the biobehavioral features of these distinct groups of animals are found to be quite distinct. One of the biobehavioral features of a bird is to guard the nests to protect the eggs and the newborns hatched out of those laid eggs in the bird nests. Normally, the reptiles hatched the eggs and left the nest-sites, without taking any effort to protect the eggs and securing the birth of the newborns, but dinosaurs,

The Evolutionary Biology of Extinct and Extant Organisms

recognized as oviraptors, guard the nests to protect the eggs laid and protect the newborns as well and it is found to be the characteristic features of birds. The two important characteristic features of birds like the presence of feathers, covering the outer surface of the body of the birds and the presence of wishbone (also called furculum) in Theropods, led the evolutionary biologists to construe the evolutionary bridge starting from reptilian ancestral stock to end in avian descendants (thelogicofscience, 2015). As for the scientists, specifically, the evolutionary biologists, who do not have any direct evidence that can help them to convince and substantiate with chronological evidence that in the “Y” epoch of “X” period, dinosaurs stop reproduced as dinosaurs (with terrestrial adaptation) and they emerged as feathery birds (with volant adaptation) with a series of ecological, morphological, anatomical, physiological, and biobehavioral adaptive changes. We do not have any such straightforward evidence that biological evolution is ultimately responsible for maintaining the dynamic journey of evolution of life on Earth. Nonetheless, the critical review of the morphological and anatomical features of the prehistoric flying bird (flight specializations indicate that it is not suitable for long flights), Archaeopteryx, has typical characteristics of the extant reptiles, including the features of extinct dinosaurs like the presence of a long bony tail, small breast-bone or sternum, lengthy forearms (with unfused digits on the hands), and the presence of teeth in the snout of the skull; all these features, which are convincingly missing in the modern bird species, left a hole in depicting continuity of biological evolution (thelogicofscience, 2015). The reptilian and avian characteristics of this iconic evolutionary link, Archaeopteryx, has been elucidated herewith: The presence of Reptilian features, possessed by Archaeopteryx: 1. 2. 3. 4. 5. 6. 7. 8. 9.

Presence of vertebral column and vertebrae are not fused. Ribs are isolated in the rib-cage. Bones are nonpneumatic. Bones in palm and meta-carpal are not fused. Although sternum appeared to be boat-shaped, there was no keel attached to it. There were around 20 pieces unfused vertebrae from the long bony tail. Presence of sharp claws in the three fingers of the forelimb (wings). Presence of teeth in both jaws. Body was covered with scales. The presence of Avian features, possessed by Archaeopteryx:

10. 11. 12. 13. 14. 15.

The entire body has been found to be masked with feathers. Forelimbs have been metamorphosed to the wings. The snout has been changed to the beak. Presence of furcular (wishbone) The bones in the cranium fused to form bony skull like modern birds. Presence of rectrices or tail feathers.

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Apparently, this discovery of this transitional entity, which looked like an ancient bird-like organism, but having predominating characteristics of dinosaurs made the scientists confused to decide whether the Archaeopteryx should be considered as an evo-link or the evolutionary stepping stone, sticking out of reptilian root-stock from which the phylogeneticists could easily draw a line of the emergence of flying bird species, scientifically recognized as avis. As paleontological studies of Archaeopteryx, would not give any strong and feasible explanation that helped to draw the continuous line of evolution from this “evo-link” to the modern birds, so far. Extensive paleontological studies of transitional fossils, specifically the evolinks between reptiles and avian species, since the 19th century, have ensured that evolutionary inheritance found to be exited from reptilian lineage and further transcended to avian lineage, but paleobotanists could not unequivocally accept that it was the Archaeopteryx, which was discovered as the maiden, iconic evo-link, that evolutionary divergence steered the journey of life to go through metamorphosis and continued its journey in form of avian species along with its ancestral lineage reptilian species. The famous paleobotanist Xing Xu, along with two associates, from the Institute of vertebrate Palaeontology and Paleoanthropology, Beijing, China have published his discovery on the transitional paleontological evidence, collected from the fossil site of Liaoning Province, China and they determined that the transitional fossil inbetween the ancient birds (belonging to Avialae) like Archaeopteryx. Anchiornis and the prehistoric dinosaurs Velociraptor and Microraptor (belonging to Deinoonychosauria) reported being evolved around 161e145 million years ago in the Jurassic period (Kaplan, 2011). Xu et al. (2011) have recognized their newly discovered transitional fossil as Xiaotingia zhengi and based on their primary level of investigations (mainly comparative morphological and anatomical features of Xiaotingia, Archaeopteryx, Archionis, Velociraptor, and Microraptor, etc.) and geological age-dating process, Xu and his colleagues tried to topple the Archaeopteryx’s placement as the iconic evo-link between reptiles and birds and Xu argued in favor of his preliminary observation, as he said: “I think Archaeopteryx’s placement was the result of both history and relatively poor sampling at the dinosaur-bird transition.” However, it requires further investigation into the details in the molecular level to draw a firm assertion on such hypothetical claim as lack of firm assertion in support of his preliminary observation has also been heard from his communication, when Xu stated further, “Because it has the position as the most primitive bird for such a long time, I am kind of nervous about presenting this result” (Kaplan, 2011). The progress of science has always been going through the trail of clutter, corrections, and acceptance of the truth. In the arena of science, there is no existence of absolute truth, as a truth of today might be proved virtual truth of tomorrow. Thus, the probability is there that discovery of Xiaotingia and multilevel interdisciplinary investigations on it would only help the evolutionary biologists to either consider it as the earliest transitional link between reptiles and birds (as well as maiden birds) or it might be proved as a hoax in future. The observation of famous paleobotanist, Thomas Holz, of the University of Maryland, USA, on his

The Evolutionary Biology of Extinct and Extant Organisms

preliminary review on Xiaotingia, which should be mentioned here, has stated: “I don’t think this is going to be the last word on this subject. You take this new Chinese species out of the mix and the argument falls apart, so the new placement is precarious at best until further evidence is dug up” (Kaplan, 2011). However, the discovery of varied forms of transitional fossils, those are in between reptiles and birds and apparently having a resemblance to Archaeopteryx, helped to build the bridge between Archaeopteryx (which is apparently considered proreptilian evo-link) to the modern birds. The discovery of 120 million years old fossil evidence of Sinornis santensis in 1992 from Cretaceous rock-bed of the Liaoning province of China, helped the evolutionary biologists to establish an evolutionary link between Archaeopteryx and modern birds by referring the features like presence of well-built sternum attached to the flight muscles, reduction of tail length and fused digits in forelimbs, all those secondary features, required for volant (flying) adaptations (Barinaga, 1992). The contemporary discovery of the fossils of Jeholornis from the Cretaceous deposit of the Rehe province of China in 2010 (Li et al., 2010) having identical features like long tail and teeth attached in the frontal-end of the snout of the skull, has also been found in Archaeopteryx but it also possesses forearm with better-flying specializations, which has found to be a helpful adaptation in long-term flight. According to the contemporary paleontologists, the recently discovered fossil of Eoconficiusornis, which has presumably been evolved around 130e125 million years ago in the Yixian fossil site (Dabeigou formation) in China, maintained a transitional bridge between Archaeopteryx, the ancient bird with teeth and the modern birds, those having its beak (Hecht, 2008). According to the paleontological experts, Confuciusornis, which has been discovered earlier from the Cretaceous deposit of Xinxiang, China, found to be evolved with beak, supposedly evolved around 125e120 million years ago, hence it has been considered to be the progenitor of the modern birds with beaks (i.e., toothless birds) (Ivanov et al., 2001; Hecht, 2008). At the same time, Confuciusornis has been considered to be phylogenetically related to the ancient birds with teeth like Ichthyosis, found in the ancient sea-birds of Cretaceous deposit from North America, those have been evolved around 95e84 million years ago (Hecht, 2008) and Hesperonis, the big, Penguin, ancient bird with teeth, reportedly been evolved between 83 and 78 million years ago, discovered from Limestone deposit of North America in late Cretaceous (Perrins, 1979). The unique features of this evo-link between the ancient and modern birds revealed that it has the common feature with reptiles like the presence of teeth, no wings, etc., whereas it supposedly adapted in swimming in the water other waterbirds with lobed or webbed-feet in their hind legs and it also maintained an evolutionary link between ancient birds and modern birds by possessing both features beak with teeth bones (Perrins, 1979). There is a structural resemblance of the feet of the Archaeopteryx and Tyrannosaurus Rex, which belong to the distinct group of dinosaur known as Theropods. The shape and structure of the feet of this reptile looked identical to the chickens and herons like modern birds. The findings of the molecular geneticists revealed that the qualitative properties of the DNA of two distinct evolutionary groups like avis and reptiles are found to be almost identical (thelogicofscience, 2015).

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The application of DNA sequencing (to determine the nucleic acid sequence or finding out the order of nucleotides in DNA) has been used since the 1970s, immediately after the innovation of it by Sanger et al (1977). DNA sequencing has been found to play an effective role in determining the close relationship between two of these phylogenetically related organisms (it determined paternity with 99% accuracy). Nevertheless, the most challenging issue is to determine the extinct and extant organism, that there is no problem in collecting a DNA sample from soft tissues of the extant organism, but the difficult task is to procure soft tissue of the fossil organism and the more challenging task is to extract DNA from that soft tissue of that fossilized specimen. Therefore, the feasible option for the scientists is the reliance on establishing the evolutionary proximity of the two distinct entities by undertaking its protein sequence or to determine the amino acid sequence, as the scientists considered that sequential arrangement of a certain number of amino acids would be responsible for the formation of the same protein and closely related species possess identical sequence of proteins. If a DNA sequence would deliver the result like the evolutionaryproximity of two phylogenetically related organisms with 99% accuracy, the amino acid sequence, as well as protein sequence, supposedly yield the results with 80%e90% accuracy. The closer proximity between mammals and amphibians has been determined by the molecular biologists already on the basis of identical protein sequences between these two evolutionary close-related organisms. In the absence of availability of the soft tissues from the Tyrannosaurus Rex, scientists failed to procure a DNA sample, to determine its proximity to the birds and other typical reptiles (apart from dinosaurs). The comparative result of protein sequences among Tyrannosaurus (dinosaur), other reptiles (apart from dinosaurs) and birds yield a unique result, though. Primarily, the results show that an identical sequence of amino acids is common in these three groups of organisms. Thus, the presence of identical nature of proteins in dinosaurs, birds, and other reptiles (except dinosaurs) have helped to determine that they are phylogenetically close related (thelogicofscience, 2015). However, the scientists were able to extract similar proteins (with an identical sequence of amino acids) from 21 living organisms and further investigations in the secondary level amazed them, as the evolutionary biologists have noticed that the protein sequence of the Tyrannosaurus (dinosaur) is exactly similar to the birds, but the protein sequence of the Tyrannosaurus (dinosaur) and from other reptiles (excluding dinosaurs) has not found to be so precisely identical between birds and Tyrannosaurus (dinosaur). It proved that divergence of birds from dinosaurs is a valid hypothesis and it also supports that its transcending dynamism of evolution, which has ensured its origin, divergence, and diversity of avian life, emerged in distinct forms of organisms out of reptilian root-stock, those are phylogenetically related to each other (thelogicofscience, 2015). The alternate way of clarification elucidates that if creationism is the ultimate essence of life on maintaining the existence of the organism as “Kind” on the Earth, then the protein sequence between the

The Evolutionary Biology of Extinct and Extant Organisms

Tyrannosaurus (dinosaur) and other reptiles (excluding dinosaurs), supposedly, have more identical or closely resembled as they belonged to same “Kind” (as par principles of Creationism) rather than the revelation of a unique result that shows that birds and the Tyrannosaurus (dinosaur) are phylogenetically, closely related than the Tyrannosaurus (dinosaur) and other reptiles (thelogicofscience, 2015). Even after the firm interpretation and assertion of scientists, Archaeopteryx would still have remained as a “hot potato” in the domain of biological evolution, on which the battle between the school of creationism and forerunners of evolution would be still on. If we try to reach out at the root of the controversies, evolutionists have a strategic advantage as the principles, they accept ascertained the existence of transitional lineages or emergence of evo-links that could have utilized to form an evolutionary bridge between two distinct evolutionary organisms and further discoveries of more transitional links, leave an opportunity to interpret the mode of evolutionary divergence of life in a better way. But if we look at another end, the supporter of creationism did not have such advantage as they principally accept the existence of any and every transitional form of an organism as distinct “Kind”, as a result, the appearance of any transitional forms of “evo-link” like Archaeopteryx led the contenders of creationism to recognize it as “Kind” rather than an “evolutionary link.” Hence, the discovery of any new transitional or evolutionary links raised a sense of inconvenience to the creationists, as it would create an initial level of denial about its existence, then it needs to be changed to the state of assertion out of compulsion as “Kind.” The expression, as well as revelation of science, has always been gone through the “interpretation of the evidence” as it often stalls the flow of “argument from ignorance to fallacy” (thelogicofscience, 2015); rather reviewing the scientific principles, which help to drive-up the predictive perceptions to expose its reality either substantiating any hypothesis or prove it wrong. It is apparently true that creationists and scientists (including evolutionists), both groups are involved in “interpreting the evidence,” but the scientists used logic to be engaged in the process of interpretation when the creationists use their personal beliefs. Mostly, it has been found that creationists “interpret the evidence” before analyzing it and apparently it seems to be a close-ended conclusion to give a predetermined observation, whereas the scientists (here evolutionists) engaged in tedious analyzing (which involved loss of time often) to interpret it, to give a logical presentation and create an open-ended opportunity.

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Walking with Cynodont to explore the uncharted evolutionary trail of mammalian lineage diverged out of reptilian

3

“Further down the river is one of the Triassic’s most bizarre animals. The cynodont is a missing link between reptiles and mammals. As he runs, his backbone moves from side to side like a reptile, but he has hair and lives down a burrow like a mammal” Kenneth Branagh

A diverse group of dinosaurs used to roam around on Earth, particularly in the “Jurassic Garden” (though geologically, Jurassic age has started around 200 million years ago [mya] and end in 56 mya) covered with a diverse group of gymnospermous flora, around 251e220 mya in the PermianeTriassic boundary. It was first time discovered by the eminent paleontologist, Richard Owen in 1887 from South Africa. The paleontological discovery ascertained that Thrinaxodon liorhinus was one of the predominant Therapsids, one of the medium-sized Cynodont, predominantly carnivorous reptile (size of a fox), which was found to live in South Africa and extended up to Antarctica (Kitching, 1977; Damiani et al., 2003). The intensive paleontological studies on Thrinaxodon liorhinus revealed that this unique carnivorous species used to rely on small insects and small-sized herbivores and invertebrates as it used to catch its prey and lived in burrowing habitat (Damiani et al., 2003). In this regard, it needs to be mentioned that paleontologists discovered that Cynodonts had been found to be preexisted before dinosaurs, evolved around 260 mya during the Permian period (Geggel, 2016). Down the trail of evolution, Monotremes, Marsupials, and placental mammals (including humans) supposedly diverged out of Reptilian lineage in the course of Cambrian radiation (Geggel, 2016). Though the scientists did not consider the Cynodonts as typical mammals, rather, they were considered as evo-links, which were predominantly reptiles, sharing the mammalian features of jaws and skull architectures (Geggel, 2016). However, the first paleontological evidence of Cynodonts has been discovered in the fossil site from the floodplains, adjacent to the Karoo basin and the age dating process revealed that it supposedly evolved around 251 mya, which is overlapping to the “Great Dying” event (one of the major mega-extinction events that were The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00003-9 Copyright © 2021 Elsevier Inc. All rights reserved.

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responsible for the extinction of 70% of terrestrial vertebrates and around 96% of oceanic life on this Earth those existed around 252 mya) (Benton, 2005; Sahney and Benton, 2008; Shen et al., 2011). The paleontological analysis of a wide range of fossil sample in the PermianeTriassic boundary of South Africa and Antarctica revealed that the land animals, particularly the vertebrates in that geological regime, were found to be dominated, represented by Therapsids like burrowing Cynodont (e.g., Triachodon), Synapsids like burrowing Dicynodont (e.g., Diictodon), and some early mammals, etc (Brink, 1954, 1955; Damiani et al., 2003). The scientists have noticed the behavioral pattern between the first Cynodont, Thrinaxodon has close similarities with Triachodon, having predominant burrowing adaptation. The scientists have critically reviewed the burrowing pattern of the Triachodon, characterized by bipartite later slopes, normally been found among the nonmammalian members of Cynodonts (Damiani et al., 2003). Accordingly, a transitional journey of evolution from reptilian lineage to mammalian lineage seems to be presented by the unique prehistoric vertebrates, evolved in the pre-Cenozoic era, and Triachodon was found to be a unique evo-link that narrowed down the gaps between two distinct evolutionary entities and building the evolutionary bridge between these two distinct evolutionary groups as a link in transit. The most unique features of one of the extinct Therapsids, Cynodont Thrinaxodon liorhinus that mesmerized the scientists were its semisprawling body posture (Brink, 1954, 1955; Branagh, 1999; Blob, 2001; Damiani et al., 2003), which were as follows: Transitional posture, horizontal, sprawling posture, found to exist in the closely related dinosaurs, Pelycosaurs, and the vertical, upright posture of mammals. Presence of hairs on the outer surface of the skin of Thrinaxodon liorhinus, instead of protective scales on the outer surface of the skin other reptiles. Females used to have mammary glands and produced milk for newborns, but their reproductive features were typically resembled the reptiles like oviparous. The movement of Thrinaxodon, one of the most important evolutionary link was noteworthy to the evolutionary biologists as their structural formation of the bones pointed out that, whenever they ran, the sidewise movement of their backbone, indicated its close semblance to the reptiles but, the standing posture it was vertically upright which had normally been found among mammals (Branagh, 1999). The ethologists and the paleontologists found that Thrinaxodon, the transitional link or evo-link between reptiles and mammals engaged in maleefemale pairing and which has found to be everlasting (as they do not swap their reproductive mate or partners like other dinosaurs) and they prefer to stay in the burrow like most of the mammals do. The basal matrix of the burrow of the Thrinaxodon had found to be covered with lichens (Branagh, 1999). The females were contemplated to be engaged in breastfeeding the newborn babies and used to incubate the eggs for 3 months after laying eggs, and after that new-born babies came out of the eggshell. The bio-behavioral patterns of the male partner of the Thrinaxodon have been contemplated to have a resemblance to mammals than reptiles as the males stay around the burrow in the daytime to protect the young kids and their female partners engaged in household works like changing the bed-litter. They also engaged in hunting and collecting food in the middle of the nighttime for other members of their

The Evolutionary Biology of Extinct and Extant Organisms

family lived in the burrow when most of the big-sized predators (like Coelophysis) fall asleep in that time (Branagh, 1999). The meticulous studies on the paleontological evidence indicated that the drastic shrinkage of the Thrinaxodon population in PermianeTriassic boundary seems to be triggered by the interspecific struggle of existence among Thrinaxodon, Coelophysis; Postosuchus for food and space (Damiani et al., 2003). In 1889, Harry Govier Seely, the great paleontologist from Great Britain has discovered the fossil remnant (comprising a skull and postcranial skeleton) of Cynodontian Therapsids collected from the fossil site of Karoo rocks of South Africa (Seeley, 1895). Further investigations indicated that it has supposedly evolved in the middle Triassic in the Southern hemisphere regions (Hall and Hallgrimsson, 2008). In 1894, after a thorough paleontological study on this fossil remnant, Seely named it as Cynagonathus crateronotus (The generic name Cynagonathus in Greek came from two words: “Kyon” means dog and “Gnathos” means jaw, together means “Dog-jawed” animal) (Seeley, 1894). Later, exploration of fossil sites in different locations of the world helped to discover it from different parts of the Southern hemisphere, ranging from Namibia to South Africa to Argentina, extended up to Antarctica (). Cynagonathus was narrated as a small dog-sized animal of 1.2 m long, had a large head (which was around 1/3rd of the body), with a wide jaw and sharp teeth. The forelimbs of Cynagonathus were found to be sprawling posture, resembled a few numbers of extant reptiles, and it also had smaller hind-limbs (Palmer, 1999; Jenkins, 2009). The paleontologists and anatomists contemplated that the absence of ribs in its upper abdomen, indicated the presence of a diaphragm, the important muscle in the middle of the body cavity, which helped mammals in better breathing; however lack of presence of any soft tissue had left such possibilities as a hypothetical scenario, rather than a reality. The diagrammatic sketch of Cynodont is presented herewith (Fig. 3.1).

FIGURE 3.1 The diagrammatic sketch of Cynodont. Courtesy Sashi Sinha.

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The evolutionary history of Lystrosaurus (In Greek, listron mean shovel and sausauros means lizard), one of the herbivorous, Dicynodont Therapsids had typical features like the presence of two tusks linked canine teeth and a horny beak, and 2.5 m long pig-like vertebrate, which had found to be an important evo-link to narrate the erstwhile existence of “mammal-like reptile” the Therapsids in prehistoric time. Dr.Elias Beadle, a missionary and an amateur “bone-hunter” (the fossil collector) from Philadelphia, USA has discovered the skull of Lystrosaurus around 1870 and communicated to the eminent paleontologist Othniel Marsh for its identification purpose, but failed to get an answer. whereas, another leading paleontologist, Edward Cope studied the fossil evidence and published his observation on this fossil in the Proceedings of American philosophical Society in 1870 (Wallace, 2000). The detailed paleontological investigations of the fossil evidence helped the scientists to find out important information about this burrowing “mammal-like reptile” noticeable for its semisprawling posture, and it reportedly evolved in the Permiane Triassic boundary and used to around in Antarctica, South Africa, and India between 270 and 250 million years ago (Damiani et al., 2003; Newitz, 2013). It was a big surprise in the world of science, specifically in the arena of biological evolution, when 95% of the terrestrial life became extinct, Lystrosaurus was an exception during mega extinction event, called “Permian extinction”. Lystrosaurus, the unique looking, herbivorous creature like a hypothetical cross-breed between the pig and lizard, reported to be survived PermianeTriassic mass extinction around 252 mya, shrunk in size, and found to be reradiated in the absence of bigger predators and interspecific competitors in the late Triassic and around 30 million years interval its population reportedly recovered from the negative impact of mega extinction and diversified further (Benton, 2005; Sahney and Benton, 2008). Upon availability of ample paleontological evidence in China, Mongolia, India, Russia, Antarctica, and South Africa in 1960 followed by its extensive investigations helped the scientists to stand behind the plate tectonics hypothesis of the erstwhile formation of the Earth and that helped to connect the dotted line of migration of terrestrial animals, dispersed throughout the world as a result of fragmentation and gradual drifting of the fragmented continental plates, those expedited the animals in prehistoric time to migrate far apart from each other (Surkov, 2005; Newitz, 2013). Eventually, this unique evo-link between Reptile and mammals disappeared forever, but its evolutionary struggle, adaptation, and its emergence as the evolutionary mother-stock of mammals helped to carry forward the history of biological evolution to continue the journey of vertebrates on Earth. The paleo-climatologists observed that preponderance of carbon dioxide and depletion of oxygen level was assumed to be the key factor for the depletion of a diverse group of vertebrates in PermianeTriassic mass extinction, but the structural adaptation like flattened, barrel-shaped chest, large-sized lungs, short size nostrils with long neural spine, and burrowing habit supposedly help those species to survive in the oxygen-deficient environment. It is an important lesson for us to note that one of the most primitive groups of reptileemammal evo-link adopted such a unique

The Evolutionary Biology of Extinct and Extant Organisms

strategy to escape a mass extinction (Newitz, 2013). For the evolutionary biologists, Lystrosaurus (scientifically recognized as Synapsid as well as Therapsids) is still a miracle in the evolutionary history of vertebrates, which endured the low light condition, breathed in poor-oxygenated air, and survived in the mud tunnel burrows to survive the mega extinction and quickly adapted to the stressful environmental conditions, endured millions of years before evolved as mammals in the Mesozoic era out of the reptilian stock of Therapsids (or Synapsids) (Newitz, 2013). Very recently, Hiroshige Matsuoka from Kyoto University, the eminent Japanese paleontologist along with his associates, discovered a dozen of fossilized teeth specimen from the fossil sites of Kuwajima, Japan, and identified that one of the fossilized-teeth specimens of a species belongs to Tritylodontidae family, which also maintained an evo-link between reptiles and mammals, nonetheless maintain the visible features of Cynodonts, especially the Synapsids, and it revealed the promammalian characteristics at the same time (Matsuoka et al., 2016). A number of plants, dinosaurs, turtles, lizards, and fishes, which supposedly shared the same niche of prehistoric Jurassic forest ecosystems, were occupied by Tritylodontids, the herbivorous reptiles that originated and evolved in Jurassic era and possessed a number of mammalian features like warm-blooded animals had a special bone in their jaws which-one the mammals used for hearing sounds. By examining the paleontological evidence of Tritylodontids, scientists ascertained that Tritylodontids survived 30 million years more than predicted by the earlier paleontologists (Matsuoka et al., 2016). Dr. Matsuoka and his colleagues assumed that Tritylodontids have radiated in early Jurassic; however, the herbivorous mammals supposedly took over the “ecological roles” of Tritylodontids to push it in the way of extinction in the late Jurassic (Matsuoka et al., 2016). Dr. Matsuoka has stated with affirmation: “This made sense because otherwise Tritylodontids and the herbivorous mammals would have competed for the same niche” (Matsuoka et al., 2016). Hence, the unique findings of Matsuoka et al. (2016) proved that the conventional biased observations that the evolution of mammals initiated the extinction of mammal-like reptiles was incorrect rather it had been witnessed that Tritylodontids survived and coexisted with mammalian species for millions of years. The inquisitive, Brazilian paleontologists, L.I. Price and Agustin Martinelli from the Federal University of Rio Grande do Sul, Brazil, studied the fossilized skull and jaw specimen of 237 and 235 million-year-old fossil, respectively, displayed in the Museum of Earth Science, Rio de Janeiro, Brazil, collected from the fossil site of Santa Cruz de Sul from the province of Rio Grande do Sul in 1946. After a thorough paleontological examination, the scientists noticed that the fossil belonged to a loafebread sized (around 30 cm long) protruding canine teeth in the upper jaw of Cynodont. From examining the teeth, it seemed to be a small carnivorous Cynodont, and this mammal-like reptile belonged to the group Probainognathidae, evolved around 237 mya (Geggel, 2016). The second fossil remnant of 15 cm long speciemen from the same fossil site was discovered to be Cynodont and recognized as Santacruzgnathus abdalai, and naming of this fossil specie has been dedicated in the memory of the famous Argentine paleobotanist Fernando Abdala, who dedicated

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his life in research of the Cynodonts from Africa and Latin America (Geggel, 2016). The discovery of these two small Cynodonts were considered to be the two early milestones in the history of origin and evolution of mammals. In 1966, Ione Rudner has discovered the fossil remnant from the fossil site of Lesotho, South Africa, the large girdle tooth of a shrew-like animal (of 10e12 cm long). Later, this fossil specimen has been identified and described as Megazostrodon rudnerae, by the paleontologists duo A. Crompton and F. A. Jenkins Jr. in 1968 (Crompton and Jenkins, 1968). According to the paleontologists and evolutionary biologists, Megazostrodon, the extinct, evo-link or transitional link between Cynodont Therapsids and crown group of extinct mammals, evolved as small shrewlike mammalian form or mammal-shaped clade around 200 mya in between late Triassic to early Jurassic period, assumed to be radiated out of the Probainognathians Cynodonts, having phylogenetic relationship with extant, crown group of mammals like Marsupials, Monotremata, and Placentalia (Rowe, 1988). The paleontologists construed that Megazostrodon, the small mammal-like prehistoric nocturnal promammalian animal used to feed small insects and lizards whenever big predators took a rest in the middle of the night. The scientists defined that the dentition of the reptiles was quite different from the dentition of mammals and the presence of fixed teeth instead of replaceable teeth and the presence of grinding teeth in Megazostrodon, proved that it emerged out of reptilian ancestral state to be evolved as early mammalian form. The unique dentine formation in Megazostrodon indicated its huge energy consumption potential, which is helpful for quick digestion of the food, the traits found among warm-blooded animals rather than cold-blooded animals (Minkoff). To compensate the reptilian advantage of teeth replacement, mammals have emerged with fixed teeth with dentine enamel, specialized with crystalline discontinuities that helped to the evolutionary divergence of crown group of mammals, out of reptilian ancestral stock, and the newly evolved dentine was equipped for consuming food having energy supplying potential for warm-blooded organisms (). Remarkable features of evolutionary adaptations have been noticed in this early evo-link between reptile and mammal as this promammalian extinct mammal, Megazostrodon evolved with four different types of teeth (Canine, incisor, premolar, and molar), whereas its evolutionary cousin, the nonmammalian Therapsids did not have such distinct type of dentine, which helped it better shearing and chewing food in terms of larger quantity and better digesting potential as the warm-blooded mammals need more energy than reptiles to survive (Savage and Long, 1986). Megazostrodon supposedly evolved with a flexible skeleton (it helped for faster movement than the evolutionary cousin, reptiles) and shorter rib-cage (shorter rib-cage could protect large-sized lungs, which helped for better respiration) that were absent in reptiles (Kemp, 2004). The evolutionary biologists contemplated further that though Megazostrodon possessed a number of transitional features of ancient oviparous mammals, they did not possess mammalian placenta but they used to breastfeed their infants after hatching till they attained the state of maturity. The evolutionary biologists

The Evolutionary Biology of Extinct and Extant Organisms

anticipated further that the environmental changes might have triggered the evolution of mammals and helped diverging out of Cynodonts out of the cold-blooded reptiles, which were slow moving and they ate less, also engaged in thermoregulation, whereas the ancient representative of mammals like Megazostrodonwas found to be fast moving, respired more, and ate more with better digestive potential and all these features supposed to ensure the existence of the warm-blooded, newly evolved mammals in the changed environment. In 1788e1801, in the second volume of “An account of the new English colony in New south wales”, the author David Collins expressed his bizarre experience in a brief note with pictorial presentation, when he came across to an “amphibian animal, of the mole species” as the small-sized (between 43 and 50 cm long) amphibian, venomous, animal possessed a number of composite characters, found in a diverse group of animals like the presence of beak-like duckbill, webbed feet like otters, and short and stout tails like otters (Collins, 1802). For three decades since 1788, the taxonomic identity of the weird-looking semiaquatic mammal was not very convincible to the renowned European explorers, naturalists, and scientists like Captain John Hunter, George Shaw, and Robert Knox, which cast a shadow of its real existence and a majority of people regarded it as a hoax (Hall, 1999; Walters and Johnson, 2003). The duck-billed platypus, which has scientifically been known as Ornithorhynchus anatinus, one of the five extant species of Monotremes (the egg-laying mammal), taxonomically comprised of the platypus (Ornithorhynchus anatinus); short-beaked-Echidna (Tachyglossus aculeatus) and three species of long-beaked Echidna (Zaglossus bruijni, Z. bartoni and Z. attenboroughi) found to be endemic in Australia; whereas, the long-beaked Echidnas are found confided in New-Guinea; but the short-beaked Echidnas are found to be spatially restricted in distribution in Australia and New-Guinea (Flannery and Groves, 1998). On the basis of the studies on the paleontological evidence of Platypus, excavated from New South Wales and Victoria, the evolutionary biologists ascertained that this unique species evolved in the lower Cretaceous (around 100 mya) and used to share the same ecological niche of Eastern Gondwana (Southern part of Australia, which was connected to Antarctica) and roamed around along with lungfish, turtles, and dinosaurs in that prehistoric time (Musser). Taxonomically, the members belonging to Monotremata (comprising Platypus and Echidnas) are characterized by the features like presence of single and common holes used as urogenital and digestive systems (Warren et al., 2008). Conventionally, Monotremata has taxonomically placed under mammalian subclass Prototheria, which was reportedly diverged from the reptilian stock of Therapsids and leading emergence to Theria. The phylogeneticists observed that Marsupialia or Marsupials and Placentalia or eutherians split out of Therian lineage in the course of evolution. Upon composite analysis of the molecular and fossil data, the molecular clock estimated further that Eutherian radiation happened around 90 mya and the ancient mammals diverged out of Sauropsida, the reptilian lineage around 315 mya. Based on the contemporary studies on molecular phylogenetics, there is a little gap in the

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point of divergence between “Monotremata-Theria,” which has supposedly evolved between 210 and 160 mya (Warren et al., 2008). The availability of the Monotreme fossil, Monotrematum suderamericanum, which was supposedly evolved around 62 mya from Southern Argentina (Patagonia), has rendered the paleontologists and geologists to contemplate that dispersal, as well as species radiation of the Monotremes in other parts of Gondwana, happened after its evolution in Australia (Musser). Though, the evolutionary history of the Duck-billed platypus was found to be the recent one in comparison to the other Monotremes as the fossil of the Obdurodon dicksonii, which was larger in size with a bigger size of the bill than that of the extant species, evolved around 20e15 mya; whereas, the earliest collection of the extant specimen was found to be 100,000 years old, which has been reported from the Australian continent (Musser, 2003). On the basis of contemporary studies of molecular phylogeneticists of Echidnas and duck-billed platypus, both groups of egg-laying mammals have reportedly evolved out of reptilian common stock around 19e48 mya and the scientists further construed that the typical reptilian bone formation in Platypus and Echidnas, particularly in the shoulder region helped this egg-laying mammals, particularly the platypus to gain more power in swimming and Echidnas for better burrowing abilities (Phillips et al., 2009). Though the bone structure and allied features like the presence of legs at the side of the body instead of mammalian feature like the presence of leg underneath of the body, duck-billed platypus has been found to have a close resemblance to the reptilian Cynodonts, especially the Synapsids, and the presence of thick brown-colored furs (instead of scales), which is found to be the characteristic feature of mammals, not merely act as a waterproof and but helped the animals to stay them warm (Grant). Another unique feature of the platypus is that it normally uses a webbed feet of the front limb for swimming, but it folds the webbed feet limb during terrestrial movement and it follows a typical mammalian walk, known as knuckle-walking, normally been found in the big apes (Grant). Yet, the egg-laying mammals maintain a clear distinction between the typical mammals and premammalian entities as the typical mammals evolved with placenta, which maintains the average body temperature around 37 C whereas platypus maintains an average body temperature much lesser, which is around 32 C (Anderson and Jones, 1967; Bethge, 1997). Although platypus does not have placenta (so it is still oviparous) and teats, but it sulks the hatched newborns by its porous milk ducts for the next 3 months since giving birth to its offsprings. The contemporary research works of the genomicists revealed that Platypus genome carry both reptilian and mammalian genes in its genome (Warren et al., 2008). The scientists found that the female platypus has a spur at the back of the leg, which carry venom. The comparative molecular analysis of the venom protein from platypus and reptiles found that they have evolved independently in reptiles and platypus from identical gene families; whereas, the milk protein genes of the platypus and other mammals are found to be identical (Warren et al., 2008).

The Evolutionary Biology of Extinct and Extant Organisms

In 2004, the reproductive biologists from the Australian National University have revealed that platypus carries 10 sex chromosomes, 5 pairs of XY in the males with respect to 5 pairs of XX chromosomes in female counterparts; whereas, most of the typical mammals carry a pair of XY and XX chromosomes in male and females, respectively (Selim, 2005). The molecular geneticists revealed that one of X chromosomes of platypus has a functional resemblance to the Z chromosome of Avis (Grutzner et al., 2004). The molecular geneticists also determined that, in the determination of sex in a higher group of animals particularly mammals, the presence of testis-determining factor as well as sex-determining region Y (SRY) protein (which is a DNA binding, gene regulatory protein, encoded by SRY gene) has been found in most of the Marsupials and placental mammals including modern human species (Berta et al., 1990). The sex-determining factor, which is regulated by the SRY gene (which is devoid of any intron) is found to be integrated into the Y chromosome of mammals; but this information is not enough for a clear understanding of the function and evolution of sex-determining genes or the molecular switches on Y chromosome (Salleh, 2014). However, the scientists observed that the SRY gene driven sex determination process is found to be the ideal sex determination factor (SDF) of those placental mammals, Marsupials, possess 1 set of XY chromosome. Recently, Dr. Paul Walters of the University of New South Wales, Australia, the eminent molecular geneticist and his research colleagues from the University of Adelaide, Australia and the University of Lausanne, Switzerland, undertook a collaborative project to study the sex-determining factor of Monotremes (Platypus and Echidnas). They have noticed that it is a cumbersome process to identify the sex-determining factor of Monotremes as the male member possesses 5X and 5Y chromosomes and Dr. Walters has mentioned in a communication: “No one had really characterized any Y chromosomes in platypus before because they’ve got quite a complex sex chromosome system.” Accordingly, the scientists opted for the examination of Y chromosomes of 15 different mammals (including Monotremes, Marsupials, Elephants, Monkeys, Humans, etc.) an alternative way to study the Y chromosome, specifically looking for a common DNA sequence found in each Y chromosome that would help to recognize the sex-determining factor of mammals. To get the best result, the scientists have set a molecular clock, to sync the fossil data to monitor the changes of DNA sequence over time. And after a stint of trial and error, they are lucky to find out a miracle biochemical compound, called AntiMullerian Hormone or AMH, the integration of which to Y chromosome found to be a determining factor of the sex of the platypus (Salleh, 2014). Dr. Walters confidently said further “If an animal has that gene it will act as a master switch to turn on testis development” (Salleh, 2014). Dr. Walters and his colleagues have gone further down the trail of evolution of sex-determining gene or molecular switch of sex determination issues in mammals by undertaking a comparative study between evolutionary pathways of SRY and AMH genes as both molecular switches act as SDF in mammals but AMH is found to have more precise analyzing potential as SDF in mammals.

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Although the presence of the Y chromosome is the ultimate SDF in mammals as it is related to the development of essential reproductive features of male members in the mammalian lineage like testes development and sperm production etc., nevertheless, Dr. Walters and his associates revealed that the unique genes that act as a sex determination factor has independently evolved in Monotremes and placental mammals around 180 mya (Salleh, 2014). Referencing to the very recent perception of the evolution of short-sized Y chromosome from the full-length X chromosome by the chromosomal aberration of gradual depletion of genes, Dr, Walters and his colleagues have contemplated that it triggered the loss of around 1000 genes in Y chromosome, and it is also observed that in comparison to its counterpart, Y chromosome is supposed to have less potential than X and it might not be functionally so important that it would determine the reproductive traits of any species. Dr. Walters stated further “It was hypothesized that the Y chromosome can’t hold anything that’s critical to life” (Salleh, 2014). To ensuring an effective way of protein production as well as coordination of all important physio-biochemical functions, two copies of a particular gene need to be present in two homologous chromosomes, but it has been found in a higher group of placental mammals, including humans where the male representative possess 1 X and 1 Y chromosome. Hence, the technical explanation of functional role-plays of genes in regulating the production of important proteins are not a very strong interpretation that could determine the expression of sex in the male counterparts, belonging to the advanced group of mammals (particularly those having 1 X and 1 Y chromosome) and which are not found to be very convincing in the advancement of biological evolution in the molecular level. However, the journey of science is not found to be straight forward always, so the understanding of the evo-link’s evolutionary expression of sex is not an exception. The statement of the famous Latin American paleontologist and the specialist on the fossil Cynodonts, Agustin Martinelli of Federal University of Rio Grande do Sul, Brazil, left an important message for us that might help to understand ourselves and our evolutionary history as modern human species in the long evolutionary journey of life and to learn from his statement “These [Cynodont] new fossils help [us] understand in more detail the evolution of pre-mammalian forms that gave rise to the group of mammals, in which we humans (Homo sapiens) are included .. ” (Geggel, 2016).

CHAPTER

One small step for amphibious fish, one evolutionary leap for moving tetrapods on Earth

4

“The lungfish is in a really great and unique position in terms of how it is related to fishes and to tetrapods . Lungfish is very closely related to the animals that were able to evolve and come out of the water and onto land, but that was so long ago that almost everything except the lungfish has gone extinct” Heather King.

Although amphibians are considered as one of the most simple and most primitive animals on Earth, this evolutionary group of animals is found to be taxonomically and ecologically diverse and equipped with a wide range of diverse structural, functional and behavioral adaptations that would help them to occupy a diverse range of habitats (ranging from terrestrial ecosystems to freshwater ecosystems) and ecological niches and able to sustain survival challenges. The transmigration of amphibians from water to land has more or less related to the execution of their adaptive safeguards, to secure their survival by enduring alleviated levels of stress. Along with birds, reptiles, and mammals, the amphibians have also taxonomically been assorted under the Superclass: Tetrapoda, the maiden group of vertebrates evolved with four limbs and transmigrated to the terrestrial habitat, leaving behind the aquatic bodies like rivers, oceans, etc. According to the evolutionary biologists, the first tetrapods were amphibians, evolved around 395 mya supposedly from the lobe-finned fish or Sarcopterygians (those are phylogenetically integrated to coelacanth and lungfish) during the Devonian period on the Earth (Schoch, 2014). It has also been discovered by the scientists that the tetrapodomorph fish (belonging to the order Osteolepiformes), reported being a phylogenetically close ally of Sarcopterygians and it has reported being disappeared from Earth around 299 mya (Lu et al., 2016). The sociobehavioral analogy of “Fish out of water” depicts a reality where survival of an organism is at stake and most often survival of any fish depends upon its breathing ability in a certain level of dissolved oxygen in water, which has been utilized by the fish, using its gills, the respiratory organ when swimming around in waterbodies, its normal habitat. Nonetheless, with little deviation out of this conventional perception, scientists identified a number of 200 extant fish species (belonging to 49 families and 17 orders), those ensured survival by performing air-breathing

The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00005-2 Copyright © 2021 Elsevier Inc. All rights reserved.

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(specially adapted in terrestrial respiration) and those have broadly been classified under two distinct categories (Graham, 1997; Wright and Turko, 2016): Bimodal breathersdThese fishes remained typically aquatic, during respiring at the water surface. Amphibious fishdIt remained in fully immersed condition, but able to breathe out of water. The scientists observed that by virtue of acquiring the organs required for terrestrial respiratory adaptation, the amphibious fishes are able to survive in terrestrial environments, so a number of people inquired about the justification of its refuge in waterbodies and sustained there in immersed state (Graham, 1997). Later, the animal biologists and ecologists observed that to secure its reproduction, foraging, averting the predatory attack, and enduring desiccation state, these amphibian fishes have sustained in the waterbodies in submerged state and this special adaptation would ensure their survival (Sayer and Davenport, 1991). The scientists revealed that there are a number of structural, physiological, and behavioral adaptations (ranging from emerged with lungs, quiridium, aestivating in the mud tunnels in prolonged summer, secretion of the mucous cocoon, etc.), the amphibious fishes adopted, when they (e.g., lungfishes, mudskippers) involved in moving to and fro in between water bodies and terrestrial plain (Wright and Turko, 2016). The scientists observed that the amphibian fishes (may also be considered as facultative aquatic fishes) usually migrate to and fro in between water and land and it seems to be an impossible task for any obligate aquatic fish species, as the physical and biochemical parameters of these two distinct habitats are not suitable for a specific respiratory organ (gills) of obligatory fish and maintaining homeostasis of any organism in between these two habitats possibly required a series of transitional adaptations those have not been found in those obligate aquatic fishes. According to the evolutionary biologists, the evolution of amphibians happened in course of time and supposedly diverged out of the osteichthyan fishes and the most unique observation of the phylogeneticists is that the tetrapods are close phylogenetic allies of the amphibious fishes (Wright and Turko, 2016). Evolutionary biologists contended that amphibians evolved more than a number of times in the last millions of years and this incident make the amphibious fishes fit for survival in terrestrial habitat, emergence with unique respiratory organs like lungs, and accustomed to aerial breathing (Graham and Lee, 2004; Randall et al., 2004). With a series of phylogenetic reviews, a large number of scientists have further concluded that acquiring a number of fixed adaptations though a number of scientists consider these acquired traits better be considered as phenotypic plasticity, and it makes them suitably surviving in terrestrial habitats, after being adapted in aerial breathing, the amphibian fishes finally paved the way to the evolution of tetrapods and began the evolutionary journey of the ancient members of vertebrates on Earth (Graham, 1997; AshleyeRoss et al., 2013; Wright and Turko, 2016). After vigilant investigations, the ecologists construed that the amphibian fishes survived in the interface between aquatic and terrestrial ecosystems, must be acclimated to a number of two different characteristics like hydration/desiccation, availability of oxygen (O2),

The Evolutionary Biology of Extinct and Extant Organisms

exposition to high/low carbon dioxide (CO2), and endurance to high and low level of ammonia (NH3) level (Wright and Turko, 2016). The evolutionary biologists further noticed that the structural formation of fins of these primitive fishes had a bony-base, rather than the fins made up of rays, and the bony-base supposedly produce limbs of the maiden amphibians. According to the contemporary phylogenetic interpretation of the evolution of Tetrapods, the amphibian fishes (e.g., Tiktaalik roseae) were considered as the transitional form between fish and amphibians that supposedly roam around in shallow water, around 375 mya. There were four groups of ancient amphibians, those played an important role in the transmigration of amphibians from water to land. The labyrinthodonts (the teeth of this extinct organism possessed a dentine, enamel coating and the cross-section of it looked like maize) had been considered as the maiden amphibian, which came out of the water to settle down on land. The animal biologists revealed that it was not a specific adaptation, rather a combination of a number of composite adaptations that assisted the amphibian organism to come out of the water to settle down at the terrestrial ecosystems, and a brief narration of the major adaptations are mentioned herewith: a. Evolution of cutaneous respiration in amphibians: Most of the amphibians, evolved with moist, permeable skin, which has been found ideal for cutaneous respiration and the outer layer of the skin remained moist and lubricated state by means of mucus secretion by mucus glands. b. Evolution of a pair of external nostrils and auricular operculum: The presence of one external nostril at each side of the mouth and connected to the internal nostril, which has been noticed among the predecessor of the tetrapods. But a pair of external nostrils has been noticed at both sides of the snout of amphibians, those are directly connected to the mouth and internal nostrils, recognized as “choanae.” The choanae have been found to play a key role in supplying a high volume of oxygen, required for air breathing by the lungs (instead of gills), and it also helped the functioning of olfactory (smell) systems, outside of water. The amphibians have been evolved with an extra bone in their ear that helped to transmit sound to their inner ear for better response to recognize prey and predators in its ambiance. c. Evolution of Lungs: As the evolution of sarcopterygian members was found to be equipped with lungs, air-bladder (which is suitable to utilize oxygen dissolved in water) was found to be the better respiratory organs it evolved with instead of gills. It requires a better respiratory organ for breathing in the terrestrial habitat where any aerobic organism needs an intermittent supply of oxygen to survive on land. d. Evolution of pedicellate teeth of amphibians: The terrestrial amphibians have been evolved with a sticky tongue to catch a diverse range of smaller size of prey along with better evolved dentine including pedicellate teeth (the root and crown of which is calcified), papilla amphibiorum, and papilla basilaris for better feeding and digestion as well.

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e. Evolution of quiridium-like limbs: The quiridium-like limbs are found to be one of the key features of amphibians evolved with, and it has immense evolutionary importance and which has been further categorized under three subcategories: i. Stylopodium: Comprised 1 bone: either humerus or femur. ii. Zeugopodium: Comprised 2 bones: radius or tibia and ulna or fibula. iii. Autopodium: Forming hands and feet, toes and fingers. The critical review of the anatomical features of these quiridium-like limbs by the scientists revealed that the stylopodium and zeugopodium were found to be originated out of the bony structured part of Sarcopterygian fins, whereas the autopodiums were found to be evolved as completely new organs or “de novo,” and found to be integrated to the evolution of amphibians on the land. The scientists contemplated further that the erstwhile members of Amphibian tetrapods like Osteolepiformes evolved with these limbs whenever roaming around in shallow, brackish, oxygendeficient water before took an evolutionary stride to transmigrate to land, and these ancient, extinct amphibians have not only been considered as the progenitor of the contemporary, extant amphibians but also recognized as the podium or evolutionary predecessor leading divergence of amniotes: reptiles, birds, and mammals. However, in 2011, Heather King, one of the graduate students of the University of Chicago Medical Center, USA has created and published a video presentation in the proceedings of the National Academy of Science, which meticulously elucidated the pelvic limbs driven locomotion (by means of the primitive locomotor organs), underneath of its body of the fishes having “eel-shaped body,” and also recognized as “lung fishes” (King et al., 2011). This unique observation has amazed the evolutionary biologists as they were familiar with such organ-driven locomotion, thought to be evolved among the ancient, land-dwelling tetrapods, whereas witnessing the same features, among the ancestral lineages of Pisces, especially in the lungfishes led the scientists to redefine the evolutionary history of transmigration of life from water to land. And such observation, supplemented with paleontological analysis, would have pondered the budding evolutionary biologists like Heather King and others of the University of Chicago Medical Center to conceptualize about the evolutionary divergence of the ancient tetrapods out of the “lobe-finned ancestor of lungfish” (Uchicagomedicine, 2011). The meticulous observations on the evolutionary studies on the African lungfish (Protopterus annectens) made the young researcher, Heather King, to state that “The lungfish is in a really great and unique position in terms of how it is related to fishes and to tetrapods,” and she further stated: “Lungfish are very closely related to the animals that were able to evolve and come out of the water and onto land, but that was so long ago that almost everything except the lungfish has gone extinct” (Uchicagomedicine, 2011). Melina Hale, the associate Professor in Organismal Biology and Anatomy, University of Chicago, and coauthor of the recently published research paper on the evolutionary history of lungfish in which she further upheld the hypothetical interpretation of Heather King as she said: “In a number of these trackways, the animals alternate their limbs, which suggested that they must have been made by tetrapods walking on a solid substrate.

The Evolutionary Biology of Extinct and Extant Organisms

We’ve found that aquatic animals with fundamentally different morphologies and that aren’t tetrapods could potentially make very similar track patterns” (Uchicagomedicine, 2011). Michale Coates, professor of the Organismal Biology and Anatomy, one of the famous researchers in evolutionary biology has earned a good name for his expertise in gait analysis of the locomotor organs of the primitive organisms, and he stated his research observation as he said: “It’s tempting to attribute alternating impressions to something like the footfalls of an early Tetrapod with digits, and yet here we’ve got good evidence that living lungfish can leave similar sequences of similar gait. The fin or limb use thought to be unique to Tetrapods is actually more general” (Uchicagomedicine, 2011). Hence, the observation of professor Coates, who co-author of the publication entitled, “Behavioral evidence for the evolution of walking and bounding before territoriality in sarcopterygian fishes,” published in Proc. Natl. Acad. Sci. USA, Dec 12, 2011, has also been found to be supportive to the earlier observation and interpretation of Heather King to recognize “African lungfish” as a transitional link or evo-link between aquatic fishes and land-dwelling tetrapods (King et al., 2011). The sketch of the African lungfish is presented herewith in Fig. 4.1. Apparently, it seems to be confusing to the scientists, whether the fins of any fish would have such load-bearing potential that would help it to walk on the terrestrial surface, but it has also been argued that its possession of the lungs rather than gills, attributed to the lungfish to breathe in substantial volumes of oxygen to make the mouth-ward part of the body buoyant, so the frail hind limbs at the tail-end could push the body front-ward to coordinate its walking. Neil Subin, professor of Organismal Biology and Anatomy, University of Chicago and one of the coauthors of the paper on evolutionary studies on lungfish, under the principal authorship of Heather King, elucidated the locomotion of lungfish in the backdrop of the evolution of its breathing organs and locomotor organs in the conjecture of transmigration of vertebrates from water to lands as she said “If you showed me the skeleton of this creature and asked me to make a bet on whether it walks or not, I would have bet it couldn’t. Their fins seem like the furthest thing from walking appendages possible. But then, it

FIGURE 4.1 The diagrammatic sketch of African Lungfish. Courtesy Sashi Sinha.

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shows what’s possible in an aquatic medium where you don’t have to support yourself with gravity” (Uchicagomedicine, 2011). In parallel to the investigations of Heather King, the discovery of 397 million year’s old fossil site from Poland helped the evolutionary biologists to have an idea about origin and evolution of vertebrates as the “Oldest Land - walker tracks found - pushes back evolution of tetrapods” (Janvier and Clement, 2010). The discovery of distinct digit marks on the limestone slabs of the fossil site raised further concern about the possibility of the existence of four-legged animals (as lobe-finned fishes do not have any digits in its place of fins) that is, tetrapods supposedly evolved at least 18 mya earlier than origin and evolution of sarcopterygian fishes on the Earth (Roach, 2010; Luskin, 2011). To clear the doubt, which challenged the amphibian succession of tetrapods, the phylogenetic tree of the tetrapods needs to be reconstructed again, where reassortment of the molecular data needs to be supplemented with paleontological data. On the other hand, the most recent investigation of a group of molecular phylogeneticists from China, under the leadership of Jing Lu of Key Laboratory of Vertebrate Evolution and Human Origins, under the parent research organization of Chinese Academy of Science, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, carried out the tomographic analysis of a fossilized skull of a predatory Devonian fish, that rendered the scientists to recognize it as Quingmenodus, a Pragian Onychodont from China (Lu et al., 2016). The age-dating process has revealed that Quingmenodus seems to be evolved around 409 mya. The scientists have observed that the ancient or stem group of sarcopterygians (like Guiyu and Psarolepis) are remarkably distinct from the recent or crown group of sarcopterygians (like coelacanths, lungfishes, and tetrapods) and the lack of any transitional form rendered the evolutionary biologists to interpret the evolutionary link between these two groups remained enigmatic for a period of time. The computer-aided tomographic analysis of the internal braincase of Quingmenodus, helped the scientists to establish an Evo-link between the stem and crown group of sarcopterygians as the ethmosphenoid portion of the skull of Quingmenodus has a strong resemblance to the skull structures of the members of the stem group of sarcopterygians, whereas the neuro-cranial characteristics of the otic region of its skull have been found identical to the members of the crown group of sarcopterygians like coelacanths (Lu et al., 2016). Apparently, Quingmenodus appeared to be an Evo-link between stem and crown group of members of sarcopterygians; but the discovery of the footprints of the tetrapods (around 397 million years old) on the limestone slabs of a fossil site in Poland that revealed the discovery of 409 million years old fossil of Quingmenodus, a sarcopterygian member, tarnished their earlier claim on the biological evolution and preexistence of tetrapods before sarcopterygian fishes (Lu et al., 2016). However, a group of immunologists and molecular biologists recently engaged in the investigation of the adaptive immune system of vertebrates in the molecular level, specifically on the evolution of the mucosal immune system in endotherms as well as the evolution of secondary “organized mucosal-associated lymphoid tissues” (O-MALT) (e.g., tonsils, adenoids, etc.) (Tacchi et al., 2015). During their

The Evolutionary Biology of Extinct and Extant Organisms

extensive research works on a wide group of organisms, the scientists discovered the existence of lymphoid aggregates (which has considered being structural and functional precursors of O-MALT, predominantly existed in the advanced group of vertebrates, including human beings) in the mucosa of anuran amphibians, which led them contemplating the evolution of O-MALT supposedly happen around 250mya (Goldstine et al., 1975; Ardavin et al., 1982). The presence of lymphoid aggregates in the lymphocyte-rich structures of epithelium tissues of the nasal region of lungfish helped to establish an evolutionary bridge between bony fishes and Amphibia in one end (Tacchi et al., 2015). On the other hand, the comparative phylogenetic analysis with lymphoid aggregates of African lungfish and the “mammalian tertiary lymphoid structure” in the molecular level ascertained that the origin of O-MALT found to be preexisted before the origin and evolution of tetrapods, which indirectly pointed out the evolutionary divergence of tetrapods, including the highest, evolved group of animals like mammals, the land-dwellers, supposedly taken place millions of years ago out of the evolutionary root-stock of the bonefish from water supposedly transcended through the amphibians to have finally emerged as vertebrates (including mammals) as the existence of mucosal lymphoid organs in the extant group of tetrapods left the molecular foot-prints behind (Tacchi et al., 2015). Along with a number of discoveries, one of the marvelous discoveries in the field of zoology in the 20th Century was the discovery of around 1 m long bluish-colored fish, having conspicuous fins, resembled the limbs of the land-dwelling tetrapods in 1938 by Marjorie Courtenay-Latimer, the curator of the Natural History Museum of East London South Africa. She had received this unusual looking fish from the local fisher-folk from a pile of fishes in a fish trawler (Smith, 1939). This naming of this newly discovered fish has been made by Professor J. Smith, the famous Ichthyologist of the University of Rhodes, South Africa, in the honor of “Marjorie CourtenayLatimer” as Latimeria chalumnae. From the evolutionary biological perspective, scientists assumed that this unusual-looking fish, which has scientifically been identified as an extant member of the coelacanth seem to be extinct in the upper Cretaceous around 70 mya (Smith, 1939). Since 1938, thus far 309 specimens of coelacanths have been collected in living conditions mainly from the East African coast, belonging to different species of Latimeria genus (Smith, 1956; Erdmann et al., 1998; Nulens et al., 2011). It needs to be mentioned here that the members of Coelacanths or Latimeria are found to be the transitional link that has established the evolutionary bridge between Pisces and Amphibia, whereas Lung fishes or Protopterus are found to be the transitional link or evo-link between bony fish and amphibians. Apparently both types of lobe-finned fishes are considered to be the ancestor of tetrapods and the advanced group of vertebrates on the land, that supposedly evolved out of such root-stock of fishes once evolved in the waterbodies. On the basis of comparative anatomical studies of the skull and vertebras of these extant coelacanths to their extinct ancestors, the evolutionary biologists and the paleontologists assumed that ancestral lineage of these extant members of Latimeria evolved around 300 mya, during Devonian (Amemiya et al., 2013). Furthermore,

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the evolutionary biologists considered Latimeria as lobe-finned fish seems to be slowly evolved, which still played an important role in the transmigration of prehistoric aquatic animals to lands from water and the evolution of tetrapods as well (Zhu et al., 2016). A number of scientists, going forward, started advocating in favor of Latimeria to be recognized as the most tenable contender of “Last Fish Ancestor” or “First Tetrapod Predecessor” to celebrate its symbolic end of the journey of a fish to crawl onto land from water as well as the symbolic start of the journey of a tetrapod to experience its maiden run on the lands in four legs (Zimmer, 1999). In the arena of molecular phylogeny and evolutionary biology, it had been remained as an unsettled issue to recognize “the first fish that crawled onto land” as the scientists narrowed down their search to either lungfish or coelacanth as the most possible contender, whenever they have screened out a wide number of species, and finally narrowed it down to an alternative contender between the Sarcopterygian fish (like lungfishes) and Crossopterygian fish (like coelacanths) (Shultze and Trueb, 1999). The comparative genomic analysis between African lungfish and African coelacanth has helped the scientists to resolve this complex phylogenetic puzzle as the lungfish has been standing out, to be the ultimate winner of this longawaited evolutionary resolution as lungfish has been emerged as the “extant sister group to the land vertebrates” as per contemporary investigations in molecular phylogenetics and genomics; though a number of evolutionary biologists considered both members of lobe-finned fishes as the predecessor of tetrapods on Earth (Meyer and Dolven, 1992; Brinkmann et al., 2004; Stamatakis et al., 2005; Amemiya et al., 2013). Stoically, the evolutionary emergence of amphibians, which has often been contemplated by some scientists more than one time in the last few millions of years history of biological evolution on Earth in the backdrop of drastic environmental changes, which transcended through a number of bottle-neck of mega extinctions, have often been appeared as analogical cascading emergence of phoenix (the bird of heaven) from its ashes, as depicted in the classic literature of Fyodor Dostoevsky in “War and Peace.” According to the contemporary phylogenetic investigations of the molecular geneticists, amphibians are such evolutionary “sentinels” those have not only witnessed the environmental changes but also endured such changes and responded to it by means of undertaking at the multilevel adaptive changes to be successful in transmigration from water to land and finally initiate the evolutionary journey of vertebrates on Earth (Brahic, 2007). The synecologists, animal physiologists, and the evolutionary biologists have noticed in their investigations that from the very beginning of their evolutionary journey, amphibians have gone through a cascade of mutations on its transmigratory swing and counter-swing between land and water as they have got in touch with the barge of mutation enhancing factors, ranging from absorbance a number of chemicals (some of those are found to be a toxin in nature, chemical mutagens, etc.), to sustain infections from a number of microorganisms (like pathogenic bacteria, fungus, etc.), to endurance of high level of exposition of UV radiations, etc. Most often such physical and physiological exposition of potential mutagens leads to another

The Evolutionary Biology of Extinct and Extant Organisms

paradigm shift to expedite or slow down the rate of divergence and diversification to cope with changing environmental conditions by means of eliciting the extent of phenotypic plasticity of the concerned organism. On the contrary, when the rate of divergence in amphibians failed to cope with the extent and magnitude of alteration of environmental changes, a drastic depletion of the population size has been witnessed, which most often ends up with the extinction of a species. The scientists contended that the occurrence of a number of major mega extinction events led to the extinction of a substantial number of amphibian species in course of evolution. Even in this regime of the Anthropocene, the critical issues like natural habitat destruction (by degrading wetlands and filling up the aquatic bodies by abrupt landfilling), habitat fragmentation (building highways through the forests), environmental pollution (discharging toxic chemical and industrial effluents to the water bodies), overexploitation of wild germplasm from natural habitat, etc. played a key role for the disappearance of a number of amphibian species on Earth. Contemporary experimental reviews on the population dynamics of amphibians (mainly the frogs) revealed that there was a sharp decline of amphibians occurred in current years, which was found to be around 43% due to anthropogenic actions either by direct consumption of it or destruction of its habitat by degrading wetlands (Brahic, 2007). Based on the paleontological reviews, the scientists found that the occurrence of a number of mega-extinction events had pushed around 30e35 prehistoric amphibians on their way to extinction and some of these were the following (Strauss, 2019): 1. Amphibamus (salamander-like) used to exist in carboniferous (300 mya) 2. Branchiosaurus (Gill lizard) used to exist in Carboniferous-Permian boundary (310e290 mya) 3. Cacops (Blind face) used to exist in Permian (290 mya) 4. Eocaecila (Dawn caecilian) used to exist in Jurassic (200 mya) 5. Eogyrinus (Dawn tadpole) used to exist in Carboniferous (310 mya) 6. Fedexia (frog like; name has been given after the globally renowned Federal Courier CompanydFedEx) used to exist in Carboniferous (300 mya) 7. Geobatrachus (Ancient frog) used to exist Permian (290 mya) 8. Koolasuchus (Kool’s Crocodile) used to exist in Cretaceous (110e100 mya) 9. Microbrachis (Little Branch) used to exist in Permian (300 mya) 10. Phlegethontia (snake like body) used to exist in CarboniferousePermian boundary (300 mya) 11. Platyhystrix (flat porcupine) used to exist in Permian (290 mya). etc. It is quite an amazing observation of the evolutionary biologists that despite facing all survival challenges, the evolutionary journey of amphibians has been remained uninterrupted and it had further been affirmed in the statement made by Kim Roelants from Vrije University in Brussels, Belgium, one of the leading molecular phylogeneticists, who stated “.their latest evolutionary tree reveals that amphibians have a remarkable capacity to bounce back from environmental changes” (Brahic, 2007).

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To the evolutionary biologists and molecular biologists, the creation of an evolutionary tree is a challenging task as paleontological evidence of amphibians are not enough to coordinate allied composite analysis like the advanced level of investigations of those fossil specimens, analyzing the DNA sequencing, extracted from its well-preserved tissue in fossil form, etc. The molecular phylogeneticists primarily depend on the genetic analysis, extracted from the extant members of amphibians to backtracking evolutionary divergence of amphibians, to understand its mode of divergence. In a contemporary review, scientists have collected around 171 samples (comprised of 120 frogs, 27 salamanders, and 24 caecilians) and extracted its DNA fragments from four nuclear genes (CXCR4, NCX1, RAG1, and SLC8A3) and one mitochondrial gene (16S rRNA), and this collection of DNA samples have been done randomly from a number of extant amphibians to track the evolutionary divergence of two new species from its common ancestor (Roelants et al., 2007). The qualitative findings of the molecular geneticists from this experiment have indicated further that extant amphibians are considered to be emerging out of recent common ancestral stock rather than emerging out more than once from the dissimilar prehistoric root-stocks (Brahic, 2007). According to the research observations of Kim Roelants et al. (2007), the contemporary amphibians were evolved out of three common ancestral lineages as well as a line of the trinity, which supposedly happens around 350 mya. The evolutionary biologists have further hypothesized that in the post-PermianeTriassic mass extinction event, which was found to be responsible for the extinction of around 95% of world biota, vacated the ecological niche that was occupied by the erstwhile organisms, paved open the origin, evolution, and diversification of a big number of species including prehistoric amphibians to colonize the vacant ecological niche. Roelants et al. (2007) revealed that erstwhile “line of the trinity” of amphibians supposedly diverged out in the geological regime between 250 and 225 mya to give rise to frogs, toads, salamanders, and snake-like subterranean amphibians called caecilians and such explosive radiation of amphibians in that specific geological regime of postPermianeTriassic mega-extinction initiated the diversification of modern amphibians on Earth. According to the critical reviews, based on molecular phylogenetic analysis, genomic investigations and a selected number of paleontological reviews, Roelants et al. (2007) came to the conclusion that another two major evolutionary surging explosions of amphibians happened immediately after the Cretaceous-Tertiary megaextinction event, which had supposedly occurred around 65 mya. It has further been assessed that around 65 mya, the Cretaceous radiation of amphibians led to 86% diversification of frog species and 81% of salamander species. The extensive research works on the various aspects of the Cretaceous-Tertiary mega-extinction and its aftermath revealed that, in the postmass-extinction regime, a wide array of flora and fauna found to be evolved and colonized the new habitat and vacant ecological niche with unique faunal elements that had been triggered at the conjectured evolution and diversification of flowering plants on Earth.

The Evolutionary Biology of Extinct and Extant Organisms

In the backdrop of radiation of flowering plants in Cretaceous, the research works successfully established the “evolutionary potential of bounce-back of amphibians” hypothesis. In 2007, Kim Roelants and his colleagues revealed that the explosive surging of amphibian populations, particularly the frogs in the postextinction regime of Cretaceous-Tertiary boundary around 65 mya, would inevitably substantiate such hypothetical stand, and it rendered Roelants to state “For instance, right after the dinosaurs went extinct 65 million years ago at the Cretaceous-Tertiary border, there was a huge explosion of frog species” (Brahic, 2007). It has been also been observed by the evolutionary biologists later that the evolution of tree-frogs and treesalamanders should be considered a unique instance of coevolution of flowering plants and those tree-dwelling amphibians during the Cretaceous period (Brahic, 2007). Apparently, the observations of conservation biologists and the evolutionary biologists on the population dynamics of amphibians seem to be apparently complex as the conservation biologists have tried to express their concern on the sharp rate of declination of the population of amphibians, particularly frogs as they have contended it as follows: “Global frog crisis defies explanation,” “Global warming fuels fungal toad killer,” etc. in the backdrop of man-made extinction in this regime of the Anthropocene (Brahic, 2007). Whereas, the evolutionary biologists have engaged in the interpolation of the evolution of amphibians on the basis of their interpretation, where it would have been influenced by mega-extinction events. However, the impact of mega-extinction events was found to be apparently beneficial for amphibians in terms of evolution, surging of its population size, and its further diversification and which has apparently supported “evolutionary bouncing back of amphibians” hypothesis. On the other hand, the evolutionary biologists who were the experts on amphibians and reptiles as well have expressed their concern whether the contemporary amphibians would have that resilience for an evolutionary bounce back or otherwise. Kim Roselants has expressed his concern with skepticism as he stated: “It is unfortunate, but then you can’t talk about super-amphibians” (Brahic, 2007). To us, the most important matters are that we could not simply predict some hypothetical scenarios as evolution has been proven to be a random process rather than a definite process and that would define further that evolution of a certain organism to a certain direction (as the newly formed habitat, created by vacant ecological niches in the new environment) might be suitable for a distinct type of organism, rather than each and every amphibian members. Hence, Roselants’s statement on such hypothetical scenarios found to be a well-judged statement, when he said: “It is likely that survivors of extinction will re-diversify, nevertheless this will probably take thousands or million of years” (Brahic, 2007).

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Evolutionary origin of amniotic egg: the transitional form between amphibians and reptiles in the doubt clear session

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“Here, we see the effects of a rather well-documented paleontological record. With such a record at hand the divisions between groups break down. The evidence of the seymouriamorphs indicates too clearly for the peace of mind of those students who wish to categorize animals within neat boundaries of classification that evolution is a continuum” -Edwin H. Colber & Michael Morales.

“Tiktaalik blurs the boundary between fish and land-living animal both in terms of its anatomy and its way of life” commented by Neil Shubin, Professor of Organismal Biology, University of Chicago, USA, immediately after his marvelous discovery of a fossil creature, Tiktaalik roseae, having composite features of primitive fishes (like the presence of jaw, scales, and fins) and the primitive tetrapods (presence of skull, neck, ribs and the locomotor limbs) found after the completion of paleontological exploration in the Ellesmere island of Arctic Canada, Nunavut territory, 600 miles away from North pole region (Gianaro, 2006; Shubin et al., 2006). Although Shubin and his colleagues have discovered this most interesting fossil remnant in 2004, which appeared to be an evolutionary link between fish, the predominant creature in water and the first animal tried to strive for terrestrialization and evolved around 375 mya on this Earth. Professor Shubin and his colleagues took 2 years for the completion of paleontological studies of the fossil samples in different aspects before publishing about it in the reputed research journal “Nature” on April 6, 2006 (Shubin et al., 2006). The availability of high-quality fossil samples (a number of specimens, ranges from 4 to 9 feet long) helped Professor Shubin and his colleagues to study the morphological and anatomical features of this unique creature and after careful investigations, they were able to describe this prehistoric creature with the flattened body with crocodilelike skull and sharp teeth that was found in mixed with carnivorous animals (Gianaro, 2006). The well-preserved fossil gave an opportunity for the scientists to study the intricate anatomical feature of the fin-bone joints along with supplementary Gate The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00002-7 Copyright © 2021 Elsevier Inc. All rights reserved.

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analysis, which ascertained that the wrist joints, elbow joints, and the well-built shoulder of this creature were found helpful for this creature to make it capable to carry its own body weight and roamed around in terrestrial habitat like a limbed animal. In support of elucidating the “Fin to Limb” hypothesis, H. Richard Lane, the director of sedimentology and paleo-biology, National Science Foundation, USA, has stated “Human comprehension of the history of life on Earth is taking a major leap forward. These exciting discoveries are providing fossil ‘Rosetta Stones’ for a deeper understanding of this evolutionary milestone - fish to land-roaming tetrapods” (Gianaro, 2006; Jha, 2006). As the scientists requested the local people who belonged to the Inuit communities in the Nunavut area of Arctic Canada and Nunavut Council, they proposed the name “Tiktaalik” in the Inuktitut language, which means “a large, shallowwater fish” (Spotts, 2006; Shubin, 200). Even Farish Jenkins, the professor of Organismic and Evolutionary Biology from Harvard University, USA has critically studied the skeleton structure of this evolutionary-link and has drawn an inference on the basis of his critical review as he said: “The skeleton of Tiktaalik indicates that it could support its body under the force of gravity whether in very shallow water or on land” (Gianaro, 2006; Shubin et al., 2006). In their detailed paleontological and geological investigations, Shubin and his colleagues came to a conclusion that the current location and environmental condition of “Arctic Canada” were different from its erstwhile location in the Devonian period, around 375 mya as it was supposedly adjacent to the equatorial region (having resemblance to tropical Amazon basin of South America) with predominating subtropical climate and “Tiktaalik,” supposedly roamed around in the shallow streams and subtropical deltas that evolved for terrestrialization for ensuring its survival after migrating from shallow water-logged basin or bogs to the adjacent lands in that time (Gianaro, 2006). The evolutionary biologists contemplated that the initial approach of terrestrialization of the land dwellers was part of an approach to commuting to and fro between two adjacent habitat, water-bodies and adjacent terrestrial eco-systems, but as time passed, a vast terrestrial habitat opened up, leading an evolutionary opportunity to the creatures like Ichthyostega to explore the terrestrial ecosystem rather than confined itself in shallow water-bodies. Thus, scientists considered Ichthyostega as an evolutionary link or transitional link as well as the maiden amphibian organisms (frogs, toads, salamanders), looked for opportunities to settle down on the land to explore a vast uncharted territory around 350e300 mya on Earth (Panciroli, 2017). By virtue of the in-born potential of adaptation, amphibians are well adapted in the diverse eco-climatic regions in farther and wider diverse nature of habitats, ranging from the Arctic Tundra to Saharan deserts in different continental parts of the Earth. Scientists noticed that since the evolution in aquatic bodies had been initiated, the amphibians slowly shifted toward the terrestrial habitats to settle down in course of transmigration to cope with the terrestrial environment through undertaking a series of physical, physiological, and behavioral adaptive changes, that helped

The Evolutionary Biology of Extinct and Extant Organisms

them to sustain in this course of terrestrialization, except in occasional return to the aquatic habitat for completion of the reproductive cycle and laying eggs nearly at the aquatic habitat. Though there was no consensus among scientists, specifically evolutionary biologists and phylogeneticists on the identity of the maiden amphibians, Eusthenopteron, one of the descendants, emerged out of the mother-stock of Crossopterygians (the lobe-finned fishes) and Dipnoans, the ancient lungfish, which was supposedly evolved around upper and middle Devonian (around 390 mya) (Hofrichter, 2000). The presence of unique features like the presence of gills and gas-permeable skin to survive with dissolved oxygen in water, the presence of primitive lungs to survive on the terrestrial habitat by breathing oxygen in the air, and the possession of leg-like limbs in place of typical fins rendered it to gain stability in favor of gravity-triggered terrestrial locomotion. Its well-built skeleton and distinct nostril and tail helped to maintain the body balance and avoid predation on terrestrial habitat for Crossopterygians and it made the scientists consider these animals with “land-like features” as first lobe-finned fishes, those attempted for terrestrialization first time. The evolutionists construed that possible palaeoclimatic changes had driven change of microenvironment of different aquatic habitats in the late Devonian and dried out ponds, deltas, caused prolonging the drought, etc. that forced the fishes out of aquatic bodies to “crossover” the land in between to reach the next ponds to get more food and ensured its survival, and the entire effort triggered the adaptive changes, helped it in its course of transmigration in long-run (Long and Gordon, 2004). The paleontologists came across to another small-sized (1.5 m long) fossiliferous specimen called “Ichthyostega,” supposedly evolved between 362 and 357 mya, which had been characterized by four legs and seven toes in each foot and the presence of these features helped the scientists to construe that the structural adaptations helped it to come out of seawater to settle on lands as they need plenty of food to survive. The number of large predators during that geological regime, whenever Ichthyostega roaming around on the land habitat, was supposed to have existed in very less number on Earth so, Ichthyostegas, were assumed to be the maiden tetrapod on the land; most likely they might not face stiff competition to compete with other land dwellers (Ward and Kirschvink, 2015). Based on the availability of fossil evidence and its contemporary analysis, the evolutionary biologists and the paleontologists contemplated that around 340 mya, amphibians diverged out of Pisces and “Temnospondyls,” was discovered to be the ancient as well as the maiden representative of amphibians, appeared on the Earth and structurally, it had a composite appearance to be somewhere in between a big crocodile and a newt (Lopez-Bosch, 2015). The other ancient amphibian member was Eryops (around 1.5 m long), which belonged to the extinct group of Rhachitomes characterized by the stout body with rib cages and backbone, and strong covering of scales, tentatively evolved around 270 mya during the Permian(Carroll, 2009). The meticulous research investigations of paleontologists, along with a wide range of exploration work in all over the world, helped the scientists to

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discover that a diversified group of extinct amphibians evolved during 300e200 mya in the boundary of Carboniferous and Permian era and they are as follows (Lopez-Bosch, 2015; Strauss, 2019): A. Aistopods: Looked like a tiny snake, used to possess incipient limb-like structures B. Diplocaulus: Had unique triangular, arrow-like, flattened head, attached to the flattened body and limbs were attached to the body C. Microsaurs: Smaller sized, primitive amphibians, used to stay bottom of a swamp D. Sauropleurs: It had long elongated body with no limbs, like snakes Since its day of emergence, amphibians were considered to be one of the fittest animals those won in the struggle of existence as it went through a diverse array of challenges in its course of terrestrialization from water to land that sustained serious issues like extreme depletion of population size in the back-drop of a number of mega-extinctions. Still, it came across a long way to exist and diversified and overcome all survival challenges to sustain in the current regime of Anthropocene. However, a series of composite survival challenges in the current climate regime like global warming, destruction of wild habitat, forests, pollution of water bodies, depletion of wetlands, usage of chemical pesticides, insecticides, and toxic chemicals jeopardize the existence of around 6000 species of amphibians in the age of Anthropocene (Gascon et al., 2005; Janke, 2010; Miller and Spoolman, 2014). Along with all these environmental and climate change related-factors, geoscientists have observed that continental drifting is a major issue in the expedited rate of natural extinction of a huge number of amphibians as they have presented a hypothetical scenario, where 5e10 cm drifting of the continental shields at a time seems to be a negligible visual impact, but transposing the same figure for 1 million years of time span, it has revealed that continental shields would move away from each other around 100 km distance; eventually, it seems to be 10,000 km away in the span of 100 million years interval. It is convincible from the continental drifting model, that broke-away plates of Pangea, the supercontinent, drifted away from each other and traversed a long distance to get in the diverse eco-climatic zone on its course of movement in the ancient, superocean of Panthalassa. The erstwhile position of the different continental shields was supposedly capable enough to have appeared as the diverse abodes of living organisms, existed around 250e300 mya and amphibians were evolved as part of that nature’s experiment (Collins and Crump, 2009; Miller and Spoolman, 2014). Although the successful beginning of the story of terrestrialization of amphibians depends on its successful evolutionary adaptations on the terrestrial habitat, the success of diversification and colonization of amphibians on Earth has always been integrated to their completion of reproductive cycle at the edge (the matrix of ecotone) of water of land to ensure that their juvenile members do not have to face the stiff competition of the predators of terrestrial origin so that they could slowly grow up and occupy the terrestrial habitat after being attained in adulthood.

The Evolutionary Biology of Extinct and Extant Organisms

As a fierce fighter in the evolutionary struggle of terrestrialization, the evolutionary history of amphibians is undoubtedly an earnest instance, yet the disadvantageous features like exogenous fertilization (fertilization of an egg by sperm outside of the body), and the course of reproduction and laying a huge number of eggs, nearby the water-bodies, have considered being disadvantageous in course of abrupt environmental changes like receding of water level of water bodies and drought, which jeopardize the normal survival and regeneration of a diversified population of amphibians in long run (Lopez-Bosch, 2015). The lack of a protective shell around its eggs attracts a big number of predators to devour its naturally regenerated juvenile amphibians. The evolutionary accumulation of a series of adaptive features by these amphibian members led this group of organisms to go down through trail of evolution to explore further how do the disadvantageous traits to be managed further by the ancient members of amphibians to go to the next level of evolutionary threshold, leading open up the divergence of reptiles in the next level of paradigm shift of biological evolution, diverged out of the ancestral amphibian mother-stock (Janke, 2010; Strauss, 2019). The beginning of the evolutionary journey of reptiles on Earth started with the phylogenetic divergence of it from amphibian root-stock and successful completion of the process of terrestrialization to become part of the terrestrial ecosystems as it had gone through the successful adaptive changes in that time that favored this unique group of organisms for successful colonization on land (Janke, 2010). Before digging deeper, let us find out the meaning of the word “reptile” in the biological world. In a literary explanation in the world of zoology, the group of organisms laid the hard-shelled eggs on the dry terrestrial habitat recognized as reptiles, whereas the amphibians laid soft eggs in and around the water bodies (Carroll, 1982; Janke, 2010; Strauss, 2019). The reptiles have been emerged with thick waterproof skins, which not only helped it to protect from the direct exposure of heat and sunlight, but rendered its inbuilt protection from loss of moisture and escaping dehydration in the severe environmental stresses like prolonged drought, and sustained in the microenvironment that had lack of water or moisture nearby its terrestrial habitat (Carroll, 1982; Strauss, 2019). The features like presence of dehydration enduring as well as water-resisting skin, bigger sized brain, stout formation of legs with strong bone and muscle, a stout bony tail and lungs (without diaphragm) helped this unique group of tetrapods to survive for millions of years in the terrestrial ecosystem prior to the emergence of mammals as an advanced group of tetrapods on Earth (Carroll, 1982; Janis and Keller, 2001; Janke, 2010). The endogenous fertilization (fertilization of the egg by the sperms of its male counterpart happens in the female body of a reptile) and its laying of eggs on the terrestrial habitat seems to be an added evolutionary advantage for reptiles to ensure maximization of its reproductive success by minimizing its potential damage from environmental and biological impediments (like predatory attacks in the aquatic bodies) (Ruta et al., 2003). The formation of a thin calcified shell outside of the

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egg, the presence of liquid nourishment and moist membrane in the reptilian egg, has rendered it enduring high level of environmental stress and indirectly help the reptiles maximizing its initial phase of colonization and diversification on Earth, followed by its emergence on Earth around 315 mya (Ruta et al., 2003). The long and extensive review of the paleontological evidence of the ancient reptiles made the paleontologists consider a number of fossil members of the reptiles as ancient members like Westlothiana. Westlothiana has a striking anatomical resemblance to the amphibians in its structural formation of the skull and wrist joint formation, and features like laying soft and leathery eggs, which seems to be an intermediate structural form of reptilian shelled eggs and amphibian eggs of the permeable and soft type, that has found to be integrated to the emergence of maiden reptiles, have evolved around 350 mya (Smithson, 1989; Strauss, 2019). Whereas the evolutionary biologists have considered another prehistoric lizard-like extinct animal, Hylonomus, (around 20 cm long), an ancient prehistoric reptile that has evolved around 315 mya and supposedly survived for 35 million years before being extinct (Smithson, 1989). The detailed investigations of the same fossil sites, from where the Hylonomus has been reported the first time, have helped the scientist to understand that Hylonomus have sustained on the prey like smaller insects such as millipedes, centipedes, and giant-sized dragonflies instead of hunting the smaller tetrapods (Smithson, 1989; Nunez-DeMarco et al., 2018). The reptile fossil experts noticed that the skulls of the ancient members of reptiles were devoid of any holes, like their modern-day counterparts, but such throwback features had also been noticed among the derived group of extant members of tortoise, turtles, and terrapins. Though it was not really easy to determine the exact time of evolution of the reptiles on Earth. On the basis of elaborative paleontological studies, scientists figured out that at the boundary of Permian/Triassic period (more precisely, between 350 and 250 mya), the ancient reptiles evolved on Earth and once the story of the evolution of Westlothiana and Hylonomus in late Carboniferous period have completed a full circle, the beginning of the evolutionary journey of next group of reptiles with more complexities in the structural formation in the Permian period have started appearing, specifically related to the formation of holes in the skull of the next generation of prehistoric reptiles (Smithson, 1989). The Anapsid member of Hylonomus had been evolved with the solid skull that has no hole in it, whereas the next level of evolutionary changes had been witnessed in the skulls of Synapsid had one hole in each side of its skull; whereas a couple of holes in both sides of the skull of Diapsids had been noticed by the scientists (Strauss, 2019). The gradual evolution of lighter skulls with more holes seems to be useful for holding an eyeball, sensory nerves, and maintaining finer adjustments with other parts of the bodies like flexible jaws, moving necks, rotating bodies, and better adaptation for catching prey, etc. The evolutionary biologists envisaged that around millions of years ago such mammal-like reptiles emerged on Earth, to which the modern human species, the supermammalian descendants had maintained a distant phylogenetic relationship;

The Evolutionary Biology of Extinct and Extant Organisms

moreover, these groups of prehistoric reptilian-mammals had been assumed to evolve prior evolution of dinosaurs, the predominant reptile groups in the Jurassic age. Dimetrodon, (around the 3 m long), the stout prehistoric reptile with spreading legs (sidewise) and big bony tail, which was studied and contemplated by the paleontologists, to be originated in the Permian age (around 280e260 mya) and roamed around for millions of years on the Earth with prancing stride (Angielczyk, 2009). The scientists had also deciphered that the mammal-like reptile Dimetrodon was predominantly nocturnal and went for hunting in the night to avoid competition with other predators (Kemp, 2004). According to the scientist, Dimetrodon, was found to be the biggest carnivorous reptiles, which used to have “two-measure teeth” (closely resembled the mammalian features), evolved in the Permian era on Earth and the ventral back of this unique looking reptile had a structural resemblance to the automobile radiator that trapped enough heat energy after the short-term exposition of sunlight (Rodbard, 1949). The evolutionary biologists further construed that mammal-like reptile or the prehistoric evo-link between mammals and reptiles, evolved as warm-blooded animals diverged out of Dimetrodon during Triassic period, whereas its internal temperature supposedly maintained a constant range of temperature, showing its unique physiological adaptations, irrespective of the outer side high exposure of sunlight (Kemp, 2004; Angielczyk and Kammerer, 2017). On the contrary, the evolutionists construed that evolution of the prehistoric reptiles like Archosaurs evolved out of Diapsids and Archosaurs, those further diverged into terrestrial groups of reptiles like Dinosaurs, Pterosaurs, Crocodiles, etc. and marine reptiles like Ichthyosaurs and Plesiosaurs (Chamary, 2014). Whereas the prehistoric members of Therapsids further evolved to form mammals (Wilford, 1982). However, the predominating ancestral lineage of reptiles, those reported to be evolved in the CarboniferousePermian boundary of the Paleozoic era had further been categorized by the evolutionary biologists into four groups (Schultze and Trueb, 1991; Benton, 2005): a. Captorhinids: The contemporary paleontological investigations supplemented with phylogenetic studies ascertained that the basal reptiles, belonging to Captorhinids, like Diadectes, Seymouria found to be evolved out of amphibian ancestors on their journey through the evolutionary transition to be diverged out as reptiles. These Anapsids were recognized as Evo-links between amphibians and reptiles, supposedly diverged into the distinct forms of ancient reptiles like Synapsid: Therapsids and Diapsids: Archosaurs. b. Millerettids: According to the evolutionary biologists and paleontologists, Eunotosaurus and Milleretta, the “lizard-looking”, ocean-dwelling reptiles supposedly evolved in the early Carboniferous and went to extinction during the Late Permian. The evolutionary biologists furthermore revealed that Mesosaurus, an ocean-dwelling reptile of this group, which had been evolved as a terrestrial organism, moved back to the ocean and adapted to the Marine environment, in the course of reverse evolution.

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c. Pareiasaurids: The largest, extinct fossiliferous members of Anapsids had been represented by two extinct members of prehistoric fossil species of reptiles like Pareiasaurs and Scutosaurus, evolved along with structural adaptation like armor shields to protect themselves from other competitors and predators. Yet, these members had been pushed on the way of extinction around 250 mya for failing to cope with the paleo-climatic upheaval. d. Procolophonians: According to the evolutionary biologists, the genera like Owenetta and Procolopon, those belonged to the group of Procolophonians, supposedly represented by the herbivorous Anapsids. The ancestral members, belonging to this group, considered to be phylogenetically succeeded by the extant reptilian lineage of tortoise and turtles. According to the analysis of paleobiologists, Seymouria, the transitional link or the Evo-link has been discovered from a fossil site of Seymour, Baylor County, Texas, USA, from which the scientific name Seymouria baylorensis has been ascribed and it has been described by the German paleontologist Ferdinand Broili for the first time in 1904 (White, 1939). The age-dating process and paleontological investigation has further ascertained that this extinct, evolutionary link between amphibians and reptiles, evolved around the Permian period in the ecotone of land and shallow water overlapping zone, and characterized by the salient features like - presence of overlapping scales, primitive lungs (without diaphragms), presence of nostrils and mouth cavities in its skull and well-built legs suitable for roaming around the terrestrial habitat. After critical reviewing the paleontological samples of Seymouria, collected from different fossil sites the scientists have tried to define its unique characteristics like a robust skeleton, stout legs with “sprawling gate” and the reptilian mode of reproduction like laying shelled eggs (which contained amnion membrane, predominantly found in the reptiles, birds, and mammals) in the land (Berma, 2000; Laurin, 2019). The eminent paleobiologist Alfred S. Romer (1928), referred it as the well statured, pre-historic reptile, evolved in the Permian period, and noticed its close resemblance to the reptile-like tetrapods, Cotylosaurs. One of the unique findings in the world of biology is the maiden discovery of calcium-coated or “shelled egg” in the tetrapod lineage, which has been noticed in the life history of the typical Evo-link Seymouria, contemplated to be 280 million years old. However, the opposing group of paleontologists, like Peter Sushkin (1925) and Theodore White (1939) put priorities on the skull formation (presence of otic cleft at the front end of the skull that reduces its strength and restricted the members of amphibians to catch bigger preys), along with secondary features like presence of sensory organs and presence of lateral lines, and pointed toward the ecological feature like affinity to the aquatic habitat of Seymouria to consider it as a close ally of “Embolomeres,” the amphibians belonged to “Labyrinthodonts” (Laurin, 2019). The diagrammatic sketch of Seymouria sp. is presented herewith Fig. 5.1. The meticulous studies of the paleontologist Zdenek Spinar in 1950 on the fossilized larval stage of Discosauriscus (belonging to the group Seymouriamorpha),

The Evolutionary Biology of Extinct and Extant Organisms

FIGURE 5.1 The diagrammatic sketch Seymouria sp. Courtesy Sashi Sinha.

revealed that in the larval stage the Seymouria was predominantly aquatic in habitat, which found to be present in the life-cycle of amphibians (Laurin, 1996). Though the bickering on the true identity of this prehistoric, evo-link, Seymouria might further take its own course, whether it was proamphibians or proreptilians, but there was no doubt in the history of evolutionary biology, specifically in the background of terrestrialization process of the biological organisms in between 300 and 200 mya, Seymouria the extinct creature lived in the ecotone of water and land, found to act as an evolutionary bridge through which tetrapods got an opportunity to be diversified and diverged out further in the form of modern-day mammals, including modern human species (Olson, 1965). The paleobiologists came across a unique, prehistoric organism, recognized as a penetrating-biter as well as Diadectes, an extinct transitional or evo-link between amphibians and reptiles, found to be evolved in the Permian period around 290e272 mya. The paleontological remnants of Diadectes has been reported first time from a fossil site of Texas in 1878, and it has been identified and described by the two famous North American paleontologists, Othniel Charles Marsh and Edward Drinker Cope (Cope, 1878; Case, 1910). The maiden discovery of 5e10 feet long, stout statured tetrapod, Diadectes on Earth, had created a buzz in the scientific world as it was supposedly the first terrestrial, herbivorous tetrapod evolved on the terrestrial habitat. The presence of unique features like well built, heavy skull, well-built rib-cages, and stout limbs with limb girdles helped the scientist to recognize this extinct species as terrestrial animal as these adaptive features found to be prevalent among most of the terrestrial tetrapods and advanced group of vertebrates, whereas the presence of “peg-like teeth”, grinding molar teeth on both sides of the jaws and the robust rib cage indicated that it supposedly contains a large-sized intestine, normally been found in the herbivores, suitable for digesting plant materials (Case and Williston, 1912; Berman et al., 1998). The presence of the characteristic features like affinity of Diadectes toward fiber-enriched food, further indicated its evolutionary connect to the primitive reptiles.

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A number of paleobiologists considered that the presence of a reptilian lineage of adaptations of Diadectes contemplated them to relate it as evolutionary descendant from the primitive amniotes like Pareiasaurs, Pelycosaurs, etc. (Kissel, 2010). The conspicuous reptilian pattern of the skeleton in Diadectes and the typical pattern of its skull (like otic notch, found to be present in the group of amphibians belonged to Labyrinthodonts), which resembled its skull to Seymouria, rendered the evolutionary biologists to recognize it as one of the transitional form or Evo-link between amphibians and reptiles (Carroll, 1990; Kissel, 2010). Maybe, the world of science would need more time to define or redefine the chronological account of the evolutionary journey of tetrapods especially the mammals that had touched down more than one transitional stopovers of Pisces, amphibians, reptiles, and birds and finally diverged out as mammals but there was no doubt that the paleontological existence of Diadectes ascertained the existence of evolutionary bridges or Evo-links was there during Carboniferous-Permian boundary (Lewis and Vaughn, 1965). According to the narratives of paleobiologists, during the early Permian (between 330 and 280 mya), whenever the Carboniferous rainforest collapsed, the members of Diadectomorpha, clad, (around 7e15 feet long) the reptile-like amphibians, evolved on Earth. The members of Diadectomorpha are partly semiaquatic and partly terrestrial and in terms of food habit the zoologists classified this group of organisms under three distinct groups of families (Carroll, 1990; Kissel, 2010): i. Diadectidae: The members were predominantly herbivorous, having reptilian adaptations. ii. Limnoscelidae: The members belonged to this family were mostly carnivores, having amphibian adaptations. iii. Tseajaiidae: The members used to have composite characteristics like partly omnivores and partly herbivores. Though the scientists noticed from their paleontological investigations that the members of Diadectomorphs used to lay amniotic eggs, the typical features had been noticed among the members of ancient reptilian members, belonged to Synapsid, but a number of Diadectomorphs were found to lay anamniote eggs with typical amphibian feature like spawning in the water bodies like larval stage of amphibians like tadpoles and fertilization of eggs reported to be taken place inside or outside of the body (Liu and Bever, 2015). The presence of transitional features of amphibians and reptiles rendered the scientists to hypothesize this group of Evo-link as an ideal instance of throwback evolution, an attempt of those animals like Limnoscelis, once settled in terrestrial habitat had tried to go back to waterbodies in search of a congenial habitat to survive to cope with environmental upheaval, though they had been pushed in the way of extinction in the course of the evolutionary journey of life (Carroll, 1967). Francois-Louis Paul Gervais, the famous French paleontologist has discovered the fossil of Mesosaurus in 1864e66, the first marine reptile (around 1 m long), reported from South Africa and South America. This carnivorous reptile, reported to be evolved during the early Permian, seems to be an instance that indicated

The Evolutionary Biology of Extinct and Extant Organisms

this prehistoric, ancient reptile gave up the terrestrial habitat, once its use to roam around to go back to the marine habitat, millions of years ago (Von Huene, 1940). On the basis of extensive studies of the fossil remnants, the paleobiologists observed that the unique features of Mesosaurus like: the presence of nostrils on the upper side of the skull, the presence of long-tail (which had a functional resemblance to the fin of the amphibians), presence of dense bone structure of the legs and webbed feet, rendered these transitional forms of animals between reptiles and amphibians that opted for settling in the marine environment (Modesto, 2006). The presence of a comb-like structure in its jaws found to be proof of a unique food-intake feature of amphibians to catch prey (like small fishes and invertebrates) in the water and filter out excess water. The presence of features like laying eggs on the land, thickened ribs, small-sized skull, and protruding jaws lead a group of scientists to consider it as water-dwelling reptiles. The careful examination of ankles and elbows of Mesosaurus, helped the scientists to understand that the Mesosaurus foot structure was good enough to walk around on the terrestrial surface. The scientists considered the presence of extended hind legs in Mesosaurus seemed to be the best fit for aquatic habitat (White, 1908). The presence of Cleithrum or dermal bone was a unique feature of Mesosaurus as this unique feature had been noticed among bony fishes and ancestral lineage of tetrapods, which indicated a common evolutionary lineage from Pisces to amphibians to reptiles and further extended to end up in mammals (White, 1908; Modesto, 2006). In 1867, Albert Gunther, the renowned German born-British reptile taxonomist, and The Royal Society Fellow as well, proposed a new order, namely Rhynchocephalia, after coordinated a taxonomic review of Tuatara and its phylogenetic extinct allies (Buller, 1871). Tuatara (means beak headed), the name has been adopted from the Maori language of the aboriginal group and it has currently been represented by two living species (Sphenodon guntheri and S. punctatus), restricted in distribution in the coastal habitat of the Karori Wildlife sanctuary, Wellington, New Zealand (Jones and Lappin, 2009). To the paleobiologists, Tuatara or Sphenodon, a lizardlike (but it is found to be phylogenetically resembled crocodiles, in the presence of ribs and bony process, rather than having an identical rib structure of lizards or snakes) animal of around 80 cm long, 1.3 kg of body weight and has survived for 60e100 years of age in wild habitat. This unique transitional form of organism between amphibians and reptiles has been recognized as the last extant descendant as well as living fossil of its ancestral lineage, as all of its phylogenetic allies have been disappeared a long time ago on Earth (Gans, 1983; Daugherty, 1990; Evans, 2003, 2008). Though it has a unique similarity with a lizard as both organisms exhibit “Caudatul autotomy” (the unique properties to get snapped off its tail end, caught by the attacking predator and regenerate it in course of time), but the reproductive features of it is strikingly distinct than lizards as male Sphenodon does not have any penis, but lizards possess two of it (Clause and Capaldi, 2006). The evolutionary biologists revealed that fossil evidence ascertained that millions of years ago, the ancient predecessors of the extant male members of

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Sphenodon used to possess external genitalia or penis, so the absence of it in the current population was an indication of throwback adaptation (Jones, 2017). The spinal vertebrae of Sphenodon have been found closely resembled the spinal vertebrae of crossopterygian fishes and amphibians. Taxonomically, Sphenodon is belonging to the prehistoric reptilian order: Rhynchocephalia, the members belonging to this group supposedly evolve around 240 mya at the beginning of the Mesozoic era. The molecular phylogeneticists revealed that the members of Sphenodon diverged out as a result of the split of Squamate-Rhynchocephalian split (comprising the reptilian members belonging to lizards and snakes), placed around 220 mya and it intrigued the molecular phylogeneticists to undertake an integrated study to unfurl the evolutionary mysteries of snakes and lizards (Gorr et al., 1998). Eventually, the primary effort to reconstruct the phylogenetic histories of Sphenodon, along with other members of Squamates, revealed its close phylogenetic relationship with a wide range of organisms, belonging to a distinct evolutionary group of amniotic tetrapods like crocodiles, snakes, and birds (Jones, 2017). The Sphenodons had been evolved with some advanced features in the reptile groups like thermoregulation mechanism with the help of the third eyelid (nictitating membrane) in each eye, involved in UV ray absorption to yield vitamin D production, used internally and sensing light and dark cycles (circadian cycles) (). Though Sphenodons are devoid of middle ear and ear-drum, yet it utilizes its afferent and efferent nerves in the brain to respond to the sound waves between 100 and 800 Hz and respond to the 40Db loud sound (Wever, 1978). Tuatara is predominantly nocturnal and goes out for hunting its prey ranges from smaller insects, snails, frogs, birds, shrimps, crickets, eggs of seabirds, and shared the burrows of the birds and basking in daytime mostly. The composite studies, comprising of molecular phylogeny and paleontological investigation revealed that on its long history of the evolutionary journey, a diverse array of ecological niches have been occupied by a number of extant groups of lizards, previously occupied by the erstwhile members of Sphenodontians. The evolutionary biologists wondered after completion of their investigations on the extinct members of Sphenodon, Pleurosaurus, a member of aquatic Sphenodontians, which was evolved around Mesozoic, seems to be well adapted to the warmer palaeoclimatic condition in comparison to the members of Tuatara, well-adapted member of extant Sphenodon, restricted in the contemporary process of diversification in the terrestrial, cold climatic condition in New Zealand in Anthropocene (Daugherty and Keall, 2007). However, the message to all who believed and concerned about the naturally maintained equilibrium state of biodiversity in the biosphere, for them, it is really an opportunity to witness and understand the journey of evolution and diversification of tetrapods that happened in the backdrop of environmental changes and through the process of transmigration from fishes to amphibians and from amphibians to fishes, it eventually ended up to the evolutionary emergence of mammals (Benson et al., 2016). Being the ultimate as well as topmost and most powerful (in terms of strategic advancement) species of mammals, it is our weakness that we are

The Evolutionary Biology of Extinct and Extant Organisms

struggling in this regime of the Anthropocene to conserve the living fossil like Sphenodon, the unique Evo-links, those are facing threat to be pushed on the brink of extinction, where the man-made conservation plan for saving this evolutionary stepping-stone has not been endorsed by entire modern human populations (Tarlach, 2017). Hence, the evolutionary history of tetrapods is at a cross-road of Anthropocene, where our course of actions would say whether our present course of actions would be ready to witness another anthropogenic history of extinction by pushing the extant species with survival threat would be pushed forward in the category of “extinct” or we would try our best as most sensitive species to reexplore the evolutionary history of tetrapods as well as the evolutionary history of ourselves by protecting the evolutionary stepping-stones like Sphenodon, effectively (Jones, 2017).

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When contemporary discoveries pushes the bony fish to ancestral or evolutionary back seat and discreetly pushes cartilaginous fish in the advanced or front seat

6

“The unknown question was where did the modern fish fauna come from and who was their ancestor? This ancient fish called Entelognathus is the missing link because it shows that the extinct armoured Placoderms fishes, which dominated the seas, rivers, and lakes of the world for 70 million years were actually the ancestors to all the living fish on the planet today” -John Long.

Professor Martin D. Brazeau from the Department of Life Sciences, Imperial College of London, Silwood Park, UK, who has dedicated almost his entire life as a meticulous research fellow that involved in the extensive studies of the wide collection of vertebrate fossils, mainly the jaws, skulls, vertebras, and solid form of hard tissues all over the world. These fossil collections are mostly formed in the Paleozoic era (those extinct organisms evolved around 540e250 mya) and helped the scientists to decipher the evolutionary history of modern vertebrates, which started with the evolution of fishes in the water-bodies. Dr. Martin Brazeau was a popular scientist in his academic circle, popularly earned the nickname in the name of a great European magician “David Blaine” alias “Great Dave,” as his critical observations and interpretation helped to resolve a number of long-drawn evolutionary issues and those that remained unresolved for a long time. During his brief research tenure in “Naturalis Biodiversity Center in Leiden,” the Netherlands, Dr. Brazeau came across a digitized picture of the skull of “Dialipina,” an extinct fish from Siberia, Russia, evolved around 400 mya. Eventually, the picture of that ancient fish fossil was posted by the Institute of Geology from Tallinn University of Technology, Estonia, which had been discovered by a group of scientists from Siberia in 1962 (Riley, 2016). As Professor Brazeau was one of the best-known scientists in the evolution of Pisces on Earth,

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the high-resolution picture of the skull of “Dialipina,” particularly the broken shaft of its skull roof that exposed the structural formation of the braincase, made him feel that he got in touch with a paradoxical paleontological treasure-trove, which required a thorough study before drawing any conclusion. Along with his colleague, Matt Friedman from the University of Oxford, UK, Martin Brazeau had placed a requisition to receive the material on loan for undertaking an advanced level of investigations (Friedman and Brazeau, 2010). After receiving the fossilized skull, the scientists had carried out the CT scan and their initial findings ascertained that the fossilized fish was wrongly identified as “Dialipina” and it had been reidentified with a new name “Janusiscus” [means two faces, ascribed in the name of Roman God, “Janus”]. Accordingly, the discovery of Janusiscus has found to be not only helpful to resolve an issue of paleontological misidentification of a fossilized sample, rather the observation of Martin Brazeau and Matt Friedman have indicated that they would able to trace out phylogenetic predecessor of the extant jawed fishes on Earth (Friedman and Brazeau, 2010). Furthermore, such meticulous investigation rendered the evolutionary biologists to assume (based on a wide range of phylogenetic and paleontological evidence) that evolution and diversification of vertebrate land-dwellers initiated in the water-bodies and substantiation of which seems to be scientifically integrated to the unfurling evolutionary mystery of Janusiscus (Callier, 2015). Mostly it has been noticed that in the absence of evidence, people rely on philosophical perceptions to elucidate any hypothetical scenarios, and the evolution of jawed fishes has found to be trapped in the middle of philosophical perceptions of the 18th century, which has desperately tried to depict the predecessors of the extant bony fish as a mystic, shark-like, cartilaginous creature, with rough skin of “small-tooth like scales” and “renewing teeth in the mouth and spines in the body, reinforcing the fins” (Riley, 2016). It was apparently as intriguing as “Cinderella Story” where oversimplistic interpretation had been put forth in the 18th century to designate “shark” (the cartilaginous fish) as the primitive fish, merely based on perception. As a result, it has been considered that being a bona fide contender ancestral, evolutionary root-stock of all extant jawed (bony fishes) fishes shark possesses a number of primitive features. According to Dr. Brazeau, such textbook-like interpretation of fish evolution and the evolution of the advanced group of tetrapods in larger aspects were found to be a convincible interpretation of philosophical perception of the 18th century, as “that [interpretation] was attractive, it was convenient and it was a good [Cinderella] story” which desperately overlooked the fragmentary scientific evidence of the 21st century as it did not fit in the footwear of runaway Cinderella and found to be lost down the evolutionary trail of vertebrates in long run. After going through a series of advance level of investigations of the Janusiscus jawed fossil, the evolutionary biologists like Brazeau (Callier, 2015), Friedman, and other Ichthyologists revealed that Janusiscus was a predominantly fish (as there was no other type of large-sized organisms with exo or endo-skeleton evolved in a Devonian period like mammals, amphibians, reptiles, etc.), evolved around 415 mya (Callier, 2015). By studying a large number of remnants of prehistoric fossils

The Evolutionary Biology of Extinct and Extant Organisms

that evolved during the Devonian period, evolutionary scientists came to a conclusion that Devonian oceans were supposed to be considered as the prehistoric evolutionary cradle of fishes as a number of transitional forms of it evolved with a diverse array of fins, tails, cartilages, spines and jaws and “placoderms” (adapted with a heavily armored interlocking bone plates, the extinct fish used to possess in Devonian period) supposedly went through the interspecific and intraspecific biological competition in the water bodies and sustained “big five” mass extinctions around 359 mya that triggered it to float through a series of evolutionary adaptations to evolve as the derived, extant bony fishes in the course of time (King et al., 2016; Zhu et al., 2016). However, the descendants of the ancestral “placoderms” have further diverged in two major categoriesd(1) Cartilaginous fishes (like sharks and rays) and (2) Bony fishes, the extant group of fishes, found to be well adapted in the diversified aquatic ecosystems ranging from saline, oceanic dwellers to the freshwater species of Pisces (Brazeau and Friedman, 2015). The simplistic assumption and kind of biased observation of the anatomists whoever considers cartilages as less evolved tissues than bones in the 19th century rendered the cartilaginous fishes to the bottom of the tree of the evolution model of Pisces. Nonetheless, a number of evolutionists and evolutionary biologists like Michael Coates from the University of Chicago, USA, strongly defied “It wasn’t founded on any well-formulated [evolutionary] argument” as the formation of the evolutionary tree of fishes were merely constructed based on perception rather than scientific judgment. Based on simplistic assumptions (those are not scientifically tested), it is absolutely unacceptable as it is too simplistic observation that the structural formation of cartilages is more simple than the bones and would not have enough merit that could substantiate a hypothesis and hold it back as “so-called” scientific interpretation origin and evolution of Pisces that end up to the evolution of tetrapods on Earth. Since the 18th Century, the cartilaginous fish like shark seems to be phylogenetically considered at the bottom of the evolutionary tree of fishes, where bony fishes have been recognized as the advanced group in such synthetic form of the evolutionary model of Pisces (Riley, 2016; Geggel, 2018). Then, the question we need to ask whether we could rule out the possibility of the ancestry of cartilaginous that could be leading to the divergence of bony fishes or not as the embryological development of tetrapod, as well as vertebrate embryos, has depicted that in the early stages of embryological development, the penultimate form of a skeleton in the embryo has been made up of cartilaginous tissues and, in the course of time, it has transformed into hard, ossified bones to form bony skeleton in the matured organisms, recognized as vertebrates. Therefore, the paleontologist Per Erik Ahlberg from Uppsala University, Sweden has considered that such embryological developmental stages of vertebrates have tendered their support to the hypothetical evolutionary development of fishes (Riley, 2016). Nevertheless, there were always a number of famous scientists (apparently notorious) who raised their voice against the stereotype perceptions of science and vertebrate paleontologist. Michael Coates from the University of Chicago was

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the forerunner among those scientists in upholding unorthodox views against the conventional perception of the evolution of fishes as he stated “It wasn’t founded on any well-formulated [evolutionary] argument . It’s the legacy of pre-Darwinian ideas imported into an evolutionary worldview” (Riley, 2016). The European paleobiologist, Matt Friedmann, from University of Oxford, who was Martin Brazeau’s colleague and Sam Giles’s research supervisor (pursued PhD in the evolution of Pisces), assisted Sam to make a comparative study of Janusiscus along with other 78 fossiliferous species of Pisces that supposedly evolved in the same geological time that had been discovered in different fossil sites and also been studied in preliminary level (Riley, 2016). Friedman and Giles have documented the detailed information of skull shape, its fissures, nerves, position of blood vessels inside, etc. of each and all of these prehistoric 79 fossil species of fishes to figure-out how they were phylogenetically related to each other in a phylogenetic tree, formed on the basis of the comparative studies (Giles et al., 2015). During that period of investigation, a stack of 3D prints of the skull of Janusiscus intrigued Friedman often to touch the skull of Janusiscus physically. Eventually, he shared his personal narrative in a research communication “Looking at the top of the skull, you get one view of what the creature is.[But] look at the other side [which is inside]: you get a very different feeling” (Riley, 2016). The modern technologyassisted studies of the skull of Janusiscus assisted the investigating scientists to draw a conclusion that there was no doubt that the roof of the skull of Janusiscus had been made up of bone, but that did not help to conclude that it belonged to the category of bony fish (Brazeau and Friedman, 2015). The team of paleobiologists comprised of Brazeau, Friedman, and Giles, who took part in the evolutionary investigations of Janusiscus to find the common ancestral root-stock of cartilaginous and bony fishes, finally revealed that the outer surface of the roof of the wrinkled skull of Janusiscus had structurally resembled the placoderm and bony fish. However, the CT scan of the internal cavity of its skull had presented a composite and unique finding like the formation of arteries inside the skull that resembled the structural formation of arteries of cartilaginous fishes whereas the sensory structures and nerves of it had closely resembled the nervous system of bony fishes (Giles et al., 2015). Janusiscus has apparently found to be appeared as “structural trinity” and a strong contender of “founding fish,” an instance of transitional link among placoderms, cartilaginous and bony fishes, which rendered the evolutionary journey of vertebrates has traversed through in a new shift of paradigm. On the other hand, a number of scientists, like Martin Brazeau, strongly believed that it was too early to draw any conclusion as he stated: “One fossil by itself doesn’t change everything” (Riley, 2016). There is a popular saying “One swallow doesn’t make a summer.” It is apparently true analogy, but what happens when 3, 4, 5 or more swallows appear on the horizon at the end of winter? Nevertheless, the term “Fish” has been ascribed to any species, out of 34,000e36,000 members belonging to the diverse group of predominantly coldblooded, vertebrates (ranging from jawless primitive, extant, hagfish to the extinct,

The Evolutionary Biology of Extinct and Extant Organisms

primitive placoderms with armored jaw; cartilaginous sharks, rays to bony fish like sea-horse, tuna, etc.), living in the water bodies that diverged out of the reticulate evolutionary lineages, rather than emerged as a distinct taxonomic group (Nelson, 2006; Reid et al., 2013). Based on the evolutionary traits that helped to recognize as an evolutionary group of animals, Pisces has been further categorized into 5e7 classes. Although the elucidation of the evolutionary journey of vertebrates on Earth further deciphered the intimate phylogenetic relationship of fish as a primitive vertebrate group of animal, acclimatized in breathing in water, its phylogenetic relationship with other four distinct evolutionary groups of animals like amphibians, reptiles, birds, and mammals needed to be understood to get a large picture. These animals had become well adapted to the terrestrial habitats and well adapted to breathe in air in course of its journey through transmigration from water to land. In the course of its evolutionary journey of tetrapod, the vertebrates, which had convincingly completed through its maiden effort of terrestrialization (that fishes already went through) had further been witnessed by the successful endeavor of amphibians and the evolution of lungs found to be the key organ, which helped this early land-dwellers to breathe-in oxygen in the terrestrial atmosphere, rather breathing in oxygen in the dissolved water by gills, like fishes. The evolution of the endoskeleton system like the formation of spine and ribs in the body of bony fish is one of the key factors in prehistoric time, that is the major shift in paradigm in the event of evolutionary metamorphosis that has rendered the placoderm to be protected under a bony armored exoskeletal system outside along with the cartilaginous tissues inside the body, mainly in the jaw areas to diverged in form of contemporary bony fishes in course of Pisces evolution. Moving forward, the microevolution of lungs in place of gills created an opportunity to evolve the African lungfishes, the evolutionary “stepping stones,” which pushed forward the macroevolution of tetrapods, has anatomically been found to possess both gills and primitive form of lungs to survive in water and on the terrestrial habitat and even sustained in the new habitat, after coming out of the water. The trend of structural changes has further been well observed in the divergence of the next stage of evolutionary groups of amphibians, the predominant dwellers in the ecotone of water bodies and land ecosystems. These amphibians maintained a bridge between proaquatic Pisces and proterrestrial reptiles, belonging to the early vertebrates. Pisces are predominantly considered to be cold-blooded animals (like two other distinct groups of vertebrates like amphibians and reptiles) as they could not control their body temperature and their body metabolism is more or less dependent upon the environmental temperature it belongs to, whereas the mammals and birds are predominantly warm-blooded. Those warm-blooded animals consume a huge volume of food for yielding a higher extent of energy to control body temperature (when it is cold outside they change their body temperature too high or vice versa) and use a little part of the food for sustaining their body mass. The evolutionary succession in the group vertebrates (i.e., the emergence of an advanced group of vertebrates out of a primitive ancestral lineage of vertebrates) has gone through the

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critical bottleneck of sequential changes like transmigration of habitat, metabolic adaptation, an evolutionary shift from cold-blooded entity to warm-blooded structure, etc. For evolutionary biologists, it is quite intriguing to notice that most of the fishes have been recognized as the predominant cold-blooded animal, some of its members must possess the molecular keys to sustain as a warm-blooded animal, which would have been transmitted or relayed to their next level of a phylogenetic successor, the amphibians. The discovery of Opah or Lampris guttatus, which has been found as a fish with a warm-blooded entity, has inevitably been recognized as an evolutionary baton changer or Evo-link between cold-blooded fishes to cross over to warmblooded tetrapod (Wegner et al., 2015; http://www.sci-news.com, May 15, 2015). The availability of a huge collection of paleontological evidence and the compilation of contemporary phylogenetic studies have revealed that evolutionary journey of fishes as well as the journey of primitive vertebrate evolution has gone through a difficult trail of evolution, which should be recognized as an amalgamation of physical and physiological adaptations that have triggered the divergence number of evolutionary lineages. The occurrence of overlapping extinctions leading disappearance of a number of primitive members of Pisces belong to a certain ecological niche, often pushed away by the better adapted, advanced group of Pisces to occupy those vacant niches. According to the conventional practices in ichthyology, the taxonomic rank of Gnathostomes (popularly known as jawed vertebrates) has been broadly categorized into two major groups: (1) Cartilaginous fishes or Chondrichthyes and (2) Bony fishes or Osteichthyes. Based on the conventional perception of evolutionary biology, ichthyologists conceived the idea for a long time that in the evolutionary context, the cartilaginous fishes like sharks and rays are relatively primitive over bony fishes as the members of Chondrichthyes did not go through the trail of evolution to be adapted in the dynamic environment they belonged to. They were contemplated to be abstained from being involved in the physiological adaptive changes like a gradual process of ossification and mineralization, which could harden the cartilage to render the hard bony structure (Brazeau and Friedman, 2014; 2015). Nonetheless, the key evolutionary groups in Pisces are as follows: A. Primitive Jawless Fish or Agnatha: The earliest paleontological evidence of Agnatha jawless fish have been discovered from North American and East European shallow, marine water habitat around 450 mya in the Late Ordovician period. It has also been construed that ancient Jawless fish have diverged out of small-sized, soft-bodied members of Cephalochordates, popularly known as filter feeders (Braun, 1996). Most of the evolutionary biologists have assumed the majority of the jawless fishes evolved during Silurian (435e419 mya) except Cyclostomes, but fossilized remnants of jawless fishes have not been found after the Devonian (419 mya) except cyclostome, which has considered to be a modern jawless fish (the earliest fossil of Lamprey from North America, has found to be 300 million years old). Fossils of placoderms and primitive bony

The Evolutionary Biology of Extinct and Extant Organisms

fishes have been discovered in the Devonian, which has helped the scientists to hypothesize that the primitive placoderms and bony fishes have pushed the ancient jawless fishes to extinction to occupy their ecological niches (Green et al., 2015; Xu and Zhao, 2016). B. Primitive Jawed Fish or Acanthodii: The Ichthyologists (the scientists engaged in scientific studies of fish) have revealed that ancient jawed fishes have evolved around 423e416 mya, started declining in the Devonian, and have disappeared in the upper Permian (around 280 mya), in the backdrop of huge ecological changes of water bodies (Bergman, 2010; Brazeau and Friedman, 2015). The primitive Acanthodian jawed fish has found to maintain the evolutionary link between bony fish in the presence of ganoid scales and the fishes with ossified skeletal system; whereas the presence of bony fin spine and gill apparatus have resembled it to the cartilaginous group of fish like sharks, rays, etc. (Woods, 2018). C. Plate Skin Fishes or Placodermi: According to the ichthyologists, the fish with bony armored or plate-like skin evolved in the early Devonian and existed till the end of the late Devonian before being replaced by the better-adapted fishes, evolved in the Devonian or a little earlier in the late Silurian (Yong, 2010). From the fossil evidence, scientists figured out that fresh-water placoderms were around 10e12 inches long, existed in the middle of the Devonian when placoderms migrated and adapted to the marine environment, it became a giant-sized placoderm (like the members belonging to Arthrodires), which was around 30e33 feet long later (Burrow et al., 2016). Placoderms were considered to be the melting pot of Pisces evolution as Chimaera, the transitional link between bony fish and cartilaginous fish had reported being originated out of marine placoderms, the giant-sized Arthrodires, whereas the primitive shark (the cartilaginous fishes) reportedly emerged out of Stensioelliformes group of placoderms (Brazeau and Friedman, 2015). The amphistylic jaws of placoderms had been considered being phylogenetically related to the bony fishes and it was considered on the basis of the presence of identical jaws of bony fishes. Those were found to be made up of the hyoid and quadrate bones, noticed in the jaws of both groups of fishes (Johanson et al., 2019; https://www. fossilhunters.xyz, Jun 11, 2019). D. Cartilaginous Fishes (Primitive Sharks) or Chondrichthyes: According to the phylogeneticists, the modern sharks, also known as Hybodont sharks, evolved in between 145.5 and 200 million years ago during the period of the Jurassic period and the modern sharks were reportedly diverged out of the primitive shark predecessor like marine “Cladoselachiformes” (Carrillo-Briceno et al., 2018). Though, two primitive groups of sharks belonged to Cladoselachiformes and Cladodontiformes and had reported evolved during Devonian (around 400 mya), became extinct in the Permian (around 251 mya). The paleontological evidence proved that Chondrichthyes supposedly evolved around 400 mya on Earth (Inoue et al., 2010). The ichthyologists have contended that the modern sharks, rays, etc. diversified in between 145 and 66 mya during the Cretaceous

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period, though the paleontological evidence along with phylogenetic studies have ascertained that three extant, modern group of sharks: Mackerel sharks or Lamniformes, ground sharks or Carcharhiniformes, and rays or Rajiformes have reported being originated around 200e145 mya during the Jurassic period (Fowler et al., 2005). E. Chimeras or Holocephali: Based on the paleontological evidence along with contemporary phylogenetic analysis, the evolutionary biologists and molecular phylogeneticists have predicted that Chimaeras, the transitional evolutionary link between the cartilaginous and bony fish, evolved during upper Devonian or immediately at the end of the Devonian mega-extinction between 400 and 360 mya, followed by a short spell of diversification and have existed till upper Cretaceous before most of their members become extinct, leaving a number of members in extant, those are popularly known as “Ratfishes” till date today (Inoue et al., 2010). The oldest fossil species of Chimaera had been discovered from Karoo of South Africa, known as Dwykaselachus oosthuizeni, found to be evolved around 280 million years old (Coates et al., 2017). The diagrammatic sketch of Dwykaselachus oosthuizeni has been presented in Fig. 6.1. A number of evolutionary biologists have assumed that the presence of characteristic gill arch in the primitive group of jawed fishes of Acanthodians and Holocephalians has contemplated them to consider that they must have a close phylogenetic relationship among themselves (Johanson et al., 2019). A number of scientists have considered that Holocephalian members possess characteristic pelvic claspers, which use to be typically possessed by the marine placoderms, known as Arthrodires, indicated its close phylogenetic proximity to the bony placoderms. On the contrary, a number of ichthyologists prioritize the presence of important features like identical pelvic claspers, placoid scales outside of the body of the fishes, absence of bones in their endo-skeletal system in the Holocephalian members of Chimaeras and the modern-day representative

FIGURE 6.1 The diagrammatic sketch of Dwykaselachus oosthuizeni. Courtesy Sashi Sinha, Ms.

The Evolutionary Biology of Extinct and Extant Organisms

Selachiian, specifically the “Ground Sharks” (belonging to Carcharhiniformes) have rendered the scientists to contemplate the evolutionary divergence of these two distinct groups of fishes likely to happen from a common evolutionary root-stock (Engelbrecht et al., 2017). F. Fleshy-finned Fishes to Sarcopterygii: The members of the Sarcopterygii, had been considered to be the prime choice of the evolutionary biologists for investigations, those engaged in deciphering the evolution of Pisces and tending to extrapolate its role in the evolution of tetrapod or evolution of vertebrates in general as the scientists had considered Fleshy-finned fishes as the evolutionary stepping stone, which triggered the evolution of tetrapod to initiate a new chapter in the history of biological evolution in this biosphere where evolutionary pilgrimage of vertebrates ended up in the ultimate evolution of us, the modern human species (Homo sapiens sapiens), the so-called superlative grade of mammal on Earth in the regime of Anthropocene. However, the paleontological evidence ascertained that the members of Sarcopterygiians, the evolutionary stepping stone between Pisces and another derived group of vertebrates, most likely evolved around 416e359 mya in early Devonian, supposedly diverged out of prehistoric jawed fish in the Silurian (more than 435 mya), predominantly colonized in the erstwhile geographical locations of contemporary Germany and adjacent location of Europe (George and Blieck, 2011). According to the extensive paleontological studies along with advanced molecular phylogenetic experiments, a group of experts on evolutionary ichthyology, declared the members of Rhipidistians, a subcategory of Sarcopterygiians as the progenitor of ancient amphibians that sustained the drastic environmental upheaval and failed to sustain the evolutionary exodus, popularly called “Transmigration” from water to land in order to secure sustainability diversification in later (Lu et al., 2016). The paleobiologists construed that in the backdrop of the abrupt paleoclimatic changes like prolonged drought and receding of water level, the members of the Rhipidistian order of Crossopterygiians, the extinct member that were diversified in the middle of the Devonian period, struggled with its pelvic and pectoral fins to crossover dried pools to the nearby water-filled ponds and initiated the first journey of the would-be tetrapods with primitive locomotor appendages (Schaeffer, 1965). The scientists notice that the amphibians are well adapted to the terrestrial environment, but they need the waterbodies to pass the juvenile stages after birth in water, which seems to indicate toward its close phylogenetic proximity with primitively aquatic vertebrates like fishes, specifically Sarcopterygiians. Unfortunately, the members of Rhipdistian have disappeared around 120 mya from this Earth in the early Permian, thus a collection of testimonials from their extant members would have been remained a dream for the evolutionary scientists till now. According to a group of evolutionary biologists, a series of phylogenetic, paleontological, physiological, structural evidence, collected and reviewed by the scientists for successful arbitration

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in favor of a few extant members of lungfish and coelacanths those phylogenetically belong to Sarcopterygiians, are considered to be the predecessor of prehistoric tetrapods. G. Ray-finned Fishes or Actinopterygii: The ray-finned fishes, belonging to the group Actinopterygii, had reportedly evolved around 400 mya in the Devonian period, diversified in its course of evolution of Pisces and vertebrates and gradually disappeared around 100 mya in the Cretaceous period (Friedman, 2015). This group of prehistoric fishes has taxonomically comprised of 42 orders, 480 families, and 26,900 extant species (Hurley et al., 2007). The molecular phylogeneticists have revealed that the bony fish or Osteichthys has two major clades that are composed of (1) the members of lobe-finned fish or Sarcopterygiians and (2) the members of Actinopterygiians or ray-finned fish. The phylogenetical review has ascertained further that Osteichthyes is the sister clade of Chondrichthyes or cartilaginous fish (e.g., sharks, rays, ratfishes, etc.) (Inoue et al., 2010). The Actinopterygiians have been broadly categorized as basal Actinopterygiians (the primitive group) and Neopterygiians (the recently evolved members of extant bony fish) (Friedman, 2015). The scientists have noticed that the order Chondrostean (comprised of two families of Sturgeons and Paddlefishes), and order Polypteriformes (having a single-family Bichirs) have been considered as Basal Actinopterygiians, which have given rise to a huge number of Chondrosteans and Holsteins. Whereas the extant members of Neopterygiians have further been categorized into three orders: a. Lepisosteiformes, the medium to large-sized predatory fishes (1e4 m long), the body of those covered with armored scales and sharp needle-like teeth found in its jaws (e.g., gars) b. Amiiformes, the medium-sized fishes (0.5e1 m long), having its characteristic dorsal fin stretched up to its entire body length (e.g., Bowfin) and c. Teleosts, the most diverse group of ray-finned, extant fishes of around 20,000 species, which are belonging to 40 orders (e.g., most living bony fishes). The distinctive features between Basal Actinopterygiians and Teleosts have critically been differentiated by the presence of characteristic tails, as the evolutionary ichthyologists have pointed out that the primitive members of basal Actinopterygiians have used to possess a heterocercal tail, the asymmetrical fin lobes (of different length), whereas the Teleosts possess a homocercal tail of symmetrical fin lobes (Hurley et al., 2007; Friedman, 2015). The evolutionary scientists have also observed that the members of Polypteriformes supposedly evolve during the early Triassic and this evolutionary group Pholidophoriformes, Teleosts, have supposedly diverged out of Ray-finned root-stock, specifically from Holostean predecessors (Clarke et al., 2016). Anyway, the evolutionary history of fishes is noticed to traverse through the labyrinth of the reticulate evolutionary history of biological evolution in the backdrop of space and time.

The Evolutionary Biology of Extinct and Extant Organisms

Nonetheless, in 2013, Min Zhu from the Chinese Academy of Science, Beijing, China, and his fellow scientists discovered a paleontological remnant of the oldest placoderm, a unique fossil of placoderm species, known as “Entelognathus” [means complete jaw], which survived between 430 and 360 mya, which was found to be evolved little earlier or in the same time that Janusiscus, had originated and evolved on Earth (Barford, 2013). Therefore, the discovery of the complete jaw of (which had been made up of a number of small bones) Entelognathus as the oldest Pisces representative, shattered the conventional perception of the evolution of bony fish, which had stereotypically been imagined to be diverged out of the cartilaginous fishes like a ray, shark, etc. The diagrammatic sketch of Entelognathus sp. has been presented in Fig. 6.2. By toppling the existing hypothesis of the origin of bony fish, that it has assumed to be diverged out of the common evolutionary stock of “cartilaginous fish,” the discovery of Entelognathus has inspired the evolutionary biologists to explore uncharted territory as the meticulous investigation of the scientists has helped to present Entelognathus as a maiden transitional link or the first stepping stone between placoderms and bony fishes (Riley, 2016). Subsequently, the discovery of more than 400 million years old fossil remnants of Pisces like Entelognathus and Janusiscus seems to be appeared as the “Founder fish,” which rendered the contemporary evolutionary biologists to construe a unique hypothesis of evolution of bony fish out of the placoderm (bony armored) rootstock, rather than nurturing the imaginary evolutionary story of the emergence of bony fish out of cartilaginous fishes (Zhu et al., 2016). Well, did it mean that the discovery of Janusiscus and Entelognathus necessarily ascertain that the earlier perception made by the earlier evolutionary biologists were completely wrong? A number of paleobiologists and molecular phylogeneticists like Michael Coates would prefer not to make any final comment as Michael Coates from Chicago University has made a comment “We have to acknowledge the fact that there’s probably quite a lot of stuff [at this evolutionary junction] that we don’t yet have a handle ondthat we don’t yet understand. we ought to expect the unexpected” (Riley, 2016).

FIGURE 6.2 The diagrammatic sketch of Entelognathus sp. Courtesy Sashi Sinha, Ms.

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The discovery of the Evo-links like Entelognathus and Janusiscus, the oldest placoderms and bony fish (to a greater extent) and cartilaginous fishes (to a lesser extent) and recognizing them as most suitable candidates to be recognized as the “Founder Fish” would render the scientists to predict that there is no doubt that placoderms, the extinct fishes evolved with the bony armor (like exoskeletons) suppose to be recognized as the most ancient Pisces that has emerged as the earliest progenitor of vertebrates on Earth (Zhu et al., 2016). Most likely, in the course of evolution, the exoskeletal bony armor had been transformed into tooth-like scales or “dermal denticules” and different form or scales, found in bony and cartilaginous fishes and internal cartilaginous skeletal systems, either remained unchanged for a group of fishes, emerged later as cartilaginous fishes and a group of fishes emerged as bony fishes, as its cartilaginous skeleton had been toughened and ossified in the course of evolutionary changes to ensure their survival stake in the ever-changing backdrop of the dynamic environment (Riley, 2016). Along with the generation of 3D pictures of the founder fish, Matt Friedman had inquisitively drawn a rough sketch (which was an effort to prepare the 2D form for print media) of Janusiscus on a scrap paper with a ball pen, which was apparently a fascinating picture of an extinct organism, the head of the creature had a close resemblance to the curved hood of the Volkswagen Beetle model, where the bony-armor was stretched out through the shoulder to be extended up to the asymmetric tail and ended up to the spines, found in all fins; the dorsal fins were found to be upward, attached to the jaws (Riley, 2016). It was a unique 2D presentation of the founder fish as anybody would hardly be supposed to find any living creature to define a visual narration of such prehistoric organism, the unique progenitor of vertebrates on this Earth, evolved million years ago and diversified in the course of evolution to ensure its survival through its descended lineages, sustained in extant form. In the long-standing evolutionary stalemate as well as the unresolved controversy of the Cartilaginous origin of bony fish, a paradoxical observation has recently been made by John Maisey, the curator of the American Museum of natural history and his research colleague, Alan Pradel as they have commented after carrying out a thorough investigation of the shark fossil, discovered in Arkansas, USA, as they state “standard anatomical textbooks say that the shark is a model of a primitive jawed vertebrate, [but] that’s all wrong” (Pradel et al., 2014). The preliminary level of paleontological investigation of a fossil specimen, made by the scientists turned out to be a discovery of 325 million years old, fossiliferous, prehistoric extinct creature of Paleozoic shark fish, further recognized to be as Ozarcus mapesae (Pradel et al., 2014). To make sure the investigation protocol is flawless and ensuring a precise age dating process, Maisey and his research teammates have carried out a series of an advanced level of investigations including CT scanning of the fossil of O. mapease, followed by a high-level X-ray imaging in the jaw areas and most surprisingly, they have observed that the presence of gill-arches of this prehistoric shark has found to be completely and structurally

The Evolutionary Biology of Extinct and Extant Organisms

resembled the Osteichthyan group of fishes rather than appreciating its perceptional resemblance to the cartilaginous fishes of the Chondrichthyan, stereotypically tendered by a number of evolutionary biologists for ages (Debecker et al., 2016). The contemporary anatomical investigations have ascertained that the jaws of modern sharks and rays are attached to their cartilaginous skull by a bunch of ligament threads (connective tissues), but the most astonishing fact to witness that the jaws of the prehistoric O. mapease, has found to be fused to the cranium straightway, without the presence of any structural interphase like ligaments and the presence of this anatomical feature has typically been noticed in the bony fishes (Debecker et al., 2016). Thus, a series of detailed investigations in broader aspects, ascertained the researchers like Pradel and Maisey to share a radical observation, that ancient sharks, as well as cartilaginous, were found to be the close phylogenetic relative of bony fishes rather than considered it as modern sharks. Furthermore, their evolutionary extrapolation indicated that the primitive cartilaginous fishes diverged out of bony fishes rather than the other way round (Pradel et al., 2014). Accordingly, going against the tide of conventional perception, the critical investigations of the prehistoric cartilaginous fishes have proved further that the conventional perception of “cartilaginous origin of bony fish” has merely been remained as a hypothetical perception, as the critical review of fossil evidence have proved that “bony origin of cartilaginous fishes” and such scientific observation must be considered over stereotypic perception to validate a hypothesis. It is difficult to be convinced with the reality that it is not the cartilaginous fishes that have given rise to bony fishes, but cartilaginous fishes, including modern sharks, diverged out of the ancient rootstock of bony fishes, though contemporary investigations have proved it (Pradel et al., 2014). Whether its Entelognathus or Janusiscus whomever we prefer to consider as “founder fish,” none has been regarded as typical prehistoric bony fish that would have given rise to the divergence of extant bony fishes on Earth rather we witness an amalgamation of composite features of prehistoric bony fishes and armored fishes, two overlapping evolutionary lineages that have been witnessed in these potential “Common ancestors.” The important twist of this story is that being an integral part of evolutionary, an advanced member of vertebrates, we, the modern human species are found in the nice conclusive end-part part of the evolutionary story of vertebrates in the backdrop of a reticulate matrix of the evolutionary history of transmigration fishes, struggling divergence of amphibians and reptiles to migrate out of from waterbodies to settle down on lands and move forward with the endeavor of terrestrialization of tetrapod of reptiles and mammals on Earth, which has been appeared as the terminal part of the story of the evolution of vertebrates and story is finally ending with the emergence and diversification of ultimate mammal, the modern human species as the most dominating animals on Earth.

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Thus, the evolutionary journey of fishes and the critical twists in it like the evolutionary journey of bony fishes, down the trail of the evolution of Pisces, which had supposedly started around 423 mya, was not an evolutionary fairytale of fishes (Riley, 2016). Rather, it was endeavoring the evolutionary biologists to check the evolutionary milestones on the trail of biological evolution on Earth, where vertebrates had started its journey around 400 mya, descended out of that prehistoric rootstock of Pisces and it had partly narrated our history of origin and reticulate evolution as modern human species who found to be successful in micromanaging and dominating over other organisms on Earth in this current regime of the Anthropocene, where we had no choice but to leave a number of phylogenetic relatives and survived with a number of phylogenetic relatives in this pilgrimage of evolutionary introspection.

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Hemichordates: the bilaterians lineage (also known as phylumDeuterostome) in the evolutionary crossroads of developmental biology

7

“Early studies from Metschnikoff (Metschnikoff, 1881) noted close morphological similarities between the early larvae of enteropneusts and echinoderms, but the significance of this observation was not fully appreciated until a series of molecular datasets, including Hox gene complements to molecular phylogenetics, robustly supported the sister grouping of hemichordates and echinoderms. The profound changes in phylogenetic relationships of the deuterostome phyla are now leading to new testable hypotheses about the early evolution of the lineage and the origins of chordates.” -Eric Rottinger & Christopher J. Lowe.

The “Chengjiang” fossil-site of Yunan Province in China (an excellent sedimentary deposit, preserving a wide array of soft tissues, which has technically designated as “Lagerstatte”) has been considered to be the unique paleontological repository to witness the surge of prehistoric biological organisms, the ancient organisms, evolved in the early Cambrian (around 541 mya), popularly known as “Cambrian Radiation” in the history of metazoans evolution (the multicellular eukaryotic organisms) and lasted for around 20 million years (Gould, 1989; Chen and Li, 1997). A number of Deuterostomians (comprising Hemichordates, Echinodermata, Xenacoelomorphs, etc.) and a number of ancient vertebrates have also been discovered in the “Chengjiang Lagerstatte” of Yunan, China (Chen et al., 1999; Shu et al., 1999), found to be evolved as the prehistoric biota of Cambrian radiation. Yunnanozoon has been discovered as the closest phylogenetic relative of chordate, as well as the maiden Hemichordates (having no notochord and myomere), and “Chengjiang Lagerstatte,” the age-dating process of which has ascertained that it has emerged during the onset of “Cambrian radiation” (Maloof et al., 2010). The diagrammatic sketch of Yunnanozoon has been presented in Fig. 7.1. Later, the prehistoric paleontological evidence of Enteropneust hemichordates with the tripartite body-plan has also been discovered from the same fossil site. The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00012-X Copyright © 2021 Elsevier Inc. All rights reserved.

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FIGURE 7.1 The diagrammatic sketch of Yunnanozoon. Courtesy Sashi Sinha. Ms.

Although the members of Hemichordata have been considered as the immediate phylogenetic relative of Chordata, a number of fossil evidence of the lower group of Chordates, the members of Urochordates or Tunicates and Cephalochordates, have also been found in the same fossil site of “Chengjiang Lagerstatte,” assumed to be evolved in the next-evolutionary stage of Chordates, emerged as Vertebrates in the backdrop of “Cambrian Radiation” (Zhang et al., 2014). A number of transitional forms of the primitive predecessor of modern chordates and vertebrates, particularly the phylogenetic allies of Yunnanozoon have been discovered from the Chengjiang fossil site of Yunan province that is supposedly the initial orchestration of the origin and diversification of vertebrates in the form of “Cambrian Radiation.” One of the primitive members of paleofauna was Xidazoon, having a “twofold” division, a big mouth with pharynx with five pairs of gill slits, but having no head in the front and the back has a structure as same as arthropods (Shu et al., 1999). The eminent Chinese paleontologists discovered another primitive Chordate, Cathaymyrus, which has some structural resemblance Yunnanozoon from the same fossil site (Chen et al., 1999). The evolutionary biologists carefully studied the composite form of morphological and anatomical features like presence of big sized rudimentary head, large-sized primitive heart, presence of zigzag myomeres (normally found in eel-fish or snakes), presence of lateral and ventral fins, gill skeleton, presence of multiple gonads and lack of true backbone and vertebra, etc. of Haikkouichtys and Myllokunmingia, have made the scientists consider these extinct animals of Chengjiang, Yunan as prehistoric vertebrates that emerged during Cambrian Radiation (Shu et al., 1999). Therefore, a detailed examination and review of palaeontological evidence of a wide array of prehistoric time of “Chengjiang Lagerstatte,” which appeared as the evolutionary cradle of Chordates and Vertebrates, have indicated that the emergence of a number of transitional forms of Deuterostomians appeared with the mosaic form of features, where the primitive members of Hemichordates supposedly took the lead in directing evolutionary divergence of vertebrates. The members of Hemichordata, the predominantly marine organisms, phylogenetically belong to the phylum of “Bilaterian” lineage, called “Deuterostome.” Hemichordata has found to be monophyletically related to the sister group

The Evolutionary Biology of Extinct and Extant Organisms

Echinodermata to form Ambulacraria clade, whereas it has been paraphyletically related to Chordata, having identical morphological resemblance and common evolutionary ancestry (Metchnikoff, 1881; Brown et al., 2008; Rottinger and Lowe, 2012). However, on the basis of morphological similarities and phylogenetic relationship, zoologists have classified Hemichordata into two major groups (Wagele and Bartolomaeus, 2014): Enteropneust worms are popularly known as acorn worms and Pterobranchs, the tube dwellers. Since 1800, a detailed investigation of the morphological affinities, close phylogenetic features, and developmental biology of Himichordata and Chordata intrigued the zoologists and evolutionary biologists to hypothesize the origin of Chordata out of Hemichordates lineage (Bateson, 1886; Morgan, 1894; Berrill, 1955; Brown et al., 2008). On the basis of morphological features, zoologists considered earlier that Enteropneusts were the primitive Chordates, which gave rise to vertebrates in the course of evolution (Bateson, 1886). Even before the studies of Metchinkoff (1881) hypothesized the phylogenetic proximity of the larval stage of Echinoderms and Enteropneusts on the basis of morphological similarity, but it failed to secure much appreciation in the arena of Zoology due to the lack of substantial evidence. But the contemporary phylogenetic evidence, particularly a number of molecular analysis in genomics, a critical review of Hox gene complements (Homeobox genes) of Deuterostomians, helped the molecular phylogeneticists to conclude that Hemichordates and echinoderms are phylogenetically close ally (Turbeville et al., 1994; Wada and Satoh, 1994; Philippe et al., 2011). The evolutionary biologists observed that the developmental genetics and genomics of Hemichordates have closely resembled Echinoderms and Chordates, and in-depth reviews of it could enlighten the issues like the origin and evolution of Deuterostome and Chordates further (Rottinger and Lowe, 2012). Before going through the evolutionary trail of chordates to reach out to the ultimate destination of vertebrates and before the formal touch-down of the transitional evolutionary milestone of hemichordates, an informal introduction of Enteropneusts or Acorn Worms is necessary. Acorn worms are predominantly marine organisms, ranging from a few centimeters to few meters in length. The threepartite bodies of these worms comprise anterior prosome or proboscis (an expandable and contractile organ, used for burrowing locomotion), a collar or mesome in the middle, and a dorsoventral axis, in which mouth is found in the ventral side and cartilaginous gill slits in the dorsal side of it. There are a number of transitional links or Evo-links that belonged to Enteropneusts and a few of those are Ptychodera flava, Sarcoglossus kowslevskii, Balanoglossus misakiensis, etc. The presence of proboscis of Enteropneusts seems to be functionally homologous to the notochord of Chordata, although lack of molecular support is there (Morgan, 1894; Peterson et al., 1999). A number of zoologists, such as Bateson (1886), Brown et al. (2008), Kaul and Stach (2010), considered that “epithelial nerve plexus” of Enteropneusts are found to be functionally homologous to the nerve cords of Chordates (Bullock, 1945; Rottinger and Lowe, 2012). The presence of the

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pharyngeal gut seems to be perforated by cartilaginous slits in Enteropneusts, which brought it phylogenetically close to the basal chordates, Amphioxus (Gillis et al., 2011). In terms of the developmental pattern of the embryonic stage of Deuterostomian organisms, two distinct patterns of development have been observed: a. Direct development: Where development of Deuterosomian organisms started from the embryonic stage to reach adulthood with a distinct body plan, without getting in via larval stage. For example, Saccoglossus kowalevskii (Lowe et al., 2004). b. Indirect development: Where development of Deuterostromian organisms started from its embryonic stage to be attained from the adulthood through a distinct “larval body plan.” For example, Ptychodera flava, Balanoglossus simodensi, etc. (Lowe et al., 2004; Miyamoto and Saito, 2010) A. Ptychodera flava: Among the indirect-developing Enteropneust, P. flava is one of the popular ones, found in the shallow waters in the Hawaiian Islands and in the shallow reef-beds of Indo-pacific, where its sexual reproduction by the spawning of oocytes happened in the month of JanuaryeDecember (Hadfield, 1975). The Oocytes have been fertilized externally to emerge as “Pelagic Tornaria Larvae” and these larvae survived a few months in this state by feeding marine planktons before getting metamorphosed in adulthood in the benthic environment (Tagawa et al., 1998). In the gastrulation phase of embryonic development, the cleavage furrow has been noticed through the egg or blastomere, forming a complete cleavage in P. flava. Immediately after cleavage, a radial cleavage has been witnessed to yield the newly formed blastomeres. Those are perpendicular to each other; the combination of holoblastic and radial cleavage leads to the formation of a hollow blastula (Henry et al., 2001). The embryologists noticed the presence of “endomesoderm” (a transitional state of endoderm and mesoderm) in the “vegetal plate” of blastula, which is found to be a transitional state as well as the penultimate stage of chordates on its evolutionary journey from nonchordate root-stock (Rottinger and Lowe, 2012). It has a striking resemblance to another Hemichordate Balanoglossus simodensis, having an identical indirect development body plan via larval stage where the characteristic feature the nonchordates (Miyamoto and Saito, 2007). B. Saccoglossus kowalevskii: S. kowalevskii is an Enteropneust worm as well as a direct-developing organism, belonging to the Hemichordate, found in the marine habitat of Eastern USA. A large number of oocytes have been released by the female member of Saccoglossus during spring and late summer, and all these free-floating oocytes are externally fertilized by the sperms, discharged by their male counterparts (Lowe et al., 2004). External heat shocks expedite the spawning of the oocytes of these worms (Colwin and Colwin, 1962). The appearance of a yellowish vitelline membrane has been noticed outside of the fertilized eggs, which have also been noticed in (Sea Urchins) Echinoderms. In the early stages of embryonic development specifically in the gastrulation

The Evolutionary Biology of Extinct and Extant Organisms

developmental stage of Saccoglossus, a similar pattern of cleavage observed in Ptychoderma flava (the combination of holoblastic and radial cleavage) has been noticed, leading to the formation of a hollow blastula with a thick vegetal plate attached to it (Colwin and Colwin, 1953). Immediately after the formation of blastula, the mesodermal coeloms at the embryonic gut region of its forms mesoderm (called enterocele) and it gets in touch with ectoderm, which forms proboscis, the collar (a transitional attachment between proboscis and trunk and the ventral mouth has found to be attached to the anterior part of the collar) and the trunk (body), in sequential order. The formation of the mouth on the ventral side appears on day 2, but the anus found to have appeared later and a pair of gill pores appeared on day 4. So, hatching of juvenile (looking apparently similar to its adult) complete on day 5 and its ready to be adapted in burrowing by giving up its initial phase of pelagic adaptation by utilizing its proboscis and gill slits. The absence of larval stages in its life cycle and the entire process of embryonic development of Saccoglossus kowalevskii looked like a prochordate developmental pattern, but the absence of notochord, nerve chord, etc. rendered the zoologists to consider Saccoglossus as a member of Hemichordata, which is phylogenetically close to Chordata (Giray and King, 1996). C. Balanoglossus simodenensis: B. Simodensis is an indirect-developing, Enteropneust worm, which belonged to Hemicohordata as well as Deuterostomes, found in the little warm and temperate, shallow marine habitat of Shimoda, Japan seas (Miyamoto and Saito, 2010). Balanoglossus, the unique bilaterally, symmetrical metazoan, has been studied by a number of zoologists and evolutionary biologists as an important transitional link or evolutionary gateway between invertebrates and vertebrates as it possesses a pallet of mosaic, overlapping features (e.g., possession of notochords, presence of branchial openings or gill slits, the existence of stomatochords, presence of tornaria larval stage in its juvenile state, possession of dorsal tubular nerve chords, etc.), which intrigued the scientists to consider Balanoglossus as an Evo-link between chordates and nonchordates (the evolutionary bridge between invertebrates and vertebrates). Since its maiden discovery in 1825, Balanoglossus has been considered as the marine worm, an organism with burrowing adaptation and typical feeding habit, prefers to grow and live in the bottom of the sand of shallow water bodies, particularly in the coastal fringes and it pointed out its primary resemblance to Nemertinea, or Proboscis worms (Tassia et al., 2016). On the basis of identical characters like identical regeneration patterns, the presence of intraepidermal nervous systems, and larval stage in the Indirect-development body plan (Actinotroch larvae in Phoronis sp. and Tornaria larva in Balanoglossus sp.) rendered Balanoglossus related to the worms, belonged to Phoronida. The formation of mesoderm and coelom in Balanoglossus sp., which has been defined as enterocoely, presence of the intraepidermal nervous nervous system, identical possession of gonads in the trunk, rendered the scientists to consider it phylogenetically close to Pogonophora or beard worms (Tassia et al., 2016). The identical shape of the

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body, feeding habit and burrowing adaptations, presence of ventral nerve chord, possession of identical blood vessels, the apparent similarity of the prostomium of Annelids, the proboscis of Balanoglossus and presence of transitional larval stage (Tornaria larva in Balanoglossus and Trochophore larva in Annelida), etc. intrigued the scientists to draw its phylogenetic proximity with Annelida. The larval anatomy and developmental biology of Balanoglossus and Echinodermata like its pelagic affinity, the formation of the anus from the blastopore, the distinct coelomic developmental pattern, the striking resemblance of medreporic vesicle of echinoderms, the heart vesicle of Balanoglossus, and the identical excretory organs like axial glands in Echinoderms and glomerulus in Balanoglossus helped a number of zoologists to consider these two distinct groups of animals that have a common ancestral origin (Tassia et al., 2016). In 1885, Bateson has been regarded the buccal diverticulum of Balanoglossus as an ancient form of a notochord, extended from the endoderm region and able to perform skeletal functions found among the early members of Chordata, but a group of scientists considered that the buccal diverticulum is not notochord as the buccal diverticulum of Balanoglossus is not strong enough to perform the skeletal function and it should not have any hole in it and the blood vessels of Balanoglossus lies below the buccal diverticulum, whereas the notochords in Chordates found to be situated above the blood vessels (Newell, 1952). The key evolutionary resemblance of Balanoglossus to the Chordates is the presence of identical gill slits. The identical gill architecture like the presence of gill bars in Balanoglossus and the members of Chordata are structurally and functionally identical. The dorsal tubular nerve chord of Balanoglossus has been found to be partially identical to the nerve cord of chordates. On the other hand, the chordates never possess any ventral nerve cord, which has been possessed by Balanoglossus. A number of mosaic characteristic features in larval and adult stage of Balanoglossus and the different members of non-Chordata, such as Annelida, Echinodermata, Nemertinea, Phoronida, and Pogonophora, and the members of Chordata rendered the contemporary evolutionary biologists to consider it as one of the bonafide members of Hemichordata, which maintained an Evo-link between non-Chordata to the Chordata, as well as playing a key role in continuing the evolutionary journey from non-Vertebrates to have emerged as vertebrates in the course of the ultimate journey of evolution of vertebrates, started millions of years ago with transmigration of animals from water to land. D. Rhabdopleura compacta: R. compacta is one of the unique members of Hemichordata, which belonged to the category of Pterobranch, and preferred to colonize in the deep-water and cold, marine microhabitat. Naturally, the members who belonged to Pterobranch are not very commonly found organisms like enteropneusts (Rottinger and Lowe, 2012). The developmental studies particularly the embryological and reproductive, developmental studies of R. compacta have successfully been made by the research biologists after a long-time hunt for this species in shallow water habitat. Although the reproductive details like the process of fertilization of this species have not been

The Evolutionary Biology of Extinct and Extant Organisms

found out so far, the larval development, as well as the indirect development process of this species, has been elucidated by the scientists as they have noticed that lecithotrophic development, free-floating or swimming larva utilized their nutrients from mother’s Yolk; of the nonfeeding, larval members of Pterobranch. The developmental growth of Pterobranch has been found to be attenuated in the month of April and July (Rottinger and Lowe, 2012). The larva of R. complacta have been found to be pigmented and locomotion of R. compacta has been supported by its structure, also found to be confined in coenobium or colony and gradually released as a swimming larva, called planula and reproduced asexually by budding (Cameron et al., 2000). However, in the field of Zoology and contemporary phylogenetic studies of Hemichordates, Enteropneusts (Acron Worms), Pterobranchia (tube dwellers), and Planctospheroidea (Planktonic) are considered to be three sister taxa. The main key feature of the Hemichordata members is the presence of stomochord, which arose in the course of embryonic development from the roof of the embryonic gut, anterior part of the pharynx. In the adult stage, this stomochord extends the pharynx to the proboscis, maintaining communication in the oral cavity (Kardong, 1995). In the field of developmental biology, it is still in a hypothetical stage. Still, stomochord in Hemichordates has been functionally considered as a functionally homologous organ like notochord in Chordates (Mayer and Bartolomaeus, 2003). Scientists have expressed their concern a number of times whether Pterobranchia is part of Hemichordates that are not present as stomochord and heart-glomerulus complexity has a shred of clear evidence in the Pterobranchian taxon Cephalodiscidia, but lack of such characteristic features remained in another Pterobranchian member like Rhabdopleura until recent investigations unveiled the presence of these key features in Rhabdopleura compacta. On the basis of the identical histologically resemblance of the stomochord of R. compacta, and the members of Enteropneusts like the presence of nonciliated, nonvacuolated cells and mono-layered epithelium (presumably of ectodermal origin), the evolutionary biologists affirmed the earlier view that Enteropneusts and Pterobranchians are closely related phylogenetic allies of Deuterostomes as well as Hemichordates (Mayer and Bartolomaeus, 2003). According to the contemporary findings of molecular phylogenetics, the members of Pterobrnchians like R. compacta are contemplated to be the important evolutionary links as it holds its evolutionary relations to other Deuterostomians as well as Hemichordates in one hand, whereas it helped to the divergence of Chordates on the other hand (Cameron et al., 2000). The contemporary molecular phylogenetic analyses ascertained that the members belonging to Pterobranchians formed the basal Deuterostomians, whereas the Enteropneusts are the derived offshoot, responsible for evolutionary divergence of Chordates and it further indicates that as a phylum Hemichordata is polyphyletic in origin (Cameron et al., 2000).

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According to the recent advancement of phylogenetic studies, Deuterostomians comprise three key phylums: Echinoderms, Hemichordates, and Chordates (Cameron et al., 2000). Hemichordates are phylogenetically close to Echinoderms in the presence of identical coeloms like hydropore, similar nervous system, and larval developmental biology. On the other hand, Enteropneusts maintained two alternatives (direct and indirect developmental pattern) development process, either a direct developmental cycle of Chordates or indirect developmental cycle via larva like nonchordates. The presence of three distinct body parts of Enteropneusts: proboscis, collar, and trunk resembled protosome, mesosome, and metasome of Chordates. Besides, the presence of allied identical characters like pharyngeal gill pores, neulated dorsal-chord, stomochord (which is considered to be the homologous organ of chordates), etc. rendered the scientists to consider Enteropneusts as transitional link or Evo-links between non-Chordata and Chordata (Cameron et al., 2000). As per the classic taxonomic system, Chordates comprise three subphylums: Urochordata, Cephalochordata, and Vertebrata (Cameron et al., 2000). However, the evolution issues of Chordates and the evolutionary relationship of Deuterostomes and Chordates have remained a matter of dispute for a long time as morphological data did not support and lack of fossil data was the main impediment to resolve the issues. The recent phylogenetic investigations ascertained the monophyletic origin of Urochordata, and it revealed that Urochordata is the separate phylum of Deuterostomia as well as a sister clade of Hemichordata rather than a subphylum of Chordata (Cameron et al., 2000). The review of the life cycle and a brief comparison of the developmental stages of the reproductive biology of Urochordates and Hemichordates revealed that both groups of Deterostomia could either complete their life-cycle with “solitary sexual mode” of reproduction, where the chance of recombination of unique characters are there, normally found in all advanced members of vertebrates. Although both groups have primitive features like completion of the life cycle in colonial form and employ “asexual mode” of reproduction by bud formation (via larval stage), the typical reproductive feature of non-Chordata. Therefore, it indicates the Deuterosomias are the evolutionary stepping stones, which lead the journey of evolution of Chordata and Vertebrata to a distinct level (Cameron et al., 2000). To elucidate and review the molecular footprints to track the evolutionary progress of life through the non-Chordates to reach out the ultimate evolution of Chordates, the examination of certain gene expressions has been reviewed of the CNS (Central Nervous System) of non-Chordate deuterostomes and Chordates (Satoh et al., 2014). To do that, a number of gene actions have been reviewed. Those might play an active role in the formation and function of CNS, like echinoderm sea cucumber Otx gene, hemichordate acorn worm Otx gene, acorn worm T-brain gene, mammalian T-brain gene, Group B Sox genes of hemichordates, and Group B Sox genes of vertebrates.

The Evolutionary Biology of Extinct and Extant Organisms

The developmental biologists noticed that echinoderm sea cucumber Otx genes are found to form ciliary bands effectively in the larval stage (Doliolaria larva) and in the metamorphosed state, responsible for nervous and sensory induced movement of the mouth of sea urchins (Shoguchi et al., 2000). The hemichordate acorn worm Otx genes have been noticed to form ciliary bands in the larval stage (Tornaria larval stage) of Hemichordates (Harada et al., 2000). The acorn worm T-brain genes are found to be responsible for creating nervous sensations in the apical organ of the Tornaria larval stage of hemichordates in controlling light sensations of eyespots (Tagawa et al., 2000). The mammalian T-brain genes are responsible for the formation of CNS in mammals and controlling the nervous impulse in the cerebral cortex (Tagawa et al., 2000). The Group B Sox genes of hemichordates are found in apical organs and express the formation of ciliary bands in echinoderm and hemichordate larva, whereas the Group B Sox genes of vertebrates are found to be responsible for the formation and development of CNS in vertebrates (Satoh et al., 2014). Accordingly, the molecular investigations of gene expression revealed that the genes responsible for the expression of ciliary bands and expressed in the apical organs in the Hemichordates and Echinoderms of Deuterostomes (Nonchordates) are expressing formation and development of CNS in Chordates (Satoh et al., 2014). The developmental geneticists and genome biologists have made immense progress in the arena of developmental gene expressions (in terms of structure and function) of the animals, look-alike or identical body plans, but those are phylogenetically distant and it helps to understand the developmental role-play of such genes on the homologous organ or body part development in those distantly related organisms or species like Amphioxus (of Chordata) and real Vertebrates (Holland and Holland, 1999). This kind of developmental studies of gene expressions helped the scientists to understand the complicated issues like the location, structure, and specific role-play of a certain number of genes present in the brain of Amphioxus (belonging to Branchiostoma, Cephalochrdata) like Otx, BF1, Hox1, Hox3, Hox4, Islet, etc. in the formation and development of CNS and it helps to understand the evolution of structural and functional development of brain and CNS of Vertebrates (Holland, 2015). The comparative account of the developmental gene expressions of the genes related to the formation and development of CNS of Amphioxus revealed that the genes mentioned earlier helped to form the CNS as well as the brain of Amphioxus and Vertebrates in a similar way and the distinct domains of the brain of Amphioxus (Chordate) and Vertebrates are found to be developed as Diencephalon, Mesencephalon, and Metencephalon, but Telencephalon part of the brain has been left out in this developmental expressions. Nonetheless, it helped to form Telencephalon in Vertebrates, which rendered the evolution of the Vertebrata brain as a better one than its immediate evolutionary ancestral Invertebrate lineage of Amphioxus. The developmental gene expressions helped the neuroscientists and evolutionary

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biologists further dealing with microanatomical investigations with electron microscopy and computer-aided investigations of brain structure and functions (Holland, 2015). As per the recent observation of molecular phylogeneticists, Amphioxus is recognized to be the extant phylogenetically of Vertebrates, which retained a number of archetypal features like simple body plans, along with acquiring a number of derived features like genomic alterations; the evolution of cis-regulatory elements, gene duplication, etc. (Wada and Satoh, 1994). A number of genomicists observed in their studies on the genes and gene clusters of Amphioxus that its archetypal organization of the genome has been characterized by the presence of a single Hox cluster of Homeobox genes, in comparison to its close ally Vertebrates as they possess four Hox clusters of these Homeobox genes (Garcia-Fernandez and Holland, 1994). Hence, the combination of a single cluster of Hox genes in its “frozen” primitive genome (as it evolved around half a billion years ago, where no major evolutionary changes of its genome have been witnessed by the genome biologists so far) and an archetypal simplest body plan like ancestral Vertebrates rendered the evolutionary biologists to consider Amphioxus as the evolutionary ancestor of Vertebrates (Pascual-Anaya et al., 2012). The developmental geneticists revealed the expression of the amphioxus genes Hox1, Hox3, and Hox4 in the structural and functional distinction of its nerve chord and it also exposed developmental homology in the hindbrain of Vertebrates and the neural tube of Amphioxus (Wada et al., 1999). It also indicates the ancestral descendants of Hox cluster genes in the segmentation of Chordates brain, once evolved by the Hox cluster in the neural tube of Amphioxus (Wada et al., 1999). Furthermore, the genome biologists observed that the evolutionary sister of the amphioxus Hox cluster, the ParaHox cluster in the other genomes, resulting out of gene duplication gave a predictive outline of gene evolution. Its expression of developmental changes of the body plan as a result of random alternation of an axial pattern (as well as alteration of “colinear” developmental expression of anterior-posterior tissues) in the emergence of a huge number of animals appeared with complex shape and body size structure and functions, as a result of Cambrian explosion (Brooke et al., 1998). The genome biologists revealed that the Homeobox genes from Hox-1 up to -Hox-10 (mainly Hox-1,-3,-4) were found to be responsible for controlling the developmental expression of the anterior part of the axial pattern and from an evolutionary point of view. These Homeobox genes are archetypal in nature (Wada et al., 1999). Hox-2 of Amphioxus has been found to be losing its function as a Hox gene and failed to express any role in the developing neural tube of Amphioxus (PascualAnaya et al., 2012). The evolutionary role-play of the Homeobox genes from Hox-5 to Hox-9 is yet to be recognized. The recently discovered Homeobox genes of Hx-11, -12, -13, -14 and the next level of phylogenetic analysis (in terms of molecular phylogenetic) revealed that these recently discovered gene clusters are responsible for developing the expression of the posterior part of an axial pattern and it is orthologous to the vertebrate

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posterior genes (Pascual-Anaya et al., 2012). The development of the posterior end of the axial pattern attributed the evolutionary edge to the Vertebrates over Invertebrates, leading to an explosive surge of Vertebrates of different sizes and shapes in the backdrop of Cambrian Radiation. It has also been extrapolated that the evolution of posterior Vertebrate genes occurred as a result of the “duplication” event of Amphioxus lineage to pave the divergence of Vertebrates and Hox-11 to Hox-14 should be considered as a derived cluster of Homeobox genes and tilting the evolutionary equilibrium. The leading preponderance of the derived group of Vertebrates and archetypal members of invertebrates shifts the expression of Homeobox genes to switching the axial pattern of development from the anterior end to the posterior end (Wada and Satoh, 1994). Amphioxus Hox-14 has considered being the enigmatic key to unlock the mystery to draw the evolutionary lineage from Invertebrates to Vertebrates and the genome biologists are engaged in tracing out the homologous form, that is, Homeobox gene cluster: Hox-14 in Vertebrates, which is yet to be discovered. In their microanatomical studies, scientists observed that Prochordates (comprising Cephalochordata and Tunicata) are lack of neural crest, an important part of the brain development in Vertebrates, particularly the evolution and development of CNS in Vertebrates, ultimately observed in the advanced group of mammals and modern human species 2019. The developmental gene expressions have indicated that Prochordates (i.e., Amphioxus, other Cephalochordates, and Tunicates) possess embryonic cell populations, having a functional resemblance to the neural crest of Vertebrates (Holland, 2015). The neural crest cells of Vertebrates are found to be formed at the juncture of the epidermis and neural plate in that location developmental expression of a number of genes took place. Likewise, in the identical location of the cell population of the Amphioxus embryo, the developmental expression of a homolog of the neural crest specific genes such as Dix, Msx, Pax3/7, and Snail has meticulously been studied. Scientists observed that neural crest cells in Vertebrates entered through the embryonic blastocoel, then migrated and subjected to differentiation in a wide array of cells. Although contemporary observations of the developmental geneticists ascertained that migration of neural crest cells would have never taken place, rather the epidermal cells adjacent to neural crest cells are looking different than epidermal cells of the other parts of the adjacent areas. Whereas the neural crest cells in the Amphioxus embryo would never enter through blastocoel and it never differentiated into a wide array cell and the cell mass at the edges of neural plate develop the neural tube (Holland, 2015). Though, the ultimate result of the developmental expression of neural crest cells in Amphioxus was found to be different from Vertebrates. The identical functional mode of developmental expression of genes indicated further that evolutionary cell precursors of invertebrates (e.g., Amphioxus) gave rise to the emergence of neural crest cells in Vertebrates (Holland, 2015). The developmental geneticists observed that Vertebrate BMP4 and BMP7 played a key role in neural crest induction, whereas their Ascidian homologs have been

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found to be expressed in the dorsal epidermis region of Invertebrates (Miya et al., 1996, 1997). Likewise, the vertebrate homolog of amphioxus DII genes, which is involved in the formation of neural crest, was found to play an identical role in the formation of neural tube cells and epidermal cells (Holland, 2015). Hence, it is proven that the gene responsible for the differentiation of neural crest cells in Vertebrates and the expression of homologous genes are found to be responsible for the differentiation of dorsal epidermis in the Prochordates (Yokoyama et al., 2019). The earliest endeavor of understanding and evolution of Vertebrates from the lineage of Invertebrates (specifically from Deuterostomia root-stock) with transitional evolutionary progress from Hemichordates to Chordates has earlier been initiated with the classical format of phylogenetic investigations in 1800. But then, it has been found by the next generation of scientists (comprising Developmental geneticists, genomicists, molecular phylogeneticists, molecular biologists, and evolutionary biologists) that the paleontological evidence of the transitional fossils between Invertebrates and Vertebrates are not so huge that would help them to draw any conclusive inference to designate/determine the specificity of an evolutionary trail as the one, which leads the shift in the paradigm of Vertebrates from Invertebrates. The real obstacles to work it out stalled by the diverse array of body-plans observed in the members of Deuterostomes (mainly Hemichordates, Echinoderms, etc.). Since 1900, the geneticists and evolutionary biologists tried to explore the uncharted territory of molecular genetics, genomics, and developmental genetics to coordinate their phylogenetic investigations in the molecular level by studying the life-cycle patterns (like direct-developmental without a larval stage and indirect-developmental cycle) of Enteropneusts and Pterobranchs, with special reference to microanatomy and embryology, the axial patterning of Deuterostomes, germ layer specifications, Homeobox gene expressions in relations to developmental changes of the body plan of Hemichordates, Echinoderms, and Chordates (Cephalochordates and Urochordates or Tunicates), etc. Furthermore, the exorbitant development in the field of molecular phylogenetics, genomics, and developmental genetics since the 1990s engaged the majority of scientific pursuits to choose Amphioxus, an invertebrate in the true sense, but it is considered to be a model for vertebrates, which is a transitional form between Invertebrates and Vertebrates to decode the mystery of the evolutionary journey of Vertebrates, happened in the backdrop of Cambrian Radiation. The expression of Homeobox genes in Amphioxus, that is, Amphioxus-Hox genes, which has been initiated to study and examined to understand its homologous structural and functional entities, that is, Vertebrate-Hox genes, started deciphering various aspects of developmental biology of vertebrates and basic ideas on the shift in paradigm from Invertebrates to Vertebrates, which has initially started with the transmigration of life from water to land.

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Since the 1990s to 2010, these two decades are not enough for the scientists to elucidate the evolutionary journey of life; particularly, the journey of Vertebrates from Invertebrates, once initiated in some water bodies and developmental genetics, is still in its early stages of development. It requires a long way to go through the evolutionary trail of evolution to narrate the brief history of Vertebrates evolution, touching down the transitional link or Evo-links of Invertebrates, in the backdrop of space and time.

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Cambrian evolution of Onychophorans: in the evolutionary labyrinth of Arthropods, Annelids, and Molluscs

8

“. Cambrian polychaetes (Morris, 1979), Onychophora (Hou and Bergstrom, 1995), and arthropods (Briggs et al., 1994) possessed antenniform outgrowths suggesting that this outgrowth is primitive. In addition, phylogenetic schemes based on both morphological characters (Valentine, 1994) and molecular evidence (Valentine et al., 1996) are consistent with the existence of a common antennae-bearing ancestor of these protostomes. Furthermore, studies of Hox genes in Drosophila and other insects suggest that the ‘ground state’ for appendage identity is the antennae because loss of Hox gene function in legs transforms tissue to antennal identity (Struhl, 1981) and loss of all Hox genes in Tribolium transforms all body segments to the antennae-bearing metameres (Stuart et al., 1991). We propose, then, that the ancestor of these higher protostome taxa bore antenniform outgrowths, and that these structures were duplicated and transformed on the trunk to parapodia and lobopodia after the divergence of the annelid and onychophoran lineages” Grace Panganiban and others

As the soft-bodied prehistoric members of Annelids and pro-Annelids decayed faster than other dead animals that have a hard-shelled body, the possibility of fossil formation and its preservation for the prehistoric soft-bodied organisms are less likely. The paleobiologists discovered a number of excellent sedimentary deposits in China and Canada, preserving a wide array of soft tissues, those have technically been designated as “Lagerstatte,” the unique abode of the rare, soft-bodied, prehistoric fossil repositories on Earth. A number of fragile, soft-bodied, multisegmented, bilaterally symmetrical, marine, worm-like creatures were devoid of the distinct head, eyes, and antennalike appendages with or without the presence of lateral appendages (like parapodia, used for locomotion), and these unique creatures have been discovered from the muddy substrate of the deep-ocean floor from a number of unique fossil sites (e.g., Chengjiang formation in China and Burgess Shale in Canada), called “Lagerstatte” (Meyer, 2013). The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00006-4 Copyright © 2021 Elsevier Inc. All rights reserved.

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The age-dating process has ascertained that most of these extinct creatures used to dominate the paleobiosphere in the Cambrian period and the molecular phylogeneticists revealed further that all these transitional forms of creatures as well as evolutionary links in between the Annelida and Arthropoda supposedly diverged out of a common Annelidan mother-stock around 600e500 mya, and Onychophora has been considered as the model organism as the Evo-link between the prehistoric Annelids and Arthropods evolved during “Cambrian Radiation” (Meyer, 2013). During a Danish Oceanographic expedition in 1952, in the East coast of Costa Rica, a tiny limpet-like creature (around 3 cm, the sample of limpet) has been collected from the “Middle America Trench” of the Pacific Ocean bed of 3750 m deep, which has been carefully studied by the Danish biologist in the exploration team Dr. Hennig Mourier Lemche (Datta, 2010). From the above, it looked exactly like a limpet-looking dorsal shell, which is a typical feature of Mollusca. Although in juvenile conditions, the spirally coiled structure of the shell resembled Gastropods (Batten, 1984; Giribet et al., 2006). During his studies, Dr. Lemche was amazed by the tiny limpet for its unique features as that living sample resembled the paleontological, extinct mollusk sample of the Cambrian-Devonian period, known as “Pilina,” disappeared from the Earth millions of years ago, which intrigued Heinnig M. Lemche to name the extant sample as well as that living fossil as “Neopilina galatheae” and he published his work in 1957 (Menzies and Robinson, 1961; Datta, 2010). The unique feature of it is found to be at the shell tip, pointed toward the head, rather than at the tail end or sidewise formation, that has usually been found in the members of Gastropods as well as typical features found in the Molluscs (Batten, 1984; Datta, 2010). Anatomically, the shell of Neopilina has resembled the Molluscs as it is made up of dorsal epidermis and inner mantle or pallium (Batten, 1984; Giribet et al., 2006). The examination of its ventral side exposed its mouth with a tentacle, without any head in it, whereas the round-shaped feet were found to be responsible for its slow locomotory movement and these features resembled Neopilina to the members of Molluscs (Batten, 1984; Giribet et al., 2006). On both sides of the foot, the presence of five gills was noticed by the scientist, resulting in its possession of a huge number of comb gills (Ctenidia), which rendered them to consider Neopilina as advance members of Molluscs (Batten, 1984). Nevertheless, the pallial cavity is missing in it (which is a typical feature of gastropod) although a pallial groove is found to be present in the mantle, foot on the side, and extended to the tail end (Giribet et al., 2006). The gill is found to be sequentially arranged in this grove, and the presence of such primordial characters in Neopilina is supposedly inherited from the ancestral root-stock of segmented worms, belonging to Annelida (Giribet et al., 2006). Neopilina was found to possess separate sexes, whereas two gonads of it fused to form a single one that produces germ cells, released through the ducts, and ejaculated in the water. Thus, it is convincible that fertilization took place in the water (outside of the body), which is a typical feature of mollusks (Giribet et al., 2006). The presence of some unusual organs like nephridia and segmented muscles, which are not found

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in Molluscs, rather found in the members belonging to Annelida, rendered the evolutionary biologists to consider Neopilina, the unique living fossil supposedly in the transitional link or the evolutionary link in between Mollusca (to a greater extent) and Annelida (to a lesser extent) (Menzies and Robinson, 1961; Giribet et al., 2006; Lindberg, 2009). Whether the evolution of Arthropods has followed the monophyletic or the polyphylatic trail of evolution has yet to be settled by evolutionary biologists. However, the members of Arthropods have some distinct features like the presence of distinct mouth and heads, segmented exoskeleton, open circulatory system, and dorsal heart etc. and they have laid yolk-laden eggs with proteinaceous shell; these features are not usually found in Annelids. The earliest endeavor of classification of Arthropods has been justified and classified on the monophyletic by Bordeaux (1979), who classified the entire arthropods in three phylums: Trilobita, Chelicerata, and Mandibulata. Nonetheless, Bordeaudx (1979) did not consider Onychophorans in his classification due to the absence of any exoskeleton in the members of Onychophora. Meglitsch and Schram (1991) have included Onychophorans in the revised monophyletic principles of classification, but they faced a barge of strong arguments from the supporter of polyphyletic origin of arthropods as it was difficult to elucidate the legs as homologous organs of wings as their distinct structural patterns. However, on the basis of primitive palaeontological evidence, Kukalova-Peck (1992) came up with a unique observation, where she recognized the ancient arthropod with a segmented leg of 11 segments followed by 8 segments of the segmented leg of a spider, 7e9 segments of the segmented leg of crustaceans, and 5 segments of the segmented leg of insects, and she assumed that its gradual reduction of a number of segments of segmented legs of arthropods leads to evolution and diversification of Arthropods on Earth. On the basis of comparative anatomical analysis and the embryological development, a number of scientists like Anderson (1973), Manton (1977), Zrzavy and Stys (1997), and Regier et al. (2010) revealed from time to time that most of the phyla evolved independently out of Pro-Annelies lineage as a result of the polyphyletic origin of Arthropods, the carrier of exoskeletons and these exoskeletal carriers extended the evolution of endoskeletal possessors, that is, vertebrates, in the course of evolution. However, in the prehistoric, main categories of Arthropods have been recognized by the evolutionary biologists, those acts as evolutionary links in the transition to put forth the evolution and divergence of present-day Arthropods on Earth (Meyer, 2013): Chelicerata: More than 70,000 species on earth (ranges from spiders, sea spiders, horseshoe crabs, ticks, mites, scorpions, etc.) Crustacea: More than 30,000 species (ranges from shrimps, lobster, crabs, copepods, amphipods, lice to barnacles, etc.) Trilobita: More than 4000 species, it includes extinct marine Arthropods, disappeared during the Paleozoic era. Uniramia: Around 1.2 million species (comprising onychophorans, centipedes, millipedes, symphylans, insects, etc.)

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The Onychophorans or “Velvet Worms,” possesses the typical “Pro-Annelidan” characters like multisegmented bodies, a pair of excretory organs (called nephridia), and possession of male and female sex organs (scientifically called monoecious bodies), and at the same time, they possess a number of typical characteristics of arthropods like the presence of incipient walking legs with claws, presence antenna, paired mandibles, presence of trachea and open circulatory system and chitinous cuticle (instead of an exoskeletal system outside of the body), which was subjected to periodical shedding or molting like the members of arthropods. A number of features of Onychophora: its identical mode of locomotion like the members of arthropods, the identical structure of the legs (e.g., millipedes, centipedes, etc.) and the comparative molecular analysis like nucleotide sequence, ribosomal RNA, etc. made the scientists construe Arthropodian affinity of Onychophora members (Anderson, 1973; Manton, 1977; Ballard et al., 1992). The contemporary cladistics analysis revealed that Onychophorans are sister clad of Arthropods and paraphyletically related to Annelids, which also indicated that the primitive members of Arthropods have some resemblance to worm-like creatures of Annelids as the multisegmented, soft-bodied, epidermal membranous outer layer of the body of Annelids might have evolved with hypersecretion of cuticular secretion to evolve with Arthropods with thick, segmented exoskeletal shell (Meyer, 2013). A group of invertebrate zoologists and the evolutionary biologists contemplated that the presence of typical features like the presence of an open circulatory system, hemocoel, and exoskeletal system intrigued them to hypothesize the monophyletic origin of Arthropods out of hypothetical “Proannelida” root-stock; whereas, a minority group of evolutionary biologists construed that in-depth palaeontological investigations of the ancient members of Onychophorans, Proannelids and primitive Arthropods, the comparative analysis of the mouthparts and lateral appendages, embryological development, etc., along with comparative molecular footprints indicates that Arthropods would have supposedly originated around four times and that indicates its polyphyletic history of origin (Meyer, 2013). However, the scientists noticed that Annelids and Onychophorans evolved with segmented excretory organs, nephridia, and the primitive excretory organs in ProAnnelids supposedly replaced by more organized excretory organs in Arthropods like coxal glands in the legs of horseshoe crabs, green-glands in the heads of crustaceans, and Malpighian tubules in the arthropod on the land ecosystem. The developmental biology of distinct forms of excretory systems in a distinct group of Arthropods, indicated toward the hypothetical polyphyletic evolutionary emergence of Arthropods, supposedly evolved multiple times, and they have gone through the process of evolutionary convergence to be recognized as a distinct phylogenetic group of organisms, called Arthropods. The one and a half to two inches long Onychophoran species, which are popularly known as Velvet worms as well as the few numbers of Peripatus and Eoperipatus species, morphologically resembled the caterpillar when it moves around the two conspicuous antennae on its head. The diagrammatic sketch of Peripatus sp. is presented in Fig. 8.1. The scientific investigations of the zoologists ascertained that

The Evolutionary Biology of Extinct and Extant Organisms

FIGURE 8.1 The diagrammatic sketch of Peripatus sp. Courtesy Sashi Sinha, Ms.

these Velvet worms are neither structurally nor physiologically close to caterpillars and the animal biologists noticed the mode of predatory acts of these unique creatures, gagged their preys by oozing out the jet-like flow of slime (https:// evolution.berkeley.edu/evolibrary/news/130905_newoldanimal, Sept. 2013). The evolutionary history of Onychophorans and the natural history of Lagerstatte, the unique fossil sites in China, and Canada are found to be closely integrated with each other. The most precious fossil sites, Lagerstatte of Chengjian formation of China and Burgess shell of Canada, preserved the range of strange-looking animals (like five eyed lobster-like exoskeletal scales with fluke like the body of Opabinia, Crustacea like body with octopus-like a couple of tentacles/tusks in the frontal end, like Anomalocaris, a slender body with long spines [resembling a porcupine-like body] of Hallucigenia, etc.) in the Cambrian. Those are not found in any other fossil sites on Earth as the Lagerstatte had a strategic advantage to preserve the soft-body part of the animals, either aquatic or terrestrial and those that decomposed faster and other fossil sites failed to retrieve the intricate body structure that Lagerstatte would have done (https://evolution.berkeley.edu/evolibrary/news/130905_newoldanimal, Sept. 2013). Cambrian Radiation has also been considered as the evolutionary surge of a huge number of animals on Earth. These unique palaeontological discoveries intrigued the phylogeneticists and the evolutionary biologists to determine the evolutionary lineage of the distinct groups of creatures, emerged in and went in the course of evolutionary divergence further in the backdrop of Cambrian Radiation. However, the critical investigations of evolutionary biologists and phylogeneticists on the palaeontological materials of Opabinia revealed further that they become extinct around the Cambrian period and did not have modern-day extant successors of it. On the other hand, a rigorous study of the paleontologists and evolutionary biologists on the Hallucigenia, as well as the pin-cushion worms, helped the scientists to discover more paleontological samples, and the micro-anatomical studies of the spike-like structures have been found to be tube-feet like structures found in the marine creatures like octopus. The ultrastructural profile of the Hallucigenia spikes has been found to be looking like stacks of ice-cream cones covered with scales (resembled jaws and claws),

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phylogenetically considered to be the marine, extinct, ancestral lineage of extant members of Onychophorans (Caron et al., 2013). The discovery of extinct species, reporting of extant members of Onychophorans and any evolutionary findings and reviews on Onychophorans inspired the evolutionary biologists and molecular phylogeneticists to establish its phylogenetic relievers like the members of crustaceans, insects, spiders, crabs, and other members of arthropods (having joint and tube legs). Therefore, it is a valid question to the evolutionary biologists whether Onychophorans are the typically primitive kind of Arthropods or not and the answer is no Onychophorans are not like the typical Arthropods as their body is soft and covered with segmented, exoskeletal shell-like arthropods. Thus, the next point is why did the evolutionary biologists considered Onychophorans as the close phylogenetically of Arthropods, is there any valid reason? Yes, there is a valid reason to consider so as if we study the life cycle pattern of Onychophorans, we would notice that Onychophorans molt few times to grow bigger in size, which is typically found in the members of Arthropods. The presence of tubes and holes, those forming the respiratory organs in the body of Onychophorans, was found to resemble the holes in the body surface of insects, called spiracles (the respiratory organs) and the molecular sequencing (Cladistic analysis) of Arthropods, Onychophorans and other groups of animals. The tree of life model revealed that Onychophorans, supposedly evolved half a billion years ago and this group has been found to be the sister clade of Arthropods, and it indicates that both groups have a universal common ancestor. So, one could try to draw a conclusion that it proves that Arthropods are not supposedly the successor of Onychophorans. As long as the ultimate result of molecular phylogeneticists is precise and correct, we could say firmly that we did not yet find the evolutionary parents of Arthropods. But then, in the world of science, it could not be tagged as an inconsequent discovery when the molecular phylogeneticists ascertained that they ascertained Arthropods are evolutionary cousins of Onychophorans as it remained the hope alive in the mind of scientists to explore the evolutionary parents of Arthropods in the future. Recently, Dr. Marin Smith, from the Department of Earth Science, Durham University, Great Britain, has shared his unique observation on the biogeographical review of the Velvet worms, which has helped to understand the evolution of Onychophoran members on this Earth around 500 mya (Smith and OrtegaHernandez, 2014; Yang et al., 2015). The palaeontological reviews along with recent phylogenetic investigations revealed that the contemporary distribution of Onychophoras in South Africa, South America, and Australia, supposedly corresponds to the Southern supercontinent “Gondwana,” and it promotes the ideas of the scientists to uphold the hypothetical perception of the Gowana origin of Onychophora (Briggs, 2003). However, its spatial distribution in South-East Asia (e.g., Vietnam) seems to be a little distracting to promote “Gondwanan Origin of Onychophorans,” which has also been elucidated by the Zoogeographers, who introduced the hypothetical migration of Onychophorans by means of “Biotic Ferry” from Gondwana to Laurasia when Gondwana plates fragmented around 150e100 mya and the breakaway

The Evolutionary Biology of Extinct and Extant Organisms

continental block drifted away from the Southern supercontinent Gondwana to the Northern supercontinent Laurasia (Smith and Ortega-Hernandez, 2014). Although the contemporary investigations revealed that the extant Onychophoran members are restricted in around 200 endemic species, the composite investigations of molecular phylogeneticists and paleontologists ascertained its emergence around half a billion years ago (Smith, 2016). The molecular phylogenetic investigations (also known as “Molecular Timetrees”) of the scientists indicated that Velvet worms left the marine ecosystems to migrate to the terrestrial environment of the maiden forest ecosystems in the Devonian period around 400 mya (Rota-Stabelli et al., 2013). The microanatomical, intricate changes (like genital openings and jaw articulations) of the first terrestrial fossil also indicated that around 300 mya, terrestrialization of this ancient invertebrate has been initiated. From an evolutionary perspective, it should be treated as one of the earliest efforts of transmigration or terrestrialization of invertebrate animals that went through further the reticulate labyrinth of biological evolution of millions of years to be emerging as the modern Vertebrates on Earth (Garwood et al., 2016). The evolutionary biologists have considered the fragmentation of Gondwana continental shelf around 150e100 mya as the key impetus that renders the prehistoric Onychophorans to diverge out into two distinct forms of evolutionary groups: The members belonging to Peripatosidae, the predominant group of Onychophorans, acclimatized in temperate Gondwana and the modern group of Onychophorans of tropical Gondwana, belonging to the group Peripatidae (Monge-Najera, 1995; Seton et al., 2012). The discovery of a 100 million years old petrified fossil of Asian Peripatid (Cretoperipatus burmiticus) in the Burmese Amber indicated the distinct regionalization of Onychophorans in the backdrop of fragmentation of Gondwanaland (DeSena et al., 2016). On the other hand, the molecular phylogeneticists ascertained after a series of investigations that the earliest members of Onychophorans came to settle in the Indian subcontinent around 65e55 mya (Murienne et al., 2014). The close morphological resemblance to the Peripatid member Cretoperipatus burmiticus and the extant members of Onychophorans in Southeast Asian region indicated that the Onychophorans members of the Indian subcontinent supposedly migrated to southeast Asian regions in Cretaceous in search of the congenial tropical climatic regime and it has been defined as “Out of India” hypothesis to elucidate the origin of southeast Asian Onychophorans (DeSena et al., 2016; Smith, 2016). However, to render a feasible elucidation of the African perapatids to Europe, the zoogeographers have promulgated a new hypothesis, called “Euro-Gondwanan hypothesis,” in which the scientists defined that the drifting away of the “Apulia Microplate” from Gondwana plate and to get closer to Eurasian plate expedited the natural migration of the Velvet worms from Africa to Europe in the Cretaceous era (Ezcurra and Agnolin, 2011). To ascertain the “Eurogondwana hypothesis” as the tenable zoogeographic theory, there must be some supporting molecular evidence that could ensure that

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the Asian peripatids should have genetic descendants from its African ancestral lineage, but the critical investigations of the molecular clock of the peripatids intrigued the molecular phylogeneticists to reveal that the divergence of Southeast Asian peripatids had taken place much earlier than the splitting off South American and African Onychophorans (Murienne et al., 2014). Rather, one of the basis of the sequence data molecular clock, the molecular phylogeneticists contemplated that the divergence of Asian Onychophorans took place around 360e210 mya, which was in between the Devonian and Cretaceous period. This is the major flaws to consider “Eurogondwana hypothesis” of erstwhile migration and diversification of Velvet worms as the geological time slot drifting off “Apulia Microplate” that did not reconcile the molecular time slot of the evolutionary divergence of Asian peripatids as observed in the “Molecular clock” (Murienne et al., 2014). Based on such observation, a number of scientists discarded the “Eurogondwana and Out of India” hypothesis and came to the conclusion that the Velvet worms were present in Lauresia, much earlier than it separated from Gondwana around 150 mya (Murienne et al., 2014). The discoveries of the 300 million years old Onychophoran fossil evidence of Helenodora from Laurasia and the discovery of the fossil of Antennipatus, the terrestrial Onychophorans from Lauresia during the Carboniferous period, rather indicated that the Velvet worms supposedly evolved in Lauresia than Gondwana (Smith, 2016). The contemporary molecular analysis of the extant representative of Velvet worms in South East Asia, along with the rest of the peripatids, revealed that the sole, living member of Velvet worm in South East Asia, found to be paraphyletic to the rest of the peripatid members and that indicates that all peripatids must have a common ancestral lineage of evolution (Smith, 2016). Hence, instead of depicting the extant representative of the Velvet worm in South East Asia as it has been interpreted by deSena et al. (2016), the molecular geneticists and phylogeneticists considered it as a living fossil and remained in such as a stable state for 100 million years (Smith, 2016). So, the living Velvet worms in South East Asia should best be regarded as the living fossil, which supposedly possesses the genetic inheritance of ancestral lineage of Onychophorans, as well as evolutionary cousins of Arthropods, those evolved during Cambrian radiations, rather than a contemporary interpretation of modern Onychophorans, the so-called outcome of biological evolution emerged during “Cretaceous Radiation” (Smith, 2016). However, the fossil evidence from the Lagerstatte of Chengjiang formation of China and Burgess shale of Canada exposed that “megadiversity of Arthropod” on Earth, happened to be exploded in the early Cambrian and that took 520 million years of time, a long ride of the evolutionary journey to have appeared in the present form (Edgecombe, 2010). To elucidate the elusive journey of biological evolution as well as the evolutionary development (Evo-Devo), the contemporary progress in the applied arena of genetics and genomics on invertebrate groups of organisms, mainly the Arthropods, specifically, the developmental genetics, molecular phylogenetics,

The Evolutionary Biology of Extinct and Extant Organisms

genomics, etc. of Drosophila sp. played key roles (Drosophila 12 Genomes Consortium et al., 2007). The extensive review of the comparative account of palaeontological, anatomical, genomic analyses between Arthropods and Onychophorans ascertained that both of these molting animals are phylogenetically close related and emerged from a “Last Common Ancestor” (Edgecombe, 2010). Around two decades ago, the “Articulata hypothesis,” which has been proposed by Cuvier in the 19th century, stereotypically narrated that segmentation throughout the body-axis of Annelids and Arthropods shared a common mother-stock and both groups of organisms have identical characteristics like the presence of body cavities or coeloms, segmented muscles, and sensory/locomotory appendages (like parapodia in Annelids and its homologous appendages like limbs in Arthropods, etc.) (Scholtz, 2002). An extensive molecular investigation on the gene expressions ascertained later that the visual resemblance of segmentation of the body, through the dorsoventral axis, has nothing to do a further phylogenetic determination of the proximity of Annelids and Arthropods. Scientists noticed that the presence of genes: engrailed, hedgehogs, and wingless; those are responsible for segmentation of polychaete AnnelidsdCapitella, Hydroides, etc., showing a distinct pattern of polarity in the segmentation of Arthropods and it indicated further that segmentation pattern is not the key characteristic feature that is supposedly possessed by the last common ancestor of these two distinct groups of organisms (Seaver and Kaneshige, 2006). The contemporary investigations of the molecular phylogeneticists revealed that Arthropods are phylogenetically closely related to the roundworms like Nematodes and another group of unsegmented worms, known as Cycloneuralians (Arthropods along with Nematodes and Cycloneuralians altogether together have been recognized as Ecdysozoa), rather than the members of Annelids (Edgecomb, 2010). However, the Arthropods were found to be phylogenetically in nesting proximity of Articulata or Ecdysozoa; the evolutionary biologists have noticed that the Arthropods were found to be phylogenetically close related to two animal phyla: a. Phylum Tardigrada (Water Bears) and b. Phylum Onychophora (Velvet Worms) The arthropod members belonging to the phyla mentioned above, have been characterized with the segmented body plans alongwith ventrolateral locomotory appendages. However, the microscopic members (body length is around 0.5 mm) of Tardigrades comprised around 960 species, living in marine-freshwater, limnoterrestrial habitat, characterized by the presence of four pairs of trunk legs, with claws at the end of a tow-like structure. On the other hand, Onychophorans are found to be less diverse, represented by 200 species, found to be inhabiting tropical and temperate forest ecosystems, and these typical carnivorous creatures are characterized by a pair of antennae, a pair of slime glands, a pair of jaws, and variable pairs of unjointed legs, called lobopods (Edgecombe, 2010). The composite assemblage of Arthropods, Tardigrades, and

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Onychophorans is altogether known as “Panarthropods” or “Aiolopoda” (Nielsen, 2001; Hou and Bergstrom, 2006). According to the contemporary effort of reconstruction of phylogenetic trees of Arthropod-Annelid assemblage, the Arthropods are reconciled as Ecdysozoans, the Annelids with distinctive “spiral cleavage” in its embryonic stage, and the “trochophore” (with distinctive ciliary bands) larva-bearing Molluscs and Platyhelminths (the flatworms) have been recognized as the clade Spiralia or Lophotrochozoa (Giribet et al., 2009). On the basis of the analysis, molecular data of 18S rRNA from Panarthropods-Cycloneuralia assemblage justify the hypothesis of the Ecdysozoan origin of Arthropods (Aguinaldo et al., 1997). The molecular phylogenetic investigations ascertained that Annelids along with Molluscs were found to be well nested in Spiralian clade and the analysis of the mitochondrial genome of Onychophorans also revealed that its protein-coding genes have shown a close phylogenetic affinity toward Ecdysozoans (Podsiadlowski et al., 2008). The review of molecular data, cuticle formation, molting pattern, and synthesizing potential of ecdysone hormones of the Ecdysozoan phyla made it phylogenetically close to Annelids, Molluscs, and Spiralia, rather than Arthropods (Edgecombe, 2010). However, the phylogenetic relationship of Arthropods with its close allies as well as transitional links or Evo-linksdEcdysozoans, Annelids, Onychophorans has gone through the labyrinth of the evolutionary trail, where the stem group of Arthropods exposed a distinct rift with its counterpart of crown groups and that indicates that the evolution of Arthropod is not an isolated chapter in the Evolutionary history of Invertebrates. Rather, it should be considered as the transitional stepping stone in the evolutionary crossroads of life on Earth; it is like a relevant parable in the Bible of the evolutionary journey of tetrapods or Vertebrates; without touching it down, the objective of the pilgrimage would have remained incomplete. Nonetheless, to understand the evolution of a group of organisms, specifically those evolved with some key appendages, responsible for better adaptation in locomotion, feeding, protection, reproduction, etc., the evolution of appendages formation and its diversification is necessary. The molecular footprints of appendages formation has found to be convincible in the best way when the molecular geneticists and genomicists concentrated their genetic investigations in the molecular level on a lower group of vertebrates and insects (Lauterbach, 1978; Hou and Bergstrom, 1995). In the year of 1997, Grace Panganiban of Department of Anatomy, Genetics and Biochemistry, University of Wisconsin, USA along with a number of research scientists investigated the gene expression of Distal-less (Dll) homeoprotein in relation to the growth of limbs of the Arthropods and the gene expression of the Dll orthologs (Dlx) in the formation and development of fish fins and the limb-buds of tetrapods, to find out whether the expressions of these regulatory genes played any cardinal role in the appendage formation in protostomes and deuterosomes. The scientists observed that Dll has been expressed in the formation and development of appendages of animals in a number phyla, like the formation of development of:

The Evolutionary Biology of Extinct and Extant Organisms

Antennae of polychaete annelid (Chaetopterus varioedatus) and distal axis of parapodia. Lobopods of Onychophoran Peripatopsis capensis. Expression of tube feet of Echinoderms. Ascidian ampullae, etc. However, the comparative morphological microanatomical and the genetical investigations indicated that the development of appendages of Cambrian Lobopodans and the prehistoric Arthropods supposedly evolved from a primitive Lobopodal ancestor (Snodgrass, 1938; Manton, 1977). The Dll gene expressions in relation to the appendage development of Arthropods and terrestrial Onychophorans, which has phylogenetically considered to be the sister group of Cambrian Lobopods, indicated that Arthropods supposedly inherit the characteristics like formation and development of appendages from the evolutionary root-stock of Cambrian Lobopodans (Panganiban et al., 1997). The contemporary phylogenetic investigations revealed that Annelids are neither the sister group of Onychophorans nor the sister group of Arthropods; so, there is no point to consider polychaete parapodia as the evolutionary successor (which has been considered earlier) of Cambrian Lobopodans; rather the independent evolution of appendages formation trends in Lobopodans seems to be more tenable hypothesis (Lauterbach, 1978; Turbeville et al., 1991; Winnepenninckx et al., 1995). The molecular phylogeneticists and paleontologists and evolutionary biologists carried out a comparative morphological study of the primitive antenniform outgrowth of Cambrian Polychaetes, Onychophorans, and Arthropods along with molecular data and paleontological reviews that helped them to render a new hypothetical elucidation of independent origin and evolution of Lobopdia and Parapodia, from sensory outgrowth traits of the evolutionary common-stock of AnnelidOnychophorans/Lobopodans (Morris, 1979; Hou and Bergstrom, 1995; Panganiban et al., 1997). The molecular investigation on the expressions of Hox genes in different insects (including Drosophila sp.) found to be responsible for masking effect of the formation of antennae in Arthropods and the loss of Hox genes in legs, rendering formation of antennae and the scientists contemplated further that the loss of Hox gene in Tribolium rendering changing the segmented body into the antennae bearing metameres (Stuart et al., 1991). It leads Grace Panganiban et al. (1997) to hypothesize that the ancestors of the modern Protostomes emerged with antenna-like appendages, that primitive appendages become duplicated and metamorphosed to the trunk-like appendages of Lobopodia and Parapodia in the course of time and it supposedly happens after the divergence of Annelids and Onychophorans. On the other hand, the evolution of Deuterostomes and their appendages are still enigmatic issues as no substantial evidence has been found so far that could interpolate that the ancestral lineage of Protosomes gives rise to Deuterostomes of the course of evolution (Gee, 1996). Rather, the phylogenetic investigations indicated that evolution of siphonaceous ampullae, the substrate-gripping locomotor organs of Ascidia, and the tube-feet like

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appendages of Echinoderms evolved from the outgrowth of the body wall of a common ancestral lineage (Panganiban et al., 1997). The evolutionary biologists noticed that in the base-line vertebrates like fishes, the evolution of fin-like appendages in fishes has no clear elucidation yet to define its outgrowth, but the formation of outgrowth of the branchial arches has been found to be regulated by Dlx gene expression and it indicates that the evolution of fins in Pisces might be controlled by the gene expressions of some identical genes (Wall and Hogan, 1995). The contemporary discoveries in the field of developmental genetics revealed that homologous genes in insects and vertebrates are responsible for the formation of important organs like the heart, eyes, and dorsoventral axis (Holley et al., 1995; Schmidt et al., 1995). It is a matter of fact that the concept of homology varies as homologous eyes and limbs in a different group of organisms structurally vary in anatomical and morphological levels. According to this hypothetical explanation, the last common ancestor of Protostomes and Deuterostomes supposedly possesses the primitive appendages, grown from the body-wall outgrowth, either sensory or locomotory appendages, changed in the course of evolutions to be appeared as the appendages like fins, flippers, or hands and legs in vertebrates, in the course of evolution (Panganiban et al., 1997). It seems to be an impossible task for evolutionary biologists to comprehend and defining the structural formation of such “Last Common Ancestor” of Protsomes and Deuterostomes as the palaeontological evidence of such primitive, invertebrate fossil in the pre-Cambrian regime was absolutely missing. However, the kind of rare discoveries of trace fossils on the shallow, sedimental layer of some erstwhile marine and aquatic fossil sites helped the paleontologists to contemplate that it seems that such hypothetical predecessor of Protostomes and Deuterostomes were structurally advanced than flatworms, coelomic, triploblastic animal, moved with primitive sensory as well as locomotory appendages, and the existence of such invertebrate organism thematically resembled Platyhelminthes like organisms (Valentine et al., 1996). The recent development in developmental genetics has found that the expression of Dll/Dlx genes in Nematodes, Annelids, Onychophoras, Arthropods, Echinoderms, and Vertebrates is found to be primarily responsible for regulating optic/sensory functions as an integral part of the functional regulator of central nervous system (CNS) of the brain (Panganiban et al., 1997). Such observation intrigued the evolutionary biologists to contemplate that the expression of Dll/Dlx genes was primarily engaged in the brain functions of the concerned animals, mainly the functional role-play of CNS before engaged in secondary functions like formation and diversification of locomotory appendages in a diverse group of Metazoa that end up in the formation and development of locomotory appendages of Vertebrates in the long run of biological evolution (Panganiban et al., 1997). Hence, in the arena of developmental genetics, the unique observation is the changes of gene expression of Dll/Dlx genes, to switch its mode of operation from nerve cells (CNS) to body cells (formation of body wall outgrowths or

The Evolutionary Biology of Extinct and Extant Organisms

appendages), which supposedly help in diversifying the evolutionary surge of the wide array of Metazoan organisms on Earth, witnessed in the backdrop of Cambrian Radiation. Since evolution, which is around 520 mya, Onychophorans (the Velvet Worm) must have gone through the topsy-turvy ride of the evolutionary journey of life that would not only help to depict the evolutionary journey of Invertebrates by acting as the mythical narrator to brief on the shift in the paradigm of life, where the invertebrate organisms with a soft body and without exoskeletal protection went through changes of time to cope with the environmental changes in its ambiance to be emerged with a unique soft-bodied organism with exoskeletal shield, around its body surface to sustain their evolutionary journey of diversification and established their domination as the competent group, called Arthropoda of organism on Earth. Relatively, Arthropods as a distinct evolutionary group clearly established its evolutionary identity as the Evo-link, which could define the shift in the paradigm of life in terms of the continuation of its evolutionary journey of diversification on Earth, from the regime of Invertebrates in the Cambrian period to the dynamic regime of Vertebrates in the Cretaceous period.

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The extent of Ctenophore uniquenessddistinctly recognized to be “quasiCnidarians” or “stunted Bilaterians”

9

“While ctenophores clearly diverged from other animals early during metazoan evolution, living species radiated relatively recently (Podar et al., 2001; Simion et al., 2014). This means that ctenophores are connected to other animals by a long branch, not due to accelerated rates of molecular evolution, but because so much time elapsed between the divergence of ctenophores from other animals and the most recent common ancestor of living ctenophores. This long branch has made it difficult to resolve their relations to other animals. It is unknown whether living ctenophores are the sole remaining subclade of a large diverse group, or if ctenophores have always had a relatively few numbers of species. Either way, there is no further reason to think that ctenophores are more similar to the most recent common ancestor of animals than are any other living animals (Grandcolas et al., 2014).” Casey W. Dunn and others1

The evolutionary journey of life, as well as depicting the evolutionary progress of animals, is conventionally defined as the acquisition of more complex traits of the recent or derived form of animals concerning its ancestral lineage, with the simplest form of an organism, gone through the gradual changes of time and space. Nevertheless, the rejection of such a biased hypothesis of biological evolution, which has logically proved that evolution is a random process than a well-programmed “bottom-up” model that could legitimately execute the principles of stereotype up-gradation to yield a Superior species down the trail of evolution. In comparison to a classical hypothesis, the contemporary phylogenetic interpretation of animal evolution elucidated that several complex traits emerged and were lost in the biological organisms over time, as all biological organisms strived to cope with dynamic changes in the environment they belonged to. It certainly revealed that it is not

1

Sally P. Leys and Steven H.D. Haddock

The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00010-6 Copyright © 2021 Elsevier Inc. All rights reserved.

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“evolutionary up-gradation” of traits that could be attributed to the progress of evolution as if the environmental changes influenced the organisms to modify themselves to go through the process of simplification which supposed to be considered as “evolutionary down-gradation.” The derived groups of animals might have emerged with simpler traits than their ancestral lineages. The phylogenetic interpretations of evolutions in the world of the animal kingdom have further been categorized under five divisions (Margulis et al., 1994; Lecointre and Guyader, 2006): a. b. c. d. e.

Porifera (Sponges) Cnidaria (Jellyfishes, Corals, etc.) Ctenophora (Comb-jellies) Placozoa (Trichoplax) and Bilateria (All other animals)

The classification of Metazoans in certain groups has been made by the taxonomists, which laid the base-work to render phylogeneticists to present the feasible interpretations of either Porifera or Ctenophora as the sister clades of the evolutionary tree-model of the remaining metazoan animals; as hypotheses, both of these have been poorly clarified as well as inefficiently defined. Superficially, Comb-jellies have a striking resemblance to the Jellyfishes in terms of sharing the marine habit (lived in suspended water column most of their life span) with translucent, gelatinous bodies and utilize tentacles to catch the prey like zooplankton and smaller animal larvae like Cnidarians (Moorhead, 2019). A careful observation helped the marine biologists to notice that when Cnidarians use tentacles to catch the prey, they use nematocysts (also called stinging cells to immobilize the prey), whereas the Ctenophores are evolved with a distinct type of organs called Colloblasts to subdue the catch of prey, and the existence of such unique organs is not found in any other metazoan representatives (Ryan et al., 2013). Instead of injecting the immobilizing chemical by nematocysts inside the body of the catch of prey, Ctenophores start exuding glue-like substance when the tentacles of the Ctenophores get in touch with prey, mainly the marine planktons, acting as a sticky trap and then contracting their tentacles to put the catch of prey in their mouth to engulf it (Moroz et al., 2014). The scientists observed that the existence of the primitive brain (comprised two nerve nets) in the aboral parts of the Ctenophores is found to control major physical and physiological actions such as controlling the gravity, coordinating chemoreception, and carrying mechanical and chemical reception. Its main function is to coordinate the locomotion by propelling actions by beating the hair-like cilia (eight in a row form unison) forming comb plates and this kind of unique ciliary movement is not found in any other Metazoans (Moroz, 2015). The evolutionary biologists considered the cilia-assisted locomotory movements of Ctenophores as primordial movements, evolved in Mesozoa, the ancient biobehavioral traits of ancient metazoans that evolved and diversified in the Metazoan groups to render the modern groups of Metazoans that struggled to come out of the water, settled on terrestrial ecosystems, and migrated all over the biosphere in the course of evolution.

The Evolutionary Biology of Extinct and Extant Organisms

As long as the cilia-mediated movement of Ctenophores or Comb-jellies is concerned, the key locomotory unit is recognized as “Ctenes” or combs, possessed by eight rows of comb-plates and each comb-plate comprised hundreds and thousands of multiciliated cells (2 mm long) (Tamm, 1982). Due to the fragile nature of the comb-jellies body, the formation of fossil is less likely to happen, which rendered the paleontologists in the dark as they could carry-out any phylogenetic investigations, and the fragile nature of its body made it difficult for the genomicists to collect the sample for this fragile organism to coordinate research works. For a long time, it was a difficult task for the systematic zoologists to place Ctenophores in the “Phylogenetic tree of life.” However, the composite studies, like morphological reviews of Ctenophores along with the review of the molecular data of ribosomal RNA made the molecular phylogeneticists contemplating Ctenophores as the sister group of all Metazoans (Moroz, 2015). Furthermore, contemporary phylogenetic studies indicated that Ctenophores were the earliest members. They diverged out of the Metazoan lineage, so they should be treated not only as of the ancient predecessor but the sister clade of all Metazoans on Earth (Borowiec et al., 2015). The contemporary investigations of the Ctenophores nervous systems, coupled with contemporary genomic analysis, helped the molecular phylogeneticists to contemplate as above (Moorhead, 2019). Comparative analyses of the structural and functional aspects of genome profiles of the members, belong to Cnidarian, Ctenophora, and Bilateria rendered the genome biologists to comprehend that Ctenophores are structurally, functionally, and phylogenetically unique organism in respect to the rest of the metazoans. In terms of developmental gene expressions, the presence of Hox genes in Bilaterians, which regulate the developmental body plan of juveniles to have emerged in the adult state, has been found to be absent in Ctenophores (Moroz, 2015). On the other hand, the “gene content data,” contained in the genome of Ctenophores, particularly in Mnemiopsis leidyi, helped with sequential development of the Ctenophores body plan such as passing through the embryonic stage to larval stage and to the next adult stage, which has been found to be absent in the rest of the Metazoans (Ryan et al., 2013). In the same way, the evolution of developmental gene expressions, which has been observed in the members of Ctenophores, particularly in Pleurobrachia sp. has not been found in other Metazoans, and it indicated that Ctenophores supposedly evolved with the lack of several traits, usually found in other Metazoans at the same time evolved with distinctively patterning genes and unique nervous systems not been witnessed among other groups of Metazoans (Moroz et al., 2014). The molecular phylogeneticists have found it difficult to determine the phylogenetic position of Ctenophores in the phylogenetic tree of life, mainly due to the following ambiguous scenarios: A. The age-dating molecular clock has determined that the prehistoric lineage of Ctenophores diverged out of the rest of the Metazoan lineages around 540 mya, during the pre-Cambrian period, which posed a challenging issue to the

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evolutionary scientists as phylogenetic signal helping to attribute and judging the phylogenetic proximity of any particular clade to its allies seems to be very faint. B. According to the evolutionary biologists, the pace of Ctenophore’s evolution happens so fast and in an overlapping pattern where the key evolutionary progress of its intermediate states (related to Long Branch Affinities, specifically) have been lost in transition. Hence, it rendered the scientist clueless in the contemporary radiation of the derived group of Ctenophores on Earth. To fix such phylogenetic impediments to determine the phylogenetic position of Ctenophores as a distinct phylum in the phylogenetic tree construction of the animal kingdom, a brief review of the “Porifera-sister hypothesis,” which claims the Porifera is the phylogenetic sister-group of all major Metazoans evolutionary lineages, needs to be done. To walk through the trail of evolution and diversification of Metazoan life, the evolutionary progress of Ctenophores (which seems to be an evolutionary stepping stone) needs to be understood to some extent, unless the shift in paradigm in the journey of life evolution from Protozoa to Metazoan would be difficult to understand. Every phylogenetic analysis gives a new perspective to the origin and evolution of a large number of animals in diverging mode and the mode of parallel evolution for the complex form of some animals. The phylogenetic classification of Pisani et al. (2015) propounded a unique hypothesis of Porifera as the sister group of other distinct groups of Metazoan but left a space for its further criticism due to inadequate substantiation of their hypothesis. The scientists noticed that the morphological, physiological, functional, molecular analyses and interpretation of data failed to corroborate the phylogenetic interpretations of conventional evolutionary format as the animals have gone through the complex and reticulate matrix of evolution. Every distinct set of the organism has not necessarily moved forward in the course of evolutionary changes from a simple form to a complex form as the interaction of its ambiance of that distinct group of the organism and the environment directs the evolutionary progress to the next level. Thus, instead of simple to complex, the nature of changes of a distinct group of organisms might go to reverse direction to ensure the survival of that evolutionary lineage. The superficial morphological resemblance does not comply with the molecular phylogenetic status of two distinct forms of animals to define their close phylogenetic proximity like the homology of choanocyte cell bearing Porifera with the Choanoflagellates group (Mah et al., 2014). The paleontological evidence of Porifera indicated that sponges supposedly originated in the Cryogenian period in between 850 and 635 mya, whereas the molecular clock of the contemporary phylogenetic analysis ascertained that Porifera emerged on Earth around 540 mya in the Cambrian period, which raised a legitimate concern about the validity of “PoriferaeSister hypothesis” of Metazoans. The apparent morphological resemblance like the absence of muscle and neuron in Porifera rendered the scientists to consider it as a simple form or organism, with respect to Ctenophora, Cnidaria, and Bilateria as these evolutionary groups possess neurons

The Evolutionary Biology of Extinct and Extant Organisms

and muscles in them. Several phylogenetic analyses claimed that Porifera is found to be closely related to Cnidarians and Bilateria, in comparison to Ctenophora and Placozoa (which does not have muscle and neuron) found to be appearing as a phylogenetic sister of Cnidarians and Bilateria as a transition between the organisms with muscle and neuron, such as Cnidaria and Bilateria and the organism without it like Porifera (Moroz et al., 2012). As long as paleontological evidence is concerned, the age-dating process of Eoandromeda, the prehistoric Ctenophore, has further ascertained that the origin and evolution of Sea gooseberries or Ctenophores happen in pre-Cambrian and Cambrian period, around 580e551 mya (Chen et al., 2007; Tang et al., 2011). Whereas the earliest fossil record of Poriferas has revealed that sponges supposedly evolved around 548 mya (Penny et al., 2014). The diagrammatic sketch of Eoandromeda is presented in Fig. 9.1. Some paleobiologists and evolutionary biologists construed that the Cambrian Radiation, which has happened around 541 mya, considered as the causal reason for the sudden surge or exponential radiation of several animal species in a short period. This had created an opportunity to evolve several evolutionary lineages of animal species as a result of the parallel evolution of a distinct line of animal species. Eventually, it expedited the divergence of several derived groups of animals with more complex tissue systems and advanced mode of functions, in comparison to their ancestral counterparts (Erwin and Valenine, 2013). So, the emergence of Ctenophores with unique epithelial tissues, neuromuscular systems, and distinct

FIGURE 9.1 The diagrammatic sketch of Eoandromeda. Courtesy Sashi Sinha, Ms.

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type of neurotransmitters to perform neurosignal transmission; the emergence of well distinct neurogenic systems with well-diversified neurotransmitters (to coordinate precise neurosignal transmission) in Cnidaria/Bilateria and the emergence of Porifera/Placozoa without any neurogenic systems has clearly validated the parallel hypothesis of evolution of Metazoan clades in the backdrop of Cambrian Radiation (Moroz, 2015). The consideration of the facts like the presence of differentiated muscles from Mesoderm and the multiciliated locomotory features of Ctenophores and at the same time the presence of a composite type of epithelia-muscular cells (that comprised part of epithelial cells and part of contractile muscles) in Cnidarians have indicated further that Ctenophores and Cnidarians are not diverged out one from another, rather these two distinct groups evolved, independently (Steinmitz et al., 2012). The diagrammatic sketch of Ctenophora is presented in Fig. 9.2.

FIGURE 9.2 The diagrammatic sketch of Ctenophora. Courtesy Goutam Saha, Mr.

The Evolutionary Biology of Extinct and Extant Organisms

A series of neuroanatomical investigations on Ctenphores have been initiated under electron microscopy since the 1960s (Horridge et al., 1962; HernandezNicaise, 1973, 1991), but they failed to catch the neuronal architecture and presenting the ultrastructural graphics of the nerve tissue of Ctenophores. So, Horridge (1974), an expert on the neurogenic interpretation of Ctenophores has analyzed and integrated these neurogenic data to establish its phylogenetic relationships with other groups of animals, as he stated “It is only an assumption that axons, synapses and sensory cell bodies seen by the electron microscopy are the same branched neurons that spread like a net over the whole surface. Only by analogy with higher animals are the synaptic vesicles thought to have this function and to be presynaptic.” The scientists have revealed that the neural system of Ctenophores is built up of four cellular stages (Tamm, 1973, 1982): a. The first layer of cell populations is made of subepithelial nerve nets (comprised neurons and neurites). b. The second layer of cell populations is made out of intramesoglea neural nets. c. The third layer of cell populations is made with neural elements in tentacles and subgastrodermal elements. d. The fourth layer of cell populations is made out of neural cells in the aboral region (comprised heterogeneous cells like gravity sensors and a statolith, having around 100 lithocytes), which regulate functions in cilia. Although true eye-spots or photoreceptors are absent in these primitive nerve tissues of Ctenophores, the presence of a primitive form of chemoreceptors and photosensors are there to carry-out neurosignal-mediated muscular movement, helped out in predation and cilia-mediated locomotion, the basic physical and physiological functions of it that would have been guided by the neural system in a distinct group of Metazoan clad (Vinnikov, 1990; Aronova and Alekseeva, 2003; Schnitzler et al., 2012). Ultrastructurally, the neurons of Ctenophores are unique and functionally well organized as the nature of synapses between the neurons and their potential effectors are found to be well-diversified, ranging from gland cells, ciliated cells, epithelial tissues, muscles, colloblasts, photosensors, and photocytes (light-emitting cells, causing bioluminescence), but the key feature missing here in Ctenophore’s neurons is polarity (Horridge et al., 1962; Hernandez-Nicaise, 1991). The unique way of synapse formation in Ctenophores has been revealed by the neuroscientists as they observed that the neuronal membrane of one cell form synapse in the other cells, forming presynaptic triads, that is present in Cnidarians, but found to be absent in Vertebrates (Anderson, 1985; Hernandez-Nicaise, 1991). Ctenophores have also possessed highly polarized synapses, occasionally (Hernandez-Nicaise, 1991). According to the recent investigations, the unique neurosynaptic transmissions of comb-jellies are recognized as “Presynaptic triad,” where any part of the nerve cell of Ctenophores (as per norms of nonpolarized morphology) or its neuron could form synapse to the adjacent nerve cell to carry-out neurotransmission, which is a distinct phenomenon not found in Bilaterian Metazoans. The neurosignal

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transmitting action of neuron or axon and the neurosignal receiving action of neuron or dendrites form asymmetrical synapse2 to coordinate such acts of neurotransmission (Moroz, 2015). The neuroscientists observed that the preponderance of asymmetrical synapse in Ctenophores made them hypothesize that Ctenophores evolved with unidirectional neurotransmission mechanisms, which supposedly took place by the unidirectional movement of biochemical neurotransmitters, usually carrying the neuronal message from one neuron to the next one (Moroz, 2015). Apart from the Asymmetrical synapse with presynaptic triads, the presence of two-way synapse with opposing presynaptic triads and Soma-soma reciprocal synapse has also been found in Ctenophores, and this unique type of two-way synapse has not usually been found in the Vertebrates (Moroz, 2015). The animal biologists, neuroscientists, molecular phylogeneticists, and interdisciplinary scientists have noticed the gap junctures in between the asymmetrical synapse of presynaptic triads of Ctenophores, which contain protein substances and act as neurosynaptic buffers to transfer neurotransmissions from one nerve cell to next one and connected to the tentacles, combs for its predation, protection, and movements, etc. Surprisingly, the diversity of “gapejunction proteins” has also been witnessed in the Ctenophores (e.g., Pleurobrachia that contains 12 types of gapejunction proteins) and “Connexin” is one of them. Eventually, the presence of “Connexin,” the gapejunction proteins (transmitted through the cytoplasmic streaming), which are present in Chordates, rendered the scientists to construe the close phylogenetic relations of Ctenophores with Chordates (Moroz, 2015). According to the biochemical investigations on the role of neurotransmitters in relation to the evolution of Ctenophores, the scientists noticed that the conventional Metazoan neurotransmitters such as acetylcholine, adrenaline, dopamine, noradrenaline, and serotonin are not found in Ctenophores, rather Ctenophores have been found to be evolved with distinct neurotransmitter, known as L-glutamate with the compatible receptor known as iGluRs (ionotropic Glutame receptors) that regulate the muscular contraction of it (Moroz et al., 2014). To understand the evolution of nerve cells and their functional integration in the development of the brain in the derived group of Metazoans, which reach out to the ultimate representative of Vertebrates, the microanatomical and physiological modes of functions of nerve cells or neurons are needed to be familiar with. The nerve cells or neurons are found to be a special kind of neurosecretory, polarized cells that have the potential in generating electrical signals to carry extracellular messages and transmitting messages to the destinations, without interfering or affecting the normal functions of neighboring cells in its periphery (Moroz, 2015). After going through several extensive investigations and critical reviews on the issues like the origin and evolution of nerve cells in Metazoans, the evolutionary biologists have come to the conclusion that the evolution of neurons and the

2

Asymmetrical Synapse: It has predominantly found in Bilaterians, where a single cell involved in neuro-signal transmission and another one is involved in receiving in polarized neuro-signal transmission.

The Evolutionary Biology of Extinct and Extant Organisms

formation of the synapse have happened more than once and independently, in the 600 million year history of the evolution of animals and it most likely happened from the Cnidarian/Bilaterian lineages, those used to possess a rudimentary nervous system rather than possessing an organized Central Nervous System (Moroz, 2015). Scientists observed that in terms of narrating the evolution of the nervous system in Ctenophores, in comparison to other Metazoans, the parallel evolutionary progress of the neural system needs to be defined well. It happened in terms of possession of the lesser diversity of genes contained in the genome of Ctenophores and these genes have controlled the functions of neuronal, synaptic, muscular, and epithelial systems found to be prevalent in Metazoan lineages. The prehistoric lineage of Ctenophores has evolved as the carnivore group of animals, inhabiting the oceanic habitat, evolved with rudimentary neuromuscular-immune systems and it has been surprisingly devoid of neuron-specific genes, found in Cnidarians/Bilaterians. The absence of typical neurotransmitters is found in Bilateria/Cnidaria (e.g., the neuron-specific RNA-binding protein-synthesizing gene Elav is absent in Ctenophores and the neurotransmitters such as Dopamine, Serotonin, and Noradrenaline, which are found to be absent in Ctenophores rather than the presence of a unique neurotransmitter Glutamate in it). It rendered the evolutionary biologists to hypothesize that the evolution of neural systems in Ctenophores happens independently in the history of the emergence of neural systems in Metazoans (Moroz, 2015). The most intriguing facts that made the scientists pick Ctenophores for further neurological investigations to unfurl the role of emergence of neuronal tissues in the course of its evolution are the following: a. The emergence of Ctenophores as pre-Bilaterian animals supposedly happens in parallel to its evolution of nervous systems and muscular tissues from the mesoderm region of the body. b. Due to the fragile nature of the body, it was difficult for scientists to study the neurobiological investigations of Ctenophores in laboratory conditions. c. The lack of presence of some conventional neurotransmitters (those usually been found in most of the metazoans having nervous systems) made the situation so difficult to understand the neurobiological functions of Ctenophores. The above scenarios, rendered the scientists to work on the emergence of neuromuscular systems in Ctenophores, the function of which has been controlled by the intracellular signaling molecule (moved through the neuronal circuits), subsequently regulated by the interactive, subset conserved gene modules in Ctenophores (Moroz, 2012; Moroz et al., 2014). Furthermore, the evolutionary biologists contemplated that the existence of such gene modules that regulated the inherent genotypic traits would have been preexisted in the common ancestors of Ctenophores, Cnidarians, and Bilaterians that triggered the evolution of unique “neurogenic, signal” molecule generating “electrical signal and polarized secretions” (Moroz, 2015). Furthermore, the scientists assumed that the “neuronal master gene” in Ctenophores might have gone through diversification to evolve the neurotransmitter “L-Glutamate” instead of other metazoan neurotransmitters to coordinate the neuromuscular functions in Ctenophores, effectively (Moroz, 2015).

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Based on the microanatomical and embryological studies, studying the formation of tissues derived from ectoderm and the endoderm layer in embryos of Ctenophores and Cnidarians is considered as “diploblastic, jellylike organisms” (Moroz, 2015). In the contemporary efforts of phylogenetic reconstruction trees of five metazoan clades (Porifera, Cnidaria, Placozoa, Ctenophora, and Bilateria), the position of Ctenophores was found to be uncertain, varied from a basal position of metazoan clades to the sister group of Bilaterians (Dunn et al., 2008; Telford, 2009; Nielsen, 2012; Nosenko et al., 2013). The early phylogenetic tree constructions have been made based on microanatomical, morphological, paleontological, and molecular data, where genomic data have not been taken into account. The very recent meticulous efforts of the genomicists to engage in molecular foot-prints of genome of a number of heterogenous organisms, carried out by a number of scientists like: Moroz et al. (2012), Moroz et al. (2014), Ryan et al. (2013) particularly in the domain of molecular phylogenetic reconstruction of metazoan clades, the scientists came forward with a firm conclusion that Ctenophores were the earliest member in the Metazoan lineage, branched out of the ancestral Metazoan lineage and Ctenophores were considered to be the sister of all Metazoan clades. According to the classical system of classifications of Metazoans, Ctenophores and Cnidarians were considered to be the sister clades, forming the clade Coelenterata (Philippe et al., 2009; Nosenko et al., 2013). However, contemporary, genomic studies along with ultrastructural studies intrigued the molecular phylogeneticists to recognize that both Metazoan clades have no phylogenetic affinity among themselves (Horridge, 1974; Moroz et al., 2014). The scientists have assumed that both groups shared the same ecological niche (deep pelagic zone), so it tends to assume the evolutionists that Ctenophores and Cnidarians might have a visible, superficial convergent evolutionary resemblance, but genomic data along with ultrastructural distinctions made them consider both groups as two distinct Metazoan clades, finally. Rather, the comparative genomic analysis along with neuronal ultrastructure and functional aspects of neurotransmitters in Cnidarians and Bilaterians firmly ascertained their close phylogenetic affinity and affirmed their sister relationship (Chapman et al., 2010; Moroz et al., 2014). Most of the time, the mode of tissue development in the ultrastructural level of any biological organism of fragile in nature has not been properly studied or not prioritized for the matter of inconvenience to prepare its sample for ultrastructural analysis, until the evolutionary studies have been undertaken to elucidate the evolutionary history of that distinct group of such animals. Based on the findings of three layers of tissues in Bilateria (ectoderm, endoderm, and mesoderm), they are recognized as Triploblastic; likewise, any organism with two layers of tissues is called diploblastic. However, the primary question about whether such mesodermal layer has exclusively been found in Bilateria only or it has also been found in other non-Bilaterians as the homologous structure of mesoderm, which has been recognized as “Mesohyl,” found in Porifera, or the presence of “Mesoglea” has been noticed in Ctenophora (Dunn et al., 2015). Instead of getting in the critical reviews of evolutionary judgment, diploblastic identity has been imposed on these Porifera,

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Ctenophora, and Placozoa groups of Mesozoans (Smith et al., 2014). In the same way, the gastrulation phase of embryonic development in Bilaterians has been studied well to define the evolutionary development of animals, whereas some diverse nature of embryonic development of gastrulation state has been examined and left under the cradle of Protostomy (Hejnol and Martindale, 2009). Another important issue regarding the evolution of Metazoan’s nervous system is to recognize that evolutionary progress has not followed the stepwise upgradation format in the Metazoan groups in the divergence of Porifera, Ctenophora, Cnidaria, Placozoa, and Bilateria in sequential order. Scientists had noticed that the emergence of nervous systems happened in Ctenophora, Cnidaria, and Bilateria, whereas it did not evolve in Porifera and Placozoa. Consequently, a stereotypical interpretation of Metazoan evolution with the nervous system from the ancient group of Metazoans with no nervous system has not been assumed to be a feasible hypothesis rather scientists count on the alternative hypothesis of homoplasy, which could present a tenable explanation of nervous systems in certain Metazoan groups and the absence of it in some groups as it put forth two possibilities: either the evolution of the nervous system in Metazoan groups happens more than once or the nervous system has disappeared from the derived group of Metazoans in the course of evolution (Dunn et al., 2014). If homoplasy is found to be the ultimate explanation of evolutionary discretion of the emergence of nervous systems in Metazoans, it contradicts the stereotypical perception about the evolution of nervous systems by simply considering an example of an organism once that has emerged with the nervous system in historical time. It has been considered as an unusual type of organism that could go through the trail of the discounted format of evolution to be reevolved as a more simple and/or less-wise organism with a simplified form, having no nervous system (get rid of its nervous system, once possessed) than its erstwhile advanced structural form (that used to have a nervous system) just for ensuring its survival on Earth. It is a legitimate concern to find out the best possible answer as it is related to understand the functionality of the biological evolution of life. However, if such gain and loss of any tissue systems would have ever been integrated into the evolutionary progress, how many times it happens? (Moroz, 2009; Ryan et al., 2013; Moroz et al., 2014; Marlow and Arendt, 2014; Ryan, 2014). Seemingly, it seems that the existence of nervous systems in any organism means that an organism seems to be more evolved and that might not be true always. As it has been noticed by the evolutionary biologists that Ctenophores have emerged with the basic or primitive nervous systems, it lacks many genes in its genome storage; whereas, Porifera and Placozoans are devoid of nervous systems, but physiologically and structurally they are considered in the advanced category of animals as they possess a very rich pool of genes that could regulate several physical, physiological, and biological expressions of these two Metazoans with no nervous system (Dunn et al., 2015). The unique combination of the rich gene pool and well-developed nervous systems have primarily been observed in Cnidaria and it has been found in the complete flourishing state (to the highest extent) in the members of Bilateria so that it further indicated that the possession of well diverse gene families along with the evolution and

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up-gradation of the nervous systems seems to be the ultimate evolutionary impetus to a particular biological organism, attributed with better sustainability than others, belonging to its phylogenetic group. Specifically, the modern Metazoan representatives traverse down the long trail of biological evolution to stay on the race of “Survival of the fittest” and Ctenophore supposed to be one of the ancestral contenders in this race to go through the transitions of the world of Metazoan animals with no nervous system (like animals with no brain) to the world of Metazoan animals with the well-developed nervous system (animals with brain or intellectual animals). Hence, a critical review on the comparative investigations of the distinct group of Metazoans has been coordinated from time to time to define and redefine the emergence of their developmental gene expressions and the evolution of distinct neuronal structures and functions that helped to override the preexisting myth of “PoriferaSister Hypothesis” (the sponges) as the maiden ancestral lineage in Metazoans rather than acknowledging the fact of the molecular footprint of life, ascribed in “Ctenophora-Sister Hypothesis” (comb-jellies) that has defined the earliest instance of Metazoan divergence (Moorhead, 2019). The lack of epithelial tissue system, nervous system, and muscular tissue system in Porifera group of Metazoans and the existence of penultimate stage of the nervous system in Ctenophora and the presence of the well-defined nervous system, epithelial tissues, and muscles in Cnidaria and Bilaterians rendered the scientists to hypothesize that evolution of nervous systems in Cnidarians/Bilaterians and evolution of the incipient state of nervous systems in Ctenophores have taken place independently and most likely it has taken place twice (Moorhead, 2019; Telford et al., 2016). In course of evolutionary diversification, Porifera has lost all ancestral traits to ensure its sustainability from complex form to simple one to fit in the changing dynamics of the environment, and conceivably this kind of unusual course of evolution has been recognized as regressive or reverse evolution (Philippe et al., 2009; Marlow and Arendt, 2014; Jekely et al., 2015). Nonetheless, a group of phylogeneticists still considered that the Ctenophorasister tree is an “Artifact” where real data have poorly fitted in the evolutionary model (here it is the CAT model), which has been criticized for LBA3 (long branch attraction) as the bias of Ctenophore’s long branches to the nonanimal species, forming the root of the phylogenetic tree, reconstructed with Telford et al. (2016). During the recent genomic studies on Ctenophores, several genome biologists observed that Ctenophores have gone through a high rate of nucleotide substitution, leading to the bias of LBA (Felsenstein, 1978). Hence, it has been observed by the molecular systematists that LBA is a kind of an unavoidable hassle of molecular systematics.

3

LBA (Long Branch Attraction): In molecular phylogenetics, LBA has been considered as a systematic error, where, phylogenetically distant related lineages are assumed to be closely related allies. This kind of systematic errors happens as a result of accumulation of morphological or molecular changes, accrued in a particular lineage that apparently resemble it to close proximity to the long branched lineage and it happens mainly due to the massive scale of changes , rather than the possibility of the both lineages having a common phylogenetic origin. When the divergence of a number of taxa, resulting formation of long branch in a phylogenetic outline, it happens.

The Evolutionary Biology of Extinct and Extant Organisms

Either due to inclusion of enough molecular data or not to include enough number of taxa, as well as the analysis of the genomic profile of those taxa at the time of modeling of any phylogenetic tree, would have jeopardize the earnest effort of phylogenetic reconstruction. The inclusion of excessive data and taxa would lead to systematic errors like LBA; so, in the phylogenetic tree reconstruction, optimization of data is an important issue to get precise results. As an example, the molecular phylogeneticists referred to the example of the erstwhile phylogenetic analyses made on the Metazoan groups and considerably less genetic data have been taken into consideration for such phylogenetic analyses. Porifera came out as the first Metazoan group, diverged out of all Metazoans and recognized to be the sister group of all Metazoans and considered to be the ancient Metazoan lineage in the history of the evolution of modern animals, specifically the Vertebrates (Medina et al., 2001; Philippe et al., 2009). Most surprisingly, the molecular phylogeneticists noticed that the inclusion of more molecular data and the inclusion of more taxa and relevant outgroups have helped them as a corrective measure to exclude flaws to get a precise result, and based on their analysis scientists strongly advocated again that Ctenophores, appeared to be the maiden distinct lineage of Metazoans, diverged out of Metazoan lineage and found to be the sister group of all Metazoans (Ryan et al., 2013; Moroz et al., 2014). Therefore, it proved a successful shift from the Porifera-sister hypothesis to the Ctenophora-sister hypothesis; it is the change of experimental protocol and handling of data that might have changed the outcome of any phylogenetic analysis. Thus, the evolutionary progress of Ctenophores (comb-jellies) in terms of the evolution of developmental patterning genes, “gap junction proteins,” “presynaptic triad,” and structural/functional complexities rendered the evolutionary biologists and phylogeneticists to contemplate Combjellies as evolutionary links between the ancestral lineage of Metazoans. The evolutionary transition that has started with “having no nervous systems” (such as Porifera, apparently having no brain) has gone through the phase of divergence to be evolved as the advanced group of Metazoans with “advanced nervous systems” (such as Cnidaria and Bilateria) and it has further stretched out the entire evolutionary journey of life being integrated itself in the shift in the paradigm of protozoan life during Cambrian radiation (of Arthropods), followed by Cretaceous radiation (of Vertebrates) of animal life to be finally emerged as ultimate descendants of Mammalia.

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The Protistan link in transition: down the evolutionary trail from unicellular Protozoa to multicellular Metazoa

10

“How might early multicellular organisms have looked like? An extant example of a very simple metazoan is Trichoplax adhaerens (Placozoa). Superficially resembling an ameba (which is, however, unicellular!), this organism is more simply organized than any other living metazoan. Even though, it already shows a high degree of cellular differentiation. Potentially, even simpler organized with regard to cellular differentiation are sponges, which have, however, a more complex body plan. Interestingly, a certain cell type of sponges, the choanocytes, resembles very much unicellular choanoflagellates. Haeckel (1834e1919) already proposed that metazoans evolved form a colonial choanoflagellate, such as Proterospongia haeckeli. Only a simple central jellied matrix is found in P. haeckeli, whereas sponges have a more complex matrix, the mesohyl” J. Maynard Smith & E. Szathmary

Till the end of the 19th century, the evolutionary progress of animals in terms of biological evolution is conceivably indoctrinated under the principle of Lamarckism. The acquisition of more complex characters seems to be considered as an inborn predisposition of the living organisms traversing down the evolutionary trail of simple ancestral form to derive a complex one. Instead of patronizing the erstwhile principles of Lamarckism, which promotes the “inherent tendency of progression,” Charles Darwin and his followers and Neo-Darwinists at the end of the 20th century engaged in promoting their principles of biological evolution, which postulates that it is the composite impetus of mutation and selection pressure. This rendered the organism to adapt to its environment to survive successfully and move forward, where it belongs to. From a visual perspective, it always appears that the domination of the recently diverged group of organisms is more complex than their simple, ancestral predecessors, but that does not necessarily prove the Lamarckian doctrine that evolutionary progress has been driven by the inherent tendency of living organisms to transcend from simple evolutionary lineage to the complex one.

The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00013-1 Copyright © 2021 Elsevier Inc. All rights reserved.

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The evolutionists and evolutionary biologists have a clear elucidation of the living and diversification process of bacteria and prokaryotic life. They are able to recognize that the bacteria and prokaryotic are well adapted to their own environment and it is an equally countable evolutionary effort, compared to the living and diversification of an advanced, complex group of mammals like whales or the human species. So, could we ignore the matter of fact that the eukaryotes are more complex in terms of the evolutionary progress of life? No, we cannot ignore that is the reality. The evolutionary biologists further hypothesized that living organisms have always gone through the nodes of “evolutionary transition,” which not only drive their physical and physiological changes but rendered them to carry the messages of such changes in genetically encrypted form to transmit it to the following generations to carry it forward (Maynard Smith and Szatmary, 1995). The most important issue in evolutionary biology is not always necessarily depicting the universal presentation of the complexities of the advanced group of animals that emerged out of the ancestral lineages of simple form in all around biosphere. Rather, instead of acquiring the complexities, a number of organisms might stop utilizing a number of features and give-up the erstwhile inheritance of physical, physiological, and genetic traits of their ancestral lineages to evolve in a much simpler, derived form of the organism. Such discounted form of evolutionary progress (e.g., like parasites, hagfishes, etc.) has helped the organisms a number of times to be adapted to their changing environment to ensure their survival. Whether it is acquiring or discounting trends of the feature of the evolutionary progress of life has been encrypted in the DNA, the ultimate genetics and molecular entity of life that determines the extent of complexity or simplicity an organism requires to stay in the evolutionary race of life to ensure its survival (Maynard Smith and Szatmary, 1995). DNA plays a role as the main storage house or like a hard drive of biological information as it acts as the ultimate estimator to determine the use and utilization of the biological information. This is to determine the complexity or simplicity of an organism in the course of biological evolution. The increase or up-gradation of the genome size to accommodate more gene and biological information is an integrated process of biological evolution too. For genomicists, it is another matter of observation to keep an eye on whether the ratio of the increased genome size and the content of the encoding protein in it is the proportionate or nonproportionate ratio of genome size of its encoding protein. This indicates that the content of noncoding protein of the concerned genome of that particular lineage of an organism is fairly high; from an evolutionary perspective, those organisms should not be assigned as the front-runner in terms of gene-environment interaction that driven changes to acquire evolutionary complexity (in a majority of the time) or simplicity (to a lesser extent) (Maynard Smith anzatmary, 1995). The scientists noticed that the major evolutionary changes in terms of genetic configurations changes or acquiring complexity usually takes place in three ways (Maynard Smith anzatmary, 1995): Duplication: According to this hypothesis, out of the set of two genes (as most of the genes found to be retained in pair, possessed by the genome of any organism),

The Evolutionary Biology of Extinct and Extant Organisms

one use to retain the original function, whereas the second one gets into the venture of evolutionary changes to explore a new form of life. Epigenesis: Normally gene expression of any organism is controlled by gene sequence, but epigenesis alters the gene expression that takes place independently without keeping track of the changes of genetic sequences. Symbiosis: The independently replicating genetic units may get in to form a symbiotic relationship. This may result in a newly formed and more complex symbiont genetic entity and successive replication of it may lead to form a more complex genetic entity in the course of evolution. The evolutionary biologists contemplated that around 1500e2000 mya, the evolution of mitochondria happens inside a Proteobacteria as a result of endosymbiosis. The evolutionary biologists principally construed the three major stages of life evolution as it has been hypothesized that it was the inorganic evolution, which sets up the base work on the proto-Earth around three to four billion years ago (Kundu, 2018). It sets the podium for the initiation of the next stage of organic evolution that was considered to be the beginning of the penultimate stages of biological evolution of life on Earth, which was supposedly initiated in the waterbodies in the unicellular form. According to the paleobiologists’ observation, the maiden cell that appeared on this Earth was a Prokaryote cell, having no definitive nucleus and they further ascertained that the prehistoric unicellular cellular entity was neither protophyta (plant), nor Protozoa (animal). It was Ernst Haeckel (1866) who studied these primitive, microscopic, cellular organism, which has nucleus apparatus (no definite nucleus) and cytoplasm that has been recognized as “Protista.” In the next stage of evolutionary transition, unicellular Protists had gone through the distinct form of unicellular plants (Protophyta) and unicellular animals (Protozoa). In the course of the evolutionary progress of life on Earth, unicellular plants or protophytes had gone through the multicellular transition of evolution to be emerged as multicellular plants or Metaphyta and the Protozoa evolved to be as Metazoans in the course of time. There is no direct evidence, which could prove that multicellular Metazoan lineage directly emerged out of ancestral, unicellular, or acellular, Protozoan lineages. The developmental studies of the embryonic stages of Metazoan organism development, indicated that evolution of life had passed through the transition from the acellular stage (noticed in the zygote stage) to attain the cellular stages (the cellular developments observed in the embryonic developmental stages such as Morula, Blastula, and Gastrula). Protists, the unicellular organisms supposedly evolved around 2000 mya, performed a series of multitasking work for ensuring its living entity. From unicellular, microscopic form of life to multicellular Metazoans to be emerged in the form of macroscopic faunal seems to be a mystery, as there is a transitional gap of fossils left by the emergence of soft-bodied Metazoans (like invertebrates) in the beginning of ancient Metazoans on Earth. This wide gap has been trying to patch up by a number of evolutionary biologists and molecular phylogeneticists by undertaking contemporary phylogenetic molecular investigations.

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However, the paleontologists revealed that the earliest palaeontological evidence of multicellular, soft-bodied animals on Earth that was discovered in Australia, known as “Ediacaran Fauna” and the age-dating process ensured that all these prehistoric, faunal representatives evolved around 670e550 mya. So far, paleontological existence of Ediacaran fauna has been considered as the earliest instance of prehistoric evolution, soft-bodied, Metazoan animals on Earth. The next level of critical reviews of the palaeontological evidence exposed that it is “Cambrian Radiation” that supposedly took place around 541 mya and last for 25 million years, effectively guided the animals’ evolution in terms of species diversity, shapes, forms, and functions to a new level of understanding about biological evolution of Metazoan animals. The scientists noticed that the majority of the paleontological evidence indicated the preponderance of hard-bodied (shelled, scaled skinned, etc.) Metazoans in the post-Cambrian Radiation era in comparison to the soft-bodied Metazoans. Naturally, it was convinced that sudden surge of Metazoans in Cambrian must be triggered by the inherent gene-environment interaction, which created a favorable ambiance for the earliest, prehistoric lineages of the soft-bodied Metazoans, those adapted to the new-environment and evolved further by acquiring the hard-shelled, scaled or skinned outlook to cope with the changing environment. The change of Metazoans soft-bodied to hard-bodied as well as the Metazoans that covered with hard-bodied protective coverings seems to be an important evolutionary milestone in the evolutionary history of Metazoans in the Cambrian period. It is difficult to substantiate whether acquiring a number of quick adaptations in a short period of time leads to a Cambrian explosion of Multicellular lineages evolution out of single-celled organism or it was the paleo-climatic changes created a congenial environmental abode, which triggered the inherent genetic profile of the unicellular organism to diverge out as a diverse group of multicellular organisms with diverse shape and sizes. Apparently, it has been hypothesized that a number of overlapping adaptations in a short period of time in Cambrian leads to promote the evolutionary emergence and diversification of multicellularity on Earth and it might be considered as the penultimate stage of the next evolutionary milestone, known as terrestrialization of organisms on the way to the ultimate evolutionary journey of tetrapods. The evolutionary biologists have further construed that the emergence of multicellularity out of unicellular lineage has been happening independently three times, leading to the emergence of three distinct groups of biological organismsdplants, animals, and fungi (Maynard Smith and Szathmary, 1995). In the next level of narration of the multicellular evolution of life, the evolutionary biologists have presented an extant, Metazoan (multicellular) model organism of Placozoa, scientifically known as Trichoplax adhaerens, which has a striking morphological and structural resemblance to the unicellular Ameba. Although zoologists considered that T. adhaerens is a simple structural form of extant Metazoan representative, functionally, a high level of cellular differentiation has been observed in it (Schierwater, 2005).

The Evolutionary Biology of Extinct and Extant Organisms

In this regard, it needs to be mentioned that the diverse species of sponges, belonging to Porifera, have apparently been emerged with simple cellular differentiation, but relatively complex body plan, the extant sponges, and its other Metazoan allies supposedly diverged out of a common ancestral Metazoan root-stock, recognized as “Urmetazoa” (Muller, 2003). In their meticulous studies to unfurl the mystery of multicellularity, the evolutionary biologists have referred a distinct type of cell pattern in the sponges called “Choanocytes” having a resemblance to unicellular “Choanoflagellates.” The Choanoflagellates are aquatic microeukaryotes, unicellular and colonial that have an apical flagellum with a feeding collar base, made up of action-filled microvilli. The unique feeding system (made up of unicellular thecate cells and rosette colonies) helped Choanoflagellates to engulf bacteria and consume it by means of phagocytosis (Dayel and King, 2014). According to the investigations from a number of evolutionary biologists, the evolution of Choanoflagellates occurred around 600 mya (Brunet and King, 2017). According to the principles of evolutionary cell biology, the scientists identified two inevitable changes that the advanced group of animals needs in their transition from unicellular to multicellular formdacquiring the maneuvering techniques for synthesizing extracellular matrix and acquiring the mechanism of cytokinesis. Furthermore, the scientists hypothesize that multicellularity in animals happens when there was a clear shift of functional changes observed at the cellular level, such as the evolution of new cells in which division of labor was well defined as they push-back the multitasking “plurifunctional” cells evolved earlier. It was a major shift from the old regime of “conversion of temporally alternating phenotypes” to get in the new regime of “spatially juxtaposed cell types,” to ensure better selective advantages to the multicellular organisms to survive in the Cambrian and post-Cambrian period on Earth (Brunet and King, 2017). In support of the unicellular origin of multicellular lineages, a number of evolutionary biologists contemplated that the evolution of Metazoans happens from the colonial Choanoflagellates, Proterospongia haeckeli, with a simple body plan, filled with “jellied matrix” inside the central cavity of it (Haeckel, 1834e1919). The diagrammatic sketch of Proterospongia haeckeli has been presented in Fig. 10.1. Most of the sponges have a little complex type of matrix, called mesophyll (Maynard Smith and Szathmary, 1995). For last decade long molecular investigations of cDNAs, which encode the protein, responsible for either celldcall or celldtissues have been cloned out of the taxa, belonging to Porifera: Geodia cydonium and Suberites domuncula. The results further affirmed that all Metazoan lineages emerged out of ancestral, Metazoan lineage, recognized as “Urmetazoa”. The evolutionary biologists tried to figure out whether multicellularity of Metazoans has an evolutionary advantage over the unicellular form of Protozoans or otherwise, although it is apparently difficult to judge and define the transition of such evolutionary lineages in terms of sustainability of Metazoans in the backdrop of paleoclimatic changes, as the interactions of developmental genetics and paleoclimatic changes were not available so far. The emergence of a diversified

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FIGURE 10.1 The diagrammatic sketch of Proterospongia haeckeli. Courtesy Sashi Sinha, Ms.

group of Metazoans in Cambrian Radiation, clearly indicates that the derived group of Metazoans (with multicellular forms) in Cambrian Radiations supposedly benefitted with “Immediate Selective Advantage” of longer sustainability by virtue of having more cells in comparison to their unicellular counterparts (Maynard Smith and Szathmary, 1995). Though the evolution of metazoan still remains as an enigmatic issue, the morphological analysis along with the supporting data on molecular phylogenetics revealed that colonial origin of Metazoans (Dewel, 2000) has gone through the hypothetical cascade of “Beklemishev’s cycle of duplication and individuation” and the colony has gone through another cycle of Individuation (the process by which an individual attained distinct level) (Beklemishev, 1969) and the prehistoric emergence of it tentatively happens around 1300e600 mya in the pre-Ediacaran period (Conway Morris, 1998). The scientists contemplated further that down the evolutionary trail of “Individuation,” multicellular systems have gone through two more cascades of

The Evolutionary Biology of Extinct and Extant Organisms

upgradation, acquiring Immune systems and Apoptotic systems1 to deal with action and counteractions to ensure the sustainability of simple sponge-like colonial Metazoans to combat with microbial and parasitic infections (Muller, 2003). It has been further observed by the molecular biologists that when the enzymatic action of “Caspases” promote the apoptotic cell death, the presence of Bcl-2 protein family in sponge population counteract the apoptotic cell death and ensure the survival of the concerned organisms and these actions and counteractions found to happen in the backdrop of cellecell and cellematrix adhesion systems, possessed by the primitive, Metazoan “Colony type of organizations” like the members of Porifera (Muller, 2003). Thus, the origin of Metazoans from the colony of flagellates, which render the cellular specialization, lead the main hypothesis regarding the origin of Metazoans, put forthColonial or Flagellate theory: The classical elucidation of Colonial or Flagellate theory has been made by Butschli et al. (1884), which has been further recommended with further modification by Metschnikoff (1886). According to the Colonial or Flagellate theory, the evolutionary biologists contemplated that the earliest multicellular organism, as well as prehistoric Metazoan, had evolved from a composite colony formed as a result of the fusion of a number of unicellular flagellates. It was construed further that intermittent adding up of unicellular individuals in the colony triggered the division of labor and distinct structural attribution and in the course of long travel down the evolutionary trail, individuality has been lost in the cellular level. The colonial multicellular entity established its structural and functional identity as a distinct Metazoan organism. The proponent of the colonial theory of Metazoan evolution, later observed that embryonic development has fit in it and they also noticed that flagellated organisms were intrigued to form colonies and they have a striking resemblance to the different embryonic developmental stages of Metazoa. The Flagellates have a close resemblance to the tailed-sperm of Metazoans and that also indicates that Metazoans are direct descendants of Flagellata. The scientists have noticed that the members of some distinct groups of Metazoans like Porifera and Coelenterata possess flagellated larvae. The Sponges possess flagellated cells, and these are designated as Choanocytes, which have identical similarity to Choanoflagellates. The base support of the Colonial theory was the Volvacid colonial structure, and those are phytoflagellates or plant-like organisms, having typical cellulosic cell wall, autotrophic nutrition, and fertilization after specialized reduction divisions, etc. It was pointed that if Volvocid phytoflagellates were considered to be the progenitor of Metazoans, then plant-like chlorophyllous organelles supposedly became vestigial in the course of evolution and instead of Volvacid colony, the aggregates of zooflagellates found to be a tenable

1

Apoptotic system: The systems, occur in the multicellular organisms, coordinate programmed cell death, by enacting a range of biochemical maneuvers, such as cell shrinkage, chromatic condensation, nuclear fragmentation, DNA fragmentation, RNA decay, etc.

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colonial model of Metazoan progenitors. The Volvox-like, hollow, spherical colony, of flagellate aggregates of Protista’s, was recognized as Blastaea, and Blastaea (it possesses an anterior-posterior axis) has a semblance to the Blastula or Coeloblastula stage of embryogenic developments of Metazoans (Butschli et al., 1884). Further cellular developments of Blastaea gave rise to the development of somatic or body cells and germ or reproductive cells. An invagination at the posterior end of Blastaea produces a double-layered sac-like structure, called Gastraea. According to the hypothetical “Gastraea theory,” the progenitor of the Metazoans has a two-walled (recognized as ectoderm and endoderm) hollow body plan and it has been found in the Gastrula stage of the embryonic development of the advanced Metazoans. According to Haeckel’s “Recapitulation theory,” the blastula and gastrula embryogenic developmental stage of derived groups of Metazoans descended out of the planula larval stage (Blastaea and Gastraea stage) of ancient Metazoans, which has been observed by Haeckel in 1869 (Reynolds and Hulsmann, 2008). Haeckel (1834e1919) has further studied the structural similarity of ancestral Gastraea, a lower group of Metazoans, such as Hydrozoan Coelanterates, sponges, etc. (Reynolds and Hulsmann, 2008). Later, Metschinkoff (1866) slightly modified the Gastraea hypothesis proposed by Haeckel, as Metschinkoff (1866) has contended that the solid gastrulation stage of the embryonic development of Coelenterates has been formed as a result of ingression, rather than invagination. As Metschinkoff (1866) contended that a part of ectodermal cells of Blastaea have modified to phagocytes, got entered in the blastocoel stage, being filled-up with ameboid cells. Furthermore, Metschinkoff (1866) has observed that such unique cellular entities have found to be interspersed within the gelatinous matrix, and started formation of solid, diploblastic Gastraea and it has been found in ancient Metazoans. The perception of solid Gastraea of Metschinkoff (1866) has been proven true when Kent (1880) discovered the existence of Proterospongia, an evolutionary transitional link between Protozoa and sponge. The microanatomical observation of Proterospongia revealed that it was nothing, but a Choanoflagellate colony, encased within a gelatinous matrix. A few numbers of collars and flagella have been lost from collard cells to transcend in the gelatinous sheath-like ameboid cells, which indicates the occurrence of ingression in it. Nonetheless, apart from the classical Colonial or Flagellate theories, there are two more hypotheses, promulgated by the evolutionary biologists from time to time to redefine the evolution of Metazoans on Earth and those are as follows: Syncytial theory: According to this hypothesis, the Metazoan organisms evolved out of multinucleate, syncytial cilia, and these are isolated and cellularized to form the intracellular boundaries. The Ciliate origin of Metazoans has been proposed by Earl D. Hanson in 1958 and Jovan Hadzi in 1963 on the basis of their experimental observations on the similarity between multinucleate Ciliates and acoelous flatworms (e.g., Turbellaria). Hadzi (1963) anticipated that the ancestral lineage of Metazoans was structurally syncytial and bilaterally symmetrical in body plan. Those were evolved as a result of cellularization of prehistoric, multinucleate, syncytial Ciliates rather than an aggregation of uninucleate Protista. Hence, the

The Evolutionary Biology of Extinct and Extant Organisms

bilaterally symmetrical, acoel Turbellaria (e.g., Convoluta) has been considered as the most primitive Metazoan ancestor according to this hypothesis. The possible extension of this hypothesis presented the members belonging to Anthozoa and Hydrozoa of the Metazoan group. Cnidaria has diverged out of rhabdocoel Turbellarians and their simple structural development and secondary adaptation changed these advanced groups of Metazoan’s body plan from bilaterally symmetrical to radially symmetrical. Based on the identical body-plan of the Muller’s larval stage of polyclad Turbellarians and Ctenophores (both share the same ecological niche), Hadzi (1963) promulgated that Ctenophores evolved from Polyclad Turbellarians and gained some important evolutionary features like Neoteny2, to leave behind the evolutionary footprints of its evolution. It has also been assumed that the conjugation process of Ciliates rendered the sexual copulation of the advanced group of organisms belonging to Metazoa. Furthermore, the striking resemblance of the organelles like the presence of trichocysts in the multinucleate Ciliates, saggitocysts in the acoelous Turbellaria, and nematocysts in Cnidarians have justified considering the acoelous Turbellaria as the primitive organism gave rise to derived groups of Metazoans in the course of evolution (Hadzi, 1963). Although the recent studies under electron microscopy partially ascertained Hadzi’s hypothesis, the observations like Hydrozoa has found to be phylogenetically primitive than Anthozoa, the appearance of radial symmetry of Coelenterates as primary features, which has evolved independently rather than diverged out of bilateral symmetrical body plan, the occurrence of flagellated sperms in Metazoans rather than Ciliates. Improper interpretation considering Anthozoans as the descendants of hermaphrodite Turbellaria put a question mark as a feasible hypothesis that failed to define the evolution of Metazoans in a full extent. Polyphyletic theory: According to this theory, the Metazoan organisms evolved out of diverse unicellular ancestral lineages. The recent phylogenetic investigations (Greenberg, 1959) ascertained that the diversification of sponges happened the way the colonial flagellates (e.g., Proterospongia) evolved and diversified, whereas, the rest of the multicellular Metazoans evolved and diversified as a result of cellularization of multinucleate, syncytial Ciliates or Protociliates. However, the contemporary findings of the molecular geneticists and phylogeneticists on rDNA revealed that Metazoa is polyphyletic rather than considered to be monophyletic earlier (Muller, 2003). Furthermore, it is ascertained that the origin and evolution of Cnidaria/Porifera happened independently, from the common ancestor or Triploblastic entity and two independent lineages formed out of the aggregation of animal-like Protists or Protozoa of distinct lineages (Christen et al., 1991). According to the earlier, microscopic analysis in the 19th century, Protozoa and Porifera have been considered in the Protozoa (Spencer, 1864). Later, on the basis of

2

Neoteny: Delaying the physiological development or growth of the organism due to extended juvenilization of the concerned organism.

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a critical review of organogenetic analysis, Porifera has been shifted to Metazoa (Haeckel, 1896). On the basis of homological comparison, scientists considered that sponge Choanocytes are similar to Chonaoflagellates and the Choanoflagellates were the sister group of Metazoans (Nielsen, 2001). A clear understanding of the emergence of multicellularity and Metazoan evolution would have remained there. As long as the molecular phylogenetic went through reorganization of a number of obscure animal taxa in the reorganization of phylogenetic trees of Metazoans on the basis of new phylogenetic data availability of such obscured organisms such as Gastrotrichs, the ciliated animals glide through substrate particles and Chaetognaths or arrow worms, the pelagic animals, etc. (Lowe and Pani, 2011). The contemporary phylogenetic investigations on the simple taxa like Xenoturbella and acoel flatworms, made by Philippe et al. (2011), rendered a stir in the domain of evolutionary biology, particularly in molecular phylogeneticists as the scientists observed in their preliminary investigations that these apparently obscured organisms supposedly branch-off the ancestral Metazoan lineages to be evolved as the most advanced group of Metazoans, called Bilaterians (Ruiz-Trillo, 1999; Hejnol and Martindale, 2009). Xenoturbella is a Pelagic organism, discovered in 1949 (the maiden species were X. bocki), apparently looked like a small (3 cm of size) flatworm, characterized by the presence of a mouth, gut, and net of neurons, underneath the epidermal layer (Kehoma Boll, 2018). The striking morphological similarity of it to the flatworm made it grouping under Platyhelminthes, but the molecular investigations in the 1990s have ascertained it as primitive Bilaterian (Kehoma Boll, 2018). In 2016e17, another five species, including a bigger sized species, X. monstrosa, have been discovered from Pacific region areas of Japan, Mexico, and the United States (Kehoma Boll, 2018). The close morphological resemblance has been observed between these two distinct organisms like the presence of an acoelomic body, presence of ventral mouth, blind gut, and diffused nervous systems that intrigued the morphologists to undertake the molecular investigations. Based on a number of characteristic features, those have been considered to be important from an evolutionary perspective, like: Presence of anterior-posterior, dorso-ventral axis Existence of mesoderm in between ecto and endoderm Possession of Central Nervous System and through guts The animals are broadly grouped into two categories: Protostomes (comparatively simpler than Deuterostomes) and Deuterostomes and such structural and functional distinctions rendered the phylogeneticists to consider Bilaterians as the advanced group of metazoans in comparison to the basal Cnidarians, Porifera, Placozoans, etc. (Lowe and Pani, 2011). In their phylogenetic investigations, Hejnol and Martindale (2009) have considered that Xenoturbella and Acoelomorpha as the “Missing Link” or Evolutionary link in between primitive Metazoan group Cnidaria and the advanced group Bilaterians down the evolutionary trail of Metazoans in the course of evolution of life on Earth.

The Evolutionary Biology of Extinct and Extant Organisms

However, the lack of resemblance in the body plans in Cnidarians and Bilaterians and absence of any intervening branch or distinct form of phylogenetic intermediates with few exceptions like Acoelomorphs in the phylogenetic analysis gave an impression to the evolutionary biologists that a kind of surging radiation of Bilaterians, puts forth multievolutionary lineages of Bilaterians, though the timing of such hypothetical event has yet to be substantiated (Hejnol and Martindale, 2009; Lowe and Pani, 2011). The accumulation of molecular data and critical review of the existing genomic datasets have intrigued the molecular phylogeneticists in the last couple of decades to construct and reconstruct phylogenetic trees of Bilaterians. The world of Molecular Biology noticed that an emerging level of consensus appeared to treat Acoelomorphs as basal Bilaterians and put it away from Protostomes and Deuterostomes. This helped to assume further the evolutionary biologists that the Metazoan lines, after splitting off Cnidarian lineage (the ancestral Metazoan lineage) put forth the early evolutionary emergence of Bilaterians (the advanced group of Metazoans) (Ruiz-Trillo et al., 1999). According to the old phylogenetic analysis (which has mainly based on morphological analysis) Xenoturbella had been considered as the closest ally of Echinoderms and Hemichordates and grouped under Deuterostomes (Bourlat et al., 2006). The recent molecular investigations on Xenoturbella and acoel flatworms done by Philippe et al. (2011) and further analyses of the molecular data on mitochondrial DNA, noncoding micro RNA or miRNA, and Express Sequence Tags or ESTs (the subsequence of cDNA library) ascertained that phylogenetically, Xenoturbella and Acoelomorpha together to be recognized as a new clade Xenacoelomorpha, placed in Deuterostomes, placed them together with Echinodermata and Hemichordata rather than placed it in its erstwhile basal position to Bilaterians, which toppled the erstwhile perception of phylogenetic base of Bilaterians (Lowe and Pani, 2010). However, the contemporary works of the molecular phylogeneticists hypothesized that the presence of short branches at the basal position of the phylogenetic trees of Bilaterians, apparently indicated that ancestral Bilaterians suddenly diverged into a number of evolutionary lineages (Hejnol, 2009). However, the animal biologists observed that Deuterostomes comprise a number of distinct animals, such as Amphioxus, Echinoderms, Hemichordates, Urochordates, and Vertebrates, characterized with a diverse range of body plans and diversified living patterns and it helped to contemplate that the ancestral lineage of deuterostomes should have been characterized by tricoelomic body plan, presence of gill pouches and pharynx (of mesodermal origin), etc. (Swalla and Smith, 2008). The comparative studies of the developmental pattern of Chordates and Hemichordates at the molecular level indicate that a “conserved network of regulatory genes” assumed to be responsible for the developmental formation of anterior-posterior axes in ancient Deuterostomes (Lowe et al., 2004). Nonetheless, the absence of such features in Xenacoelomorpha along with its loss of coeloms and guts and its integration to the Deuterostomes, pointed out that most likely the morphological and molecular loss of complex traits has gone through the selection pressure to render evolutionary emergence of Xenacoelomorpha in a simple form after the secondary loss or adaptive simplifications (Lowe and Pani, 2011).

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In the molecular level qualitative appraisal of gene expressions, particularly the expression of Hox genes in Xenacoelomorpha and the presence and absence of some characteristic traits indicate that Hox gene supposedly plays some regulatory role in regulating gene expressions, which might trigger some secondary loss of complex traits of the concerned organisms resulting evolutionary emergence of penultimate lineages of Bilaterians, the well-diversified lineages of Metazoans and leading the evolution of the animal kingdom from the metaphoric gateway of Cambrian Radiation to get through the ultimate metaphoric gateway of Cretaceous Radiation on this blue planet, Earth (Hejnol and Martindale, 2009). To decipher multicellularity, Dictyostelium discoideum has been recognized as a model organism, provided an in-depth insight into cell biology on deciphering the evolution of multicellular organisms (Parfrey and Lahr, 2013). Dictyostelium sp, belongs to Dictyostelid family, under the eukaryotic clade Amoebozoa and these members of Dictyostelids are popularly known as slime molds or social amebae (Lahr et al., 2011). The members of slime molds maintained cellecell connections, having a structural, functional, and molecular resemblance to epithelial cells of advanced Metazoans. Based on such observation, a group of evolutionary biologists hypothesized that multicellularity is an ancestral trait, witnessed in the clade Amorphea or erstwhile group called Unikonts, which contain fungi, animals, and Amoebozoa (Parfrey and Lahr, 2013). As a hypothesis, the ancestral lineage of Dictyostelid rendered multicellularity sounds intriguing, but in reality, molecular phylogeneticists proved it just as a unique hypothesis as the contemporary phylogenetic investigations screened out that developmental gene expressions of Vinculin and a-Catenin lead to discarding the single-origin hypothesis of a-Catenin in Dictyostelium and Metazoans. The scientists noticed that functionally a-Catenin in Dictyostelium found identical to the a-Catenin in Metazoans, but a-Catenin gene in Dictyostelium is not found to be an ortholog of an a-Catenin gene in Metazoans, rather a-Catenin in Dictyostelium has found to be originated as a result of gene duplication of Vinculin genes, a couple of copies of it found in Dictyostelium (Dickinson et al., 2011). The critical investigations of the molecular phylogeneticists ascertained that the single origin of the Amorphea clade would have to have adaptive “loss of multicellularity” in a number of unicellular lineages in this clade (Parfrey and Lahr, 2013). Rather, a number of lineages of multicellularity have been found to be evolved independently in a diverse group of eukaryotes more than 25 times, including three such occasions that have been traced out in Amorphea clade (Grosberg and Strathmann, 2007; Knoll, 2011). On the basis of molecular data analyses in the contemporary phylogenetic investigations, scientists tried to reach a consensus on the multiple emergences of multicellularity as well as the emergence of Metazoans out of the ancestral unicellular root-stock as a result of the occurrence of convergent evolution, which exerting similar selective pressures on the animals, Dictyostelids, having characteristic features like cellecell connections to form multicellular structures (with a distinct type of cells in terms of structure and functions) at the end of the evolutionary trail (Grosberg and Strathmann, 2007).

The Evolutionary Biology of Extinct and Extant Organisms

To give a new perspective of multicellular lineages evolution out of unicellular mother-stock, a number of scientists have hypothesized that to avoid the predation pressure and to secure long sustainability, multicellularity has been evolving as an evolutionary safeguard to overcome biological competition. Experimental observation of the preyepredator relationship between the algae Chlorella vulgaris and its flagellate predator Ochromonas valencia revealed that the free-floating individuals of C. vulgaris sustained huge pressure of predation and it triggered these individuals to form colonies, those emerged to safeguard protections against the flagellant predators of O. valencia (Boraas et al., 1998). Another evolutionary benefit of the multicellularity has been envisaged by the scientists as the emergence of cellular differentiation like different cells-types with distinct functional attributions like somatic cells (dealing with body functions, growth, cellular replenishment, etc. It has been normally enacted by mitotic cell division) and the germ cells or reproductive cells (dealing with the formation of eggs, sperms, their fusions to form new embryos, etc. and it has been enacted by meiotic division or reduction division followed by equal division) and this feature of the Metazoans has been revealed for the first time by Weismann (1834e1914), referred by Mayr (1985) in his review article “Weismann and Evolution.” The evolutionary biologists considered that Proterospongia haeckeli has occupied the evolutionary stepping stone or the transitional link that needs to be reached out and studied further at the molecular level to understand the true identity of the evolutionary link Proterospongia haeckeli. This could further decipher the evolutionary journey of life, particularly the Metazoans from Protozoa to Sponge or Porifera, which is a stop-gap journey of the life evolution, integrated into the ultimate evolutionary history of Vertebrates on Earth. The evolutionary diversification of cells in multicellular organisms, particularly with the somatic and germ cells, leading to diversification of entire Metazoan lineages to end up with the evolutionary journey of tetrapods in the emergence with the ultimate mammal, Homo sapiens, sustained in its evolutionary journey of Anthropocene.

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Evolutionary mysticism of Euglena: a sagacious soul of a plant in the body of an animal

11

“The origins of photosynthetic euglenophytes (includes the well-known genus), diatoms, golden algae and brown algae happened later in time by secondary endosymbiosis events, wherein a photosynthetic protist (a red or green algae) was engulfed by or incorporated into a heterotrophic protist. In this event, both the host cell and the new endosymbiont were eukaryotic cells (Katz and Bhattacharya, 2006). The ‘engulfed cell’ became the dominant cell line, with the engulfed endosymbiont slowly being reduced to essentially its photosynthetic chloroplasts, which are now characterized by three outer membranes (rather than two as in the green algae and red algae that resulted from primary endosymbiosis). The third membrane is in most cases believed to be the remains of the outer cell membrane of the engulfed cell, which has ‘shrunk’ around the chloroplasts.” David Zeigler

The erstwhile inclusion of fungi in plants in the classical taxonomic classifications of living organisms has absolutely been changed in the contemporary phylogenetic classification of biological organisms made by Robert Whittaker around 4 decades ago, popularly recognized as “five-kingdom classification,” under which entire biological organisms have been categorized under following five kingdoms: a. KingdomdMonera: It comprises unicellular, prokaryotic organisms, having no well-defined nucleus and no organelles. The cell wall may or may not be present out of its cell. According to the mode of nutrition, some are autotrophic and some are heterotrophic. For example, cyanobacteria, bacteria, mycoplasma, etc. b. KingdomdProtista: It comprises unicellular, eukaryotic organisms, having some appendages like cilia, flagella, and pseudopod for locomotion. It has both autotrophic and heterotrophic modes of nutrition. For example, diatoms, protozoans, etc. c. KingdomdFungi: It comprises multicellular, eukaryotic organisms, having a cell wall, made up of chitin. The mode of nutrition is heterotrophic, specifically saprophytic (get nourishment from decomposed organic matter). For example, black mold, mushroom, and yeast species of fungi. The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00016-7 Copyright © 2021 Elsevier Inc. All rights reserved.

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d. KingdomdAnimalia: it comprises multicellular, eukaryotic organisms, having cell membrane instead of the cell wall. It has a heterotrophic mode of nutrition. In terms of evolutionary transitions at cellular level, in the tissue systems, in the structural and functional appearance of organelles, in the mode of functions of unique locomotory appendages, and in the distinct mode of metabolism, a great deal of diversity has been noticed in the different phyla under the Kingdom Animalia, such as Porifera, Coelenterata, Annelida, Mollusca, Arthropoda, Echinodermata, Chordata and Vertebrata, etc. If the extent of structural and functional complexities are concerned to define the evolutionary transitions in the different phyla, belonging to the kingdom Animalia, it has been meticulously observed in the distinct type of metazoans, ranging from hydra, earthworm, snail, insect, starfish, hagfish, to rhinoceros, etc. e. KingdomdPlantae: It comprises multicellular, green, eukaryotic organisms, having a cell wall, made up of cellulose. Almost 99% of the plants are photoautotrophic and prepared their own food by means of photosynthesis. On the basis of structural diversities and functional complexities, the plants have further been classified under distinct divisions, such as Thallophyta, Bryophyta, Pteridophyta, Gymnosperms, and Angiosperms. For example, Chlamydomonas, Riccia, Pteris, Ginkgo, Acer saccharum, etc. Since the publication of the five-kingdom classification of Whittaker and Marguilis (1978), Fungi has been treated as a distinct kingdom along with Animalia and Plantae, after segregating it from plant scientists found in their meticulous phylogenetic studies that the distinct kingdoms such as Animalia, Fungi, and Plantae have diverged from ancestral protistan lineages of uncertain affinities (Baldauf and Palmer, 1993). The erstwhile phylogenetic analyses based on the cumulative studies on the rRNA, tRNA, and multiple protein sequencing, plants have been considered as the sister group of animals (Gouy and Li, 1989). On the basis of his critical investigations on the evolutionary emergence of an ancestral group of organisms such as fungi, prokaryotic organisms, and prehistoric eukaryotic organisms, Cavalier-Smith (1987) has promulgated that two distinct lineages of organisms like fungi and animals derived from the ancestral lineage of protists, the common-stock of choanoflagellates. However, based on phylogenetic analyses of ribosomal RNA (rRNA) sequences have alternatively assigned either plants or fungi in equally frequent proximity of animals (Hasegawa et al., 1985; Krishnan et al., 1990; Hendriks et al., 1991; Wainright et al., 1993). But the contemporary phylogenetic analysis of rRNA, specifically the comparative analysis of Elongation Factor-1a or EF-1 sequences proved that phylogenetically, Animalia is the sister group of Fungi (Hasegawa et al., 1993; Wainright et al., 1993). To resolve the phylogenetic mystery, these three distinct groups of organisms, Baldauf and Palmer (1993) have reexamined the issue by examining the sequence of a number of 25 proteins, having predominantly four number of insertionedeletion sequences, viz. actin, a-tubulin, b-tubulin, and elongation factor 1-aach of the protein has been screened out in a wide range of eukaryotic organisms, specifically found in Animals and Fungi in relation to Bacteria,

The Evolutionary Biology of Extinct and Extant Organisms

Protista, and Plants. At the time of primary screening out 25 proteins, the following prerequisite criteria have been taken into consideration, which was as follows: To make sure the proteins comprise more than 300 amino acids long. All these proteins must be available in the protistan lineage. These proteins should be available in different species of animals, plants, and fungi. To make sure that these proteins are free from the problems like gene splitting, duplication, substitution, or horizontal gene transfer between relevant evolutionary lineages. More than 100 years of molecular studies on molecular genetics and genomics of the model fungus, yeast, or Saccharomyces cerevisiae, which has earned the recognition of ancestral lineage of model eukaryotes, and it has been recognized as the microbial model system as well. The monophyletic relationship of Fungi and Animals and its common evolutionary descendant from Protistan lineage creates an opportunity for the evolutionary biologists to review critically the microbial model in the evolution of the derived group of eukaryotic animals including modern human species that could be found unique to the researchers to traverse down the evolutionary trail, “from yeast to man” (Baldauf and Palmer, 1993). It would have further been deduced that all four insertions/deletion protein sequences have uniquely been found in two taxonomic groups (Animals-Fungi) out of three (Animals, Fungi, and Plants). The molecular phylogeneticists further hypothetically contemplated that Animal and Fungi, these two evolutionary lineages are monophyletic origin, excluding plants and protists; moreover, it has also ascertained that fungi and plants are not monophyletic in origin (Baldauf and Palmer, 1993). In the molecular phylogenetic studies, bootstrap analysis is an essential experimental protocol, which replicates or interpolates rearrangement of the DNA data sequence and the bootstrap analysis did not affirm the likelihood of Plant-animal or Plant-Fungi monophyly, based on the experiment coordinated by Baldauf and Palmer (1993). Rather, the supporting molecular data available from their phylogenetic studies, the molecular phylogeneticists pronounced congruence on the monophyly of Animal-Fungi with further contemplation on the independent evolution of plants. The prehistoric Protistan members hold a unique evolutionary position to initiate the evolutionary diversification of animals in terms of complex structure and better functions from microscopic unicellular eukaryotic life in millions of years ago to the derived group of massive mammals like elephants and whale in the current regime of Anthropocene. The evolutionary success of eukaryotes in the Anthropocene has been initiated with Cretaceous radiation after going through the evolutionary transition of terrestrialization when aquatic, unicellular and multicellular eukaryotes went through the evolutionary course of migration from water to land. But every success story has a preface. The penultimate stage of aquatic, prehistoric eukaryotes has been initiated with the evolutionary journey of unicellular, eukaryotic protistan lineage,

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such as the beginning of the evolutionary journey of Euglenids in water bodies in millions and millions of years ago, on the blue planet. However, Euglenids (comprised Discoba, Euglenida, Euglenozoa, and Excavata) are free-living, single-celled (15e100 mm in size), aquatic, flagellates, which has scientifically been categorized under the kingdom “Protista” under five kingdom classification of Whittaker and Margulis (1978); eventually, it shows a wide range of nutrition (Breglia et al., 2013; Zakrys et al., 2017), ranges from: EukaryovorydConsume big size prey cells like most of the eukaryotes. BacterivorydConsume smaller sized cells including bacteria. PhotoautrophydHaving potential trap solar energy to synthesize own food, those are mostly recognized as “euglenophytes” OsmotrophydThe microeukaryotes absorb nutrients from their environment. Due to the presence of photoautotrophic and phagotrophic modes of nutrition in this group of microscopic organisms, the taxonomic experts in zoology and the taxonomic experts in Botany tried to engage in classification of this unique group of plants according to the guidelines of International Code of Botanical Nomenclature and International Code of Zoological Nomenclature without recognizing the evolutionary uniqueness of the Euglenids as it is neither a plant nor an animal (Zakrys et al., 2017) as per perceptional dichotomous identity of organisms rather it should better be considered as the transitional link between animals and plants, a third evolutionary distinct group, synapomorphic descendants of which has helped to contemplate about common ancestral lineage of plants and animals, which supposedly through the sequential shift in paradigms of inorganic evolution followed by organic evolution, successively followed by biological evolution in the backdrop of spatiotemporal matrix on Earth. The earliest Euglenid-like fossiliferous member has been discovered from the Silurian fossil deposit known as Moyeria, which has a morphological and structural affinity to the photoautotrophic Euglenids, known as Monomorphina, though a number of fossils Euglenids (with the clear distinctive feature) have been discovered in the fossil deposits of Tertiary (Gray and Boucot, 1989). The key cellular and ultracellular characteristic features of eukaryotic organisms have been observed in the member of Euglenids like the presence of cytoplasm, distinct nucleus, mitochondria, golgi bodies, vacuole, lysosomes, etc. Normally, the excretion of the nitrogenous substances has been excreted by the process of diffusion from the body surface of the Euglenas in a conventional way of respiration like absorption of oxygen and giving out of carbon-dioxide instead. It has been noticed by the scientists that the water the outside of the body surface, get in the euglenoid cell by endosmosis, through the permeable membrane of pellicle and the elimination of excess water, mixed with nitrogenous excretory materials, pumped out of the body through the contractile vacuoles. Apparently, it appears that there is no specialized system, such as the excretory system developed in this group of organisms, that can extend the journey of evolution to evolve with an advanced form of structural organs and new functional systems, that could back-up the unique metabolic systems, and that an organism needs to secure its survival in the marathon of biological evolution on this Earth.

The Evolutionary Biology of Extinct and Extant Organisms

Recent observation of the molecular phylogeneticists on a eukaryovorous, freshwater Euglenid species, Heteronema scaphurum, noticed that these unique species have been evolved with cytoproct, a special pore in the pellicle, an exocytose vesicle (functionally act as part of the excretory system, like anal pore), through which the solid pellets of nitrogenous excretory products, thrown out of the body and presence of such preliminary form of the excretory system, which has been found in Ciliates, carry forward the evolutionary journey further down from animal-like simple form of Protists to be further appeared in form of Mammals with well distinct excretory system, with integrated to the metabolic, digestive, respiratory systems, down the spatiotemporal trail of evolution (Breglia et al., 2013). So far around 1400 species of Euglenids have been discovered, in which it has been considered only the 1/3rd of the total species diversity of Euglenids existed on the earth and the wide array of morphoanatomical, behavioral diversities elucidate the key evolutionary events like the emergence of autophototrophic, osmotrophic, and phagotrophic food habits, the occurrence of mutations in molecular level in regulating developmental mechanisms and secondary endosymbiosis (Leander, 2008). The evolutionary biologists construed further that in the history of biological evolution of living organisms on this Earth, the emergence of photosynthesis in eukaryotes has emerged as a tentative one or more than one time symbiotic association of photoautotrophic prokaryotes and heterotrophic eukaryotes (Patterson and Sogin, 2000). In the evolutionary history of blue-green algae or cyanobacteria, the evolutionary biologists observed that a number of symbiotic relationship happen between the blue-green cyanobacteria and the primitive eukaryotes. According to the hypothetical explanation of a group of evolutionary biologists, the occurrence of symbiotic assemblage and emergence of the photosynthetic eukaryotes has been taken place as a result of the cumulative evolutionary action of independent genetic expression of a photosynthesizing prokaryotes or their descendants and functionally and genetically assimilated and controlled by the eukaryotic cell, which has heterotrophic profile earlier. The entrapped or assimilated autotrophic photosynthesizing, green part became integrated like an accidental but successful grafting of chloroplast in the eukaryotic cell to make it as photosynthesizing eukaryotes (Patterson and Sogin, 2000). The contemporary ultrastructural investigations exposed that the plastids or chloroplasts are a membrane-bound organelle, encased with two or more membranes, freely suspended in the cytoplasmic matrix or attached to the nuclear envelope or attached to the “cytoplasm and residual nucleus of eukaryotic endosymbiont” (Patterson and Sogin, 2000). In course of evolutionary succession, the primary plastids of prokaryotic origin have gone through evolutionary changes and appeared with secondary associations in the descendant lineages of eukaryotes. The evolutionary biologists have noticed further that at least two prehistoric protists (e.g., Chlroarachniophytes and Cryptomonads) have been integrated with plastids after forming the symbiotic association ship with prehistoric, eukaryotic algal species to evolve as photosynthesizing protists or algal protists and such integration

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of plastids of prokaryotic origin in the penultimate stage of eukaryotic evolutionary lineage, has physiologically been recognized as “Secondary Endosymbiosis” (Patterson and Sogin, 2000). According to the contemporary phylogenetic analysts, the critical studies of morphostasis1 of characteristic features in a number of species are inevitable for the reconstruction of evolutionary history as well as determining the distinct evolutionary lineages of those species apparently seems to be the successor of any prehistoric ancestral lineage and a number of overlapping, complex features in the derived group of members, diverged out of any common evolutionary stock. As the evolutionary molecular biologists have revealed that emergence of traits such as an evolutionary transition from phagotrophy to the photoautotrophic mode of nutrition has occurred independently more than one time in the eukaryotes, particularly in the members of Euglenidshe diverse group of Flagellates, leading to the emergence of a distinct type of derived Flagellate lineages having a diverse trait of nutritions to cope in a diverse type of dynamic environments (Yamaguchi et al., 2012). The emergence of photoautotrophic Euglenids from the phagotrophic lineage of Euglenids as an integrated acquisition of secondary symbiotic association with green algae, leading to a unique evolutionary accident or experiment of nature (Yamaguchi et al., 2012). Recently, the scientists carried out the ultrastructural (like scanning and transmission electron microscopy) and comparative molecular analysis (rDNA sequences) of the marine Euglenid, popularly known as “Green grasper” or Rapaza viridis and the marine algae, Tetraselmis sp., sharing the same ecological niche and biological stakeholders of the same ecosystems (Yamaguchi et al., 2012). The critical investigations ascertained that the phototrophic Euglenid species, such as Rapaza viridis predate the marine green algae Tetraselmis sp. and presence of pellicles strips (16 plus one short whorls) the structural pattern of the chloroplast of Green grasper is found to be identical in other phototrophic Euglenids (Yamaguchi et al., 2012). The presence of composite features such as the presence of the two different sizes of flagella, euglenoid movement of the Green grasper, characteristic food habit, and ultrastructural features of the feeding apparatus (which is composed of short microtubules) indicates its mixotrophy2 along with photoautotrophy act as an ideal instance of morphostasis, which supposedly play a cardinal role in the evolution of the diverse group of Euglenids put forth a hypothetical evolution of phototrophic Euglenids out of eukaryovorous lineage, as a result of probable integration of chloroplasts of green alga in the eukaryotic protists (Yamaguchi et al., 2012).

1

Morphostasis: It is an ability of a biological system to maintain its structure, unchanged, in the backdrop of changing environment. 2 Mixotrophy: It is an organism, use mix of diverse source of carbon and energy source for its nutrition, instead of following stereotypic uni-trophic mode of nutrition, it has accustomed to physiologically and behaviorally adapted to be autotrophic (which has helped it long-term utilization of nutrition) in one end and the heterotrophic mode of nutrition in other end (which immediately cater its nutrition demand) and it would ranges from Prokaryotes to Eukaryotes organism.

The Evolutionary Biology of Extinct and Extant Organisms

The contemporary phylogenetic investigations ascertained that Green grasper is the sister clade of the rest of the photo-autotrophic Euglenids and it ascertained the primary assumptions of the evolutionary scientists who hypothesized the evolution of the derived lineages of photoautotrophic Euglenids, out of an ancestral phagotrophic lineage of Euglenids as a result of secondary symbiosis, often contemplated as an evolutionary accident (Yamaguchi et al., 2012). However, the synecologists observed that the autotrophic and osmotrophic Euglenids grow in the water column of the freshwater environment, whereas the phagotrophic counterparts (comprised of bacterivorous and eukaryovores) found in the mud and water-columns ranging from marine to freshwater habitat, including brackish water habitat (Brown et al., 2002). Most of the Euglena species possess two flagella, found in the flagellar pocket but a number of evolutionary lineages have more than two flagella (e.g., Tetreutreptia). The diagrammatic sketch of Euglena has been presented in Fig. 11.1. The scientists have noticed carefully that the eukaryvorous Euglenids engulf the green algal eukaryotes with special feeding apparatus and the hook-like flagella helped to immobilize the algal prey cells, such as Chlamydomonas, with the help of mucous secretion. The flagella of Euglenids having paraxonemal rods arranged side by side, each comprised of two central and nine peripheral microtubules or axonemes and the ultrastructural pattern of paraxonemal rods varies in differently located flagella as it has been arranged in whorls in the dorsal flagella, where it has been arranged lattice-like structure in ventral flagella (Leander, 2008). The flagellar axonemes are hooked-up to the base of the flagellar pocket the anchorlike basal bodies. The scientists noticed that the “flagellar apparatus” form the center of origin of other cytoskeletal elements of the Euglenoid cells-like the microtubules attached to the cell surface at the juncture, called “Pellicle,” feeding organs, etc. (Hilenski and Walne, 1985; Willey and Wibel, 1985; Belhadri and Brugerolle, 1992; Shin et al., 2001). Furthermore, it has been revealed that ultrastructurally, pellicles in Euglenozoa are made-up of parallel proteinaceous strips and microtubules, called “articulins,” clasping in between outer plasma membrane and the inner endoplasmic reticulum (Marrs and Bouck, 1992; Leander and Farmer, 2001; Leander, 2004). In crosssection, the pellicle is typically S-shaped, having an arch region and a heel region in articulation, give an appearance of the euglenoid cells and the changes of articulation leads to changes of the cell and expedite the movement of euglenoid cells, called “metaboly,” which is triggered as a result of engulfing or devouring large size of eukaryotes or eukarovory (Leander, 2004; Leander et al., 2007). It has also been contemplated by the scientists that metaboly related to a set of evolutionary chain reactions either gave rise to osmotrophic Euglenids or it has assumed to be originated parallel to the eukaryvory, paved the next stage of the evolutionary event, secondary endosymbiosis that subsequently paved the following evolutionary event, called photosynthesis, resulting origin of photoautotrophic Euglenids (Leander et al., 2001a; Leander, 2004).

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FIGURE 11.1 The evolutionary biology of extinct and extant organisms. The diagrammatic sketch of Euglena. Courtesy Sashi Sinha, Ms.

According to a group of evolutionary biologists, the metaboly has been found predominantly existed in the Euglenophytes (in photoautotrophic and osmotrophic Euglenids) but it becomes vestige in euglenozoa (in eukaryvores and bacterivores) (Leander et al., 2001b). Phylogenetically, the photosynthesizing Euglenids or Euglenophytes form a single subclade, recognized as Euglenophyceae, the plastids with conspicuous pyrenoids and paramylon molecules, and these unique plastids are Ultrastructurally encased by three consecutive layers of membranes and contemplated

The Evolutionary Biology of Extinct and Extant Organisms

to be evolved as a result of secondary endosymbiosis between the parental lineage of phagotrophic, eukaryvorous Euglenids and the green algae, belong to Pyramimonadales (Zakrys et al., 2017). The molecular phylogeneticists further revealed that there are three distinct evolutionary lineages diverged out of the photosynthesizing lineage Euglenids, the basal lineage has been represented by myxotroph, Green grasper or Rapaza viridis, along with two other photosynthesizing Euglenid lineages, belong to Euglenales, thriving in freshwater habitat and the Eupterales, the predominant photosynthesizing Euglenids. The order Euglenales has further been divided into two families (Zakrys et al., 2017). Phacaceae: It has three monophyletic generadDiscoplastis, Lepocinclis, and Phacus. Euglenaceae: It has comprised of seven monophyletic generadColacium, Cryptoglena, Euglenaformis, Euglenaria, Monomorphina, Strombomonas, and Trachelomonas. The morphological feature has been studied for more than 100 years based on the outer cell coverings of Euglenids, called pellicle and the organization of it has found to be integrated into the mode of nutrition and the cellular movement of it (Zakrys et al., 2017). Likewise, the formation of tree rings formation of pellicles (which is multigenerational) have some resemblance as the number of pellicle strips outside of cell found to be doubled prior commencement of cytokinesis, though the daughter cells inherit a certain number of pellicles from their ancestors has been found that formation of pellicles found to be started from anterior part to end in posterior part but that happens in Euglenozoas rather than Euglenophytes (Leander et al., 2001b; Esson and Leander, 2008).t has resulted in the formation of incomplete strips of pellicles form a number of whorls in between anterior-posterior body plan of the osmotrophic and photoautotrophic euglenas, which is an evolutionary important factor to the qualitative assessment of evolutionary diversities of Euglenids (Esson and Leander, 2006, 2008). However, the evolutionary biologists noticed that the formation of a number of pellicle strips upon the cell periphery of any Euglenid, ascertained the locomotion pattern and nutritional diversities of the distinct evolutionary group of Euglenids the Bacterivores (engulfing minute size of bacteria as preys) having small rigid cells of longitudinally arranged pellicle strips, are equal or less than 12 in number and the eukaryovores (engulfing large size of eukaryote preys) accustomed to metaboly have a range of helically arranged pellicle strips 20e60 number. On the other hand, the photoautotrophic and osmotrophic Euglenids have a large number of pellicle strips, which range from 16 to 120 and adapted to metaboly (Leander et al., 2007). According to the critical review of the molecular phylogeneticists, the origin of endosymbiosis in eukaryovores has rendered the photosynthesizing potential among this simple form of animals, which has emerged in course of the independent lineage of evolution and they further observed that the photosynthesizing or photoautotrophic, prehistoric Euglenids, then ancestral predecessor of its recently evolved descendants have possessed

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40e50 pellicles Euglenids having more than 50 or less than 40 pellicle strips, considered to be the derived groups of Euglenids (Leander and Farmer, 2000; Esson and Leander, 2008) such as Euglena obtusa has 120 pellicle strips. Phacus sp. has around 32 pellicle strips. The photoautotrophic Euglenids are especially noticed that possession of less number of pellicle strips found to be integrated to loss of the potential of metaboly in course of evolution (Leander, 2008). On the basis of molecular phylogenetic analysis and the presence of a number of eukaryovorous characteristics among osmotrauphs, the evolutionary biologists have contemplated that the photoautotrophs, the derived group of Euglenids have emerged out of eukaryvores and the osmotrauphs diverged out of photoautotrophs lineage in the middle of it and it subsequently changes the possession number of pellicle strips as well (Leander et al., 2001a). The microanatomists noticed that alteration of pellicle strips found to be broadly categorized under three categories, shaping the evolutionary alteration of cytoskeletal changes of Euglenids in the long run (Leander et al., 2001b, 2007; Leander, 2004): Asymmetrical or unequal separation of the pellicle strips to transcend it to daughter cells. Doubling of pellicle strips in offsprings. Halving of pellicle strips in the derived groups, in respect to its possession of parental pellicle strips. The feeding apparatus in Euglenids that has been found diversified in the phagotrophic members ranges from simple form of microtubule reinforced pockets (Mtr) to rods and vanes (Leander et al., 2007). The ultramicroscopic examination reveals that the Mtr formed at the base of the ventral flagellar apparatus (e.g., Notosoleus) and the feeding apparatus in some bacterivores and eukaryovore Euglenids are found to be more complex, comprising 2e3 feeding rods, made up of a bunch of microtubules (e.g., Dinema, Entosiphon) (Leander et al., 2007). The mode of feeding of eukaryovore and bacterivore Euglenids has a similarity to the mode of sap-sucking creatures like vampires as the phagotrophic members inject the feeding rods, piercing the cell of prey animals to get the cell content of prey to fill-in the “phagosomal vacuole” (Leander, 2008). The feeding rod in phagotrophic members much complex and articulated (such as in the size of length and ultrastructural formation) in comparison to its presence in photoautotrophic and osmotrophic counterparts as the evolutionary shift from phagotrophy to photoautotrophy and osmotrophy by means of adaptive changes like secondary endosymbiosis and surface absorption changed the food intake pattern of the Euglenids (Willey and Wibel, 1985; Shin et al., 2001). The scientists observed that the eukaryovorous Euglenids feed on a substantial volume of photoautotrophic eukaryotes, such as single-cell green algae and diatoms, in their regular diet.

The Evolutionary Biology of Extinct and Extant Organisms

At the same time, the phagotrophic Euglenids or Euglenozoa did not have any earlier evolutionary track record of photoautotropism (Leander, 2004). Whereas, the evolutionary biologists contemplated that the photoautotrophic Euglenophytes, originated monophyletically out of eukaryovorous lineage (the predators), have gone through evolutionary changes to establish secondary endosymbiosis with the green algal (prey) cells (Gibbs, 1978; Leander, 2004). The Euglenid chloroplasts are covered with three-layered membranes, having a distinct pyrenoid in most of the members, and it is responsible for RuBisCO enzyme production (though a number of Euglenids like Phacus, Lepocinclis, etc. are devoid of pyrenoids) and three stacks of thylakoids. The carbohydrate storage molecules, paramylons, are found to be dispersed in the cytoplasm throughout and related to the presence of pyrenoids in the euglenoid cells. On the basis of environmental conditions alongwith the availability of light intensity, that directly or indirectly regulates the mode of nutrition, the chloroplasts of Euglenids are found to be morphologically diverse and it range from a disc, star, or shield-shaped organelles. These diverse type of Euglenoid chloroplasts are primarily responsible for long-term sustainability and evolutionary diversification of it in a certain environmental state without light or a in a different mode of nutrition that not only alters the photosynthesizing abilities of a number of Euglenophytes but given rise the evolution of Euglenids, those have no photosynthesizing abilities (which indicates the loss of chloroplasts or it has become functionally vestige in the derived lineages in course of evolutionary journey) (Hachtel, 1998), such as: Ancestral lineage of Hyalophacus gave rise to the descendant Phacus, Ancestral lineage of Astasia longa gave rise to the descendant Euglena longa etc. But it has also been observed that though the chloroplast is in a physiologically inactive state still it exists as a vestige in a number of osmotrophic Euglenid members, proved that the derived members of nonphotosynthesizing Euglenids have maintained synapomorphic relation with photo-autotrophs (Hachtel, 1998). The flagella-induced movement of Euglenids has been stimulated by light and shade photoreception impetus that has been controlled by chloroplasts to some extent. Literally, in Greek, “Euglena” means “good eye” though it does not possess any real eye like an animal it possesses carotenoids, an orange-colored photoreceptive biomolecule that regulates the flagella-driven locomotory movements, called “phototaxis” of the members belonging to Euglenid (Schaechter, 2012). The microbiologists and proto-zoologists have observed in their experiments that outside of the euglenoid chloroplasts, there is an apparatus called “extraplastidic apparatus,” which is responsible for photoreception and coordinating photoreceptive swelling of the flagellum and moving toward the source of light and initiates gliding movement in the water-columns they lived in; at the same time, the photoreceptive molecules, carotenoids, which have been located at the flagellar pocket and called “eyespot” or “stigma,” from which the swimming flagella protrudes out (i.e., the flagellar base), control the retracting movement in dark conditions and the composite action of the flagellar movement helped the Euglenids to come up to an optimum

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level of the water column that ensures the absorption of optimum light required for its photosynthesizing process (Kuznicki et al., 1990). The photoreceptive, propelling actions of long, slender flagella of the Euglenas render these unique microorganisms to move forward in twisting, gliding, or crawling pattern in the aquatic environment, like other microorganisms and as long as it gets closer to the optimal light source, the rate of food production, as well as accumulation of procurement, has found to be increased for the photosynthesizing Euglenids. Convincingly, in a favorable environment, the entire aquatic ecosystem has been overcrowded of Euglenophytes that boosts up the population surge of minnows, crustaceans, tadpoles, mussels, etc. (Spellman and Drinan, 2001). It has critically been observed by the scientists that there are some eukaryovorous Euglenids with no chloroplasts, but the similar physiological action of photosensory swelling of flagellar and the stigma-induced movements have been noticed in some species, such as Urceolusts predatory action of engulfing the photoautotrophic eukaryotes like single-cell algae and dinoflagellates in the photic zone indicates that eukaryovorous origin of photoautotrophic Euglenids seems to be a valid hypothesis and it also indicates that either evolution of photoreception in ancient Euglenids seems to be much earlier that the secondary endosymbiosis and evolution of chloroplast possessing derived group of Euglenids or evolution of photoreceptive features in Euglenids evolved independently more than one times (Leander et al., 2001b). As the spermatogenesis and embryogenesis have not been found in this evolutionary stepping stone between animal and plant organisms, the composite evolutionary biological entity like “Euglenozoa-Euglenophyta” transitional group, these organisms found to be reproduced by the asexual reproduction, orchestrated by mitotic division of nuclear material, followed by cytokinesis (like duplication of cytoskeletal systems like formation of flagellar bases or roots, formation of pellicles strips, and formation of eyespots) (Esson and Leander, 2006). Although the presence of mitochondria in the Euglenids noticed by the scientists but the functional part of it is enigmatic. The mitochondrial genomic analysis revealed that mitochondria of a protistan species, such as Petalomonas cantussygni, showed that it contained kDNA type of nuclear structure, which has been found in the kinetoplastids, but it has not further been confirmed by subsequent studies (Leander et al., 2001a; Roy et al., 2007). The confusion still persists regarding the nature of DNA particle possessed by the Euglenids as some protistan members found to possess circular-shaped DNA molecule, called “maxicircles,” that would encode proteins directly and some members possess kinetoplastid DNAs, called “minicircles,” encoding proteins via rRNA or ribosomal RNA, those have normally been found in the advanced group of Eukaryotes (Leander, 2008). However, the molecular geneticists observed that genome sequencing of Euglenoid organisms cumbersome process due to big size (around 2 Gbps in size) and complex orientation (around 80% of the genome has repetitive sequence) and the occurrence of such genomic alteration has tentatively occurred as a result of an evolution of a number of secondary endosymbioses (O’Neill et al., 2015).

The Evolutionary Biology of Extinct and Extant Organisms

Along with a cascade of secondary symbiosis, the Euglenid genome has gone through a series of molecular changes like eukaryotic epigenetic alterations, histone acetylation, etc. often leading formation of DNA methylations integrated complex genomes (the modified genomes, found to possess glucosylated hydroxythymidine or modified nucleotide base J and exotic nature of kinetoplastids) and all such structural and functional modifications have stalled the normal polymerase chain reaction or PCR to stall the progress of DNA sequencing of the concerned organisms (Borst and Sabatini, 2008). During undertaking the DNA sequencing of the Euglena sp., the scientists further noticed that the high pace of transcription and instantaneous processing of excessive mRNA alters the sequence, which ultimately stalled the protein translation process (Tessier et al., 1992). Hence, for the evolutionary biologists, it is difficult to adjudge the identity and functions of the complete set of proteins, or proteome to decipher from the Euglenoid genome (O’Neill et al., 2015). To overcome such hassles to enable the genome sequencing and elucidating the metabolic potential of Euglena sp., the genome biologists undertook an alternative investigation of sequencing the transcriptome3 or transcript analysis of Euglena gracilis (Rismani-Yazdi et al., 2011; O’Neill et al., 2015). The scientists revealed that there were around 22,814 protein-encoding genes in phototrophic Euglenid members, whereas it was around 26,738 in heterotrophic Euglenids, around 32,128 nonredundant proteins, and 8890 splice-site variants4 (O’Neill et al., 2015). The investigators contemplated further that most of the genes remained functional in cellular metabolic activities by maintaining the production of a number of carbohydrates, vitamins, and amino acids through the functional aspects of a number of novel proteins have remained unexplored. The unique observation of such transcriptomic analysis revealed that evolution of a derived or advanced form of the genome (which is found as complex also) in Euglenid members happened as a result of horizontal gene transfer, shared from multiple sources of heterogeneous organisms, rather than as a result of a cascade of vertical inheritance of genes from predecessors to successors (Henze et al., 1995). The evolutionary biologists further contemplated that such horizontal transfer not only helped to enhance biosynthesis potential such as the production of unique enzymes or proteins to form unique cellular organizations or better immune systems of the derived Euglenid members in a cellular and molecular level that helps evolving unique metabolic potential of derived groups and it supposedly helped the evolutionary advancement of the next level of the eukaryotic evolutionary group

3

Transcriptome: A transcriptome represents the full range of messenger RNA or mRNA molecules, possessed by an organism. It has a functional difference with the genome of the concerned organism as the identity of the genome is much more stable or constant in nature which hardly changes, but the nature of transcriptome is pro dynamic as it changes, triggered by the impetus of internal developmental changes or external environmental changes. 4 Splice-site variants: It results a genetic change in the sequence of DNA, which happens at the borderline of splice site as well as the juncture of exon and intron. It causes alteration of protein coding sequences by disrupting usual RNA splicing, caused by gaining of introns or loss of exons.

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of successors when such complex genomic inheritance carried forwarded from Euglenids to the next level of the derived group of a eukaryotic organism (O’Neill et al., 2015). Multiple successful attempts of horizontal gene transfer and a number of secondary endosymbioses have been noticed by different evolutionary biologists during their investigation o the complex genome structure and its function of Euglenids, which is integrated into its evolution. The genome biologists have contemplated that around billion years ago, whenever Euglena has phylogenetically seperated from the rest of Eugenozoa (Parfrey et al., 2011), supposedly received a number of genes from the phylogenetically distant allies like "red algal endosymbiont" through horizontal gene transfer, and those archaic genes of red algal descent have been lost from the gene-pool of red algal lineage since then (Maruyama et al., 2011). The next level of gene transfer of Euglena has happened from green algal endosymbiont, which shared a number of its genes (including chloroplast maintaining gene) from its nucleus by horizontal gene transfer (Martin et al., 1992). The molecular geneticists and genomicists observed that the composite genomic treasure trove of Euglena has received and enriched with the exotic genes through horizontal gene transfer from heterogeneous, ranging from prehistoric protozoa, such as Trypanosoma and Leishmania, alpha-proteobacteria, red algal symbiont, green algal symbiont, and blue-green algal symbiont (Hallick et al., 1993; Maruyama et al., 2011; Spencer and Gray, 2011). It was a unique observation of the genome biologists that the core nuclear genome of Euglena has a close resemblance to ancestral protozoal members, Trypanosoma, rather than its so-called close phylogenetic proximity to the eukaryotic algae (O’Neill et al., 2015). The unique evolutionary history of Euglena has been opened-up from an unexpected level of information, available from its transcriptome, which is the treasure trove of a huge number of proteins or metabolic enzymes, acquired by the euglenoid genome in the course of complex evolutionary exploration for the last 1.6 billion years since its divergence from unicellular ancestral lineages of plants and algae (O’Neill et al., 2015). It is quite amazing to find that acquiring diverse genes from a distinct domain of biological organisms of a wide range of diversities has been successfully accomplished by Euglenids, to be evolved and revolved in unique structural and functional entity to carry forward the evolutionary journey of eukaryotes from simple unicellular form to the complex multicellular form. It is quite fascinating to understand and accept that in the complex journey of biological evolution of life, Euglenids hold a key transitional position where a shift in paradigm has been integrated into the evolutionary journey of eukaryotes in terms of a shift from unicellularity to multicellularity. It further ramifies the horizon of molecular exploration as it reveals that horizontal gene transfer played a key role in the journey of evolution of vertebrates as the most derived groups of eukaryote like mammals might not be evolved so fast unless the horizontal gene transfer would not play its cardinal role in the evolution of the most derived groups of eukaryotes in Anthropocene.

The Evolutionary Biology of Extinct and Extant Organisms

Perhaps it would sound like science fiction or just remained to be a hypothetical perception (unless evolutionary biologists could prove its truth with certainty in the future) to comprehend that we, the Homo sapiens, the most intelligent species on Earth are still inheriting the genes of some heterogeneous group of organisms, including protozoa and algae, through horizontal gene transfer (Riley et al., 2013). In addition, our origin and evolution have not exclusively driven down the vertical trail of evolutionary descendant, rather our enigmatic evolution is a result of cumulative molecular evolution, where we acquired a million number of genes to be evolved with a unique genome, shared from a wide group of organisms, through horizontal gene transfer to be emerging as the ultimate mammalian species on Earth that supposedly took place billions of years.

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Virus: a stepping stone in transition in the course of evolutionary journey from the world of “nonliving” to the world of “living” entity

12

“Viruses are part of life. Outside of a host cell, a virus particle, a virion is not alive as it has no metabolism and cannot reproduce. A virion is a biochemical machine that functions to get it or its genetic code into a host cell where it is reproduced. Whereas for cellular life, it is believed that there is a last universal common ancestor (LUCA) and there is no presumed common ancestor for viruses. Viruses have seven distinct genome structures which may have evolved separately. The living stage of the virus is when it has parasitised the host cell’s translational machinery and is making new copies of the virions. It is a kind of borrowed, or maybe stolen life” Peter Foster

After traversing a long-winded labyrinth of the evolutionary trail in quest of the origin and evolution of life on Earth, scientists and evolutionary biologists resorted to the conventional theory of abiogenesis to conceive and share the perceptional explanation of the origin and evolution of the living entity out of nonliving entities. However, lack of pragmatic elucidations of such occurrence had led the hypothetical explanations under the doubt of a few shades of cloud as none has a clear idea of how it could happen. The most convincing visual outcome of the abiogenesis hypothesis was “primordial soup,” the ancient treasure trove of heterogeneous organic matter on the blue planet Earth. Those organic molecules have evolved as a result of the inorganic evolution as a number of inorganic matters have gone through the metamorphic and interactive changes in the backdrop of paleoclimatic changes of planet Earth since the journey of proto-Earth initiated around 4 billion years ago; eventually, the proto-Earth has been metamorphosed from dark, gray-colored, moisturefree, oxygen-deficient earliest form to oxygen and water enriched, blue planet Earth in course of time (Georgia Tech Press Release, 2016; Javelosa, 2016; Kundu, 2018). It has further been contemplated that once the primordial soup, the primary

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product of organic evolution has been developed after through the composite interactions of chemical (physical, and organic) and palaeoclimatic changes Earth went through for millions of years. The cascade of cosmological impetus like the lightning, thunderstorms, frequent expositions to the gaseous clouds, intermittent fluctuations of the solar vortex and scorching flashes of heatwaves, gradual exposition of increasing level of oxygen, incipient level of moisture, and ionic-exposition of cosmic rays render the organochemical changes of organic matters leading the formation of the simple form of admixture of the primordial soup assumed to be evolved as proteins as well as enzymes, and the primitive but unique form of “gene soup,” the ultimate footprints of modern genetic codes (Georgia Tech Press Release, 2016; Javelosa, 2016; He et al., 2017). The team of evolutionary biologists like Christine He, Isaac Gallego, and others from the School of Polymer and Biomolecular Engineering, Georgia Institute of Technology, USA has envisioned that there must have an existence of thickener in the proto-earth, even that assumed to be preexisted before life evolved on it, which gradually thickened the puddles of gene soup to have thick enough to make it as “gene-like strands” that took control over evolution and diversification of life on this earth for more than billions of years (Javelosa, 2016; He et al., 2017). Furthermore, the scientists of Georgia Institute of Technology, USA used off the shelf viscous thickening ingredients to coordinate in their experiment, and they revealed that the precursors of the genetic code, which has been called as “genetic soup” used to possess self-replication potential as they existed prior the emergence of the enzyme (Javelosa, 2016; He et al., 2017). In the language of Martha Grover, the Research coordinator from School of Polymer and Biomolecular Engineering, Georgia Institute of Technology, USA on the prehistoric existence of precursor of genetic code, elucidated this evolutionary driven natural incident in a simple way as she said “A simple and robust process like this one could have operated in a variety of environments and concentrations making it more realistic in moving evolution forward” (Javelosa, 2016; He et al., 2017). From the stereotypes perceptional background, the progress of evolution in the biological world means an increase in the taxa complexity at structural and functional levels. But then, it might be conceivable to downgrading or decreasing of structural complexity too to adapt to a changing environment. Nonetheless, sticking to the perceptional views of acquiring complex form and traits and the inherent driving factors (which are a conceptually genetic entity) triggers such as transitional changes, stored in the biological information system of the concerned taxa to transmit to the next and following generations, to understand the progress of biological evolution, the sheer understanding of inorganic and organic evolution needs to be read out, encrypted on stones, inorganic and organic molecules, preserved in a natural condition since prehistoric times (like permafrost in the Arctic) to assess the dynamics of complexity for qualitative appraisal of progress of the evolution of the concerned organism (Maynard Smith and Szathmary, 1995).

The Evolutionary Biology of Extinct and Extant Organisms

Scientists, particularly the evolutionary biologists opined that DNA acts as a biological black-box, to keep a record to the progress of the evolutionary data to present the progress of the evolutionary history of many taxa, which has primarily been assessed from the increasing size of the concerned taxa genome (Maynard Smith and Szathmary, 1995). However, the protein-encoding potential of the genome is not precise as the size of the genome that varies from one taxon to another depends on the accumulation of noncoding DNA in that genome. In the gene level, the accumulation of complex trait would have been triggered in three ways (Maynard Smith and Szathmary, 1995): Gene duplication: In the course of duplication, when a gene holds the ancestral traits, another one (of the allele) explores a new venture of adaptation, required for undertaking the evolutionary progress of life. Symbiosis: According to this hypothesis, two or more genetic entities come together to form a composite, symbiotic relationship to yield a new evolutionary lineage. The evolutionary scientists cited the example of the evolution of mitochondria (which supposedly took place between 1500 and 2000 years ago), diverged out of the symbiosis of a-proteobacteria. Epigenesis: It has been considered a process, which took place as a result of a change of gene expressions rather than the change of gene sequence. To define major transitional changes that drive up biological evolution in terms of the more complex form of structure and advance level of function of the derived taxa, the experimental observation of Maynard Smith and Szathmary (1995) needs to be referred as they have commented: “Major transitions are major changes in the evolution of complexity that involve a change in the level of organization and hence the level of selection.” The scientists have hypothesized further that the emergence of a gradual, complex form of life, which roll-on evolutionary progress, happens as a cumulative result of an innumerable occurrence of major transitions, rather than one big major transitional changes, such as the following: Transition from a solitary form of organism to colony-forming organism. The emergence of one type of multitasking cell to functionally and structurally differentiated cells (observed in Protists, fungi, animals, etc.). Evolutionary journey of Prokaryotes to Eukaryotes. Migration of organisms from aquatic habitat to terrestrial habitat. Asexually reproduced populations to sexually reproduce populations. Shift from RNA to DNA and proteins as predominating genetic material. Evolution and diversification of hominid lineage from hominoid lineage. In 1962, Alexander Rich has theoretically proposed the “RNA World hypothesis,” though the actual term has been coined by Walter Gilbert in 1986. According to the “RNA World Hypothesis,” the evolutionary history of life has primarily been initiated in the podium of “RNA World,” where RNA acts as a selfreplicating molecule, existed on Earth before the origin and evolution of DNA and protein as the genetic material. The assumption of such hypothesis is primarily

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based on the storing and replicating potential of genetic information, which has been regulated by RNA enzyme or Ribozyme (which act in an identical way of how the DNA enzyme works) (Cech, 2012; Neveu et al., 2013; Zimmer, 2014). The evolution of the genetic code was a major transitional shift in paradigm that liberalizes the structural and functional perception of genes, integrated into the nature of nucleic acid, the ultimate power button, which is responsible for the switch over the regulation of functionalities of evolution from RNA to DNA (Maynard Smith and Szathmary, 1995). The strategic switch over from RNA to DNA in the domain of nucleic acid has played a fundamental role in promoting the extent and multitude of biological evolution as RNA as well as Ribozyme itself used to play two-in-one action as it acts as gene and acts as an enzyme, which led an overlapping limited functional opportunity of the nucleic acid as a gene-driven information storage system and enzymatic functional system supposedly limit each other functional potential (Maynard Smith and Szathmary, 1995). Consequently, it would further indicate a tentative situation where evolution would never unfurl its full-fledged functional potential to let evolve and diversify a big number of organisms that would fail to create an ambiance of trial and error in full-fledged execution of this evolutionary game-ball on Earth. The emergence of a big number of organisms would supposedly get a wide opportunity of adaptive screenings in the backdrop of intermittent environmental changes. But strategic switch-over from RNA to DNA for streamlining evolution further demarcates the functional arena of nucleic acid (gene action) and protein (enzymatic action). Though this part of this functional switch-over is not clear the substantial evidence indicated that to achieve specific functional potential, which is assumed to be triggered by the selection pressure in its ambiance, DNA (which functionally deal with only nucleic acid) had overtaken the front seat and RNA (which deals with nucleic acid and protein) became the secondary genetic material in the regime of the precise division of labor. The shift of structural and functional identity of the gene in the domain of nucleic acid, that is, from DNA to RNA, leading the emergence of a unique role of genetic interpreter, called translation, which maintains liaison between the driving potential of nucleic acid (actually reading out the sequential arrays of nucleotides) and determine the nature of proteins yields as a result of gene expression (carry in a genetic message, generated by the sequence of nucleotides and engaged in sequencing the amino acids to form a specific protein or enzyme as per genetic message-driven out of nucleic acid end) (Maynard Smith and Szathmary, 1995). Furthermore, the scientists observed that in the execution of translation a genetic code is necessary, which could help in the flawless execution of genetic message from nucleic acid end to protein end, but to dig deeper for its further elucidation, three major issues need to be clarified here, which are as follows: Whether there is any strategic advantage of segregation of genetic information storage functions from enzymatic functions on evolutionary dynamics (whether it is progressive or regressive)?

The Evolutionary Biology of Extinct and Extant Organisms

Apparently, the RNA molecule, as well as Ribozyme, is capable to perform both functions like storage information and enzyme functions, so the separation of these two integral functions into two distinct functions creates confusion. The scientists noticed that the larger size of the genome needs enzymes to carry-out functions, therefore a large-sized genome could store in a large array of genetic information, for its full-fledged functioning it requires a big pool of enzymes. Besides, the scientists also noticed that separation of one function from another is like division of labor, which enhances catalytic efficiency in one hand and reduced mutational load at the time of replication (Maynard Smith and Szathmary, 1995). As the replication of genetic material has intermittently been continued from one generation to the next, so the replication of genetic material is likely to be considered as a precise, error-free, and biological copycat. To clarify this part of the problem, scientists tried to present an analogical reference, where they took an example of making a machine with 100 pieces of parts and they put two options either all of these parts are to be categorized in 20 types or 4 types. Thus, a logical interpretation pointed out that there would be less chance of error in the case of the parts belong to four broad categories rather than 20 micro or specific categories. Hence, it is convincible that a genetic code comprises of a combination of four nucleotides supposed to coordinate error-free replication and reduce mutational load (Maynard Smith and Szathmary, 1995). The scientists further construed that the active hypothetical gene machine is made up of four monomers. Accordingly, if the machine is made up of four nucleotides, there would be 44 or 256 active catalytic sites whereas if the same is made up of 204 amino acids, there would have 1660 active catalytic sites of the machine (Maynard Smith and Szathmary, 1995). Therefore, by virtue of holding more catalytic sites, enzyme, as well as protein function, has created a strategic opportunity to expedite the evolutionary dynamics by enhancing the chance of adaptive potential of selection, whereas the DNA has played its role in storing genetic information system. How did the coordination among nucleotide-amino acids evolve and what is the advantage of such coordination to achieve any evolutionary benefit? Apparently, the hypothetical explanations, such as “division of labor,” a clear distinction between storage of genetic information and function of enzymes, etc., have rendered the separation of functions of nucleic acids and proteins (enzymes). The separation of these two important evolutionary driven mechanisms evolved in the backdrop of the evolution of genetic code (triplet nucleotides that encode certain amino acids) and scientists also considered that a number of back-up mechanisms helped in the evolution of genetic code (Maynard Smith and Szathmary, 1995). The molecular biologists tried to make a brief, comparative review of the mode of the Ribozyme functions and the synthesizing potential of Protein enzymes to focus on the division of labor between nucleic acids and protein enzymes. The molecular biologists referred the oligopeptides, the coenzymes in Ribozymes, supposedly gone through modifications to evolve as part of the peptide chain involved in a full-fledged enzymatic activity; hence, theoretically, ribozyme has been considered

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as the precursor of enzyme protein (Maynard Smith and Szathmary, 1995). Yet, it would not clarify the evolution of close coordination between the amino acids and the triplet nucleotides (or codon). To give a theoretical explanation (which has not been tested yet), the molecular biologists further contemplated that the amino acids were most likely to act as coenzymes of ribozymes. To be linked and is a functional state of coenzymes, the amino acids were subjected to carry a trinucleotide identifier (like a destination board in front of a public transporting bus) and possibly linked to such nucleotide “destination boards” to the amino acids (the public transporting bus) in the ancestral ribozyme entities. This might have rendered the evolution of the earliest form of the “enzyme protein” entity, which would have evolved out of the ancestral cradle of the ribozyme (Maynard Smith and Szathmary, 1995). However, in the next level, the scientists tried to find out whether the mix-match of triplet nucleotide and the amino acid was random and it apparently appears that the relationship of genetic code to codon assignments as a “frozen accident” or not, but a critical review helped the scientists to construe that assignments of codon to amino acids were not a random process for the following reasons (Maynard Smith and Szathmary, 1995). They noticed that identical amino acids have identical codons, the first codon position maintained “biosynthetic kinship with amino acid” and the second codon has been found to be associated with the polarity of the specific amino acid it codes for. On the basis of their analysis, the scientists came to the conclusion that the evolution of genetic codes with codon assignment protocol has not to be considered as “frozen accident,” rather it has assumed to be evolved for minimizing the “mutational load” to offset negative effects, which escalate errors during translation (i.e., from mRNA to enzyme protein formation) and fix it. The encoding potential of one codon for more than one amino acids considered to be an instance of an ambiguous alteration of the original assignment of codon evolution that encodes for a specific amino acid (Maynard Smith and Szathmary, 1995). It has also been noticed by cell biologists that the ribosome is the key cell organelle that coordinated the protein translation mechanism in all living organisms (Wessner, 2010). More or less genetic code is universal in nature and the functional distinctions of it are based on the typical pairing between nucleic acids and proteins has certainly been considered as a major shift in paradigm in the process of evolutionary transition. Unique process of functionality of genetic code has helped us to witness the preliminary achievement of the evolutionary success of life by regulating the expression of specific protein trigerred by specific sequence of nucleic acid, that is the greater part of functional protocol of genetic code. Furthermore, the molecular geneticists and evolutionary biologists have witnessed that the ultimate evolutionary diversification of metazoan lineage out of the archaic protozoan root-stock of life and the tertiary origin and evolutionary diversification of the ultimate mammalin the animal kingdom, in this contemporary regime of Anthropocene, that is the emergence of modern human species in the blue planet has directly or indirectly streamlined by the ubiquitious mode of functionality of the genetic code.

The Evolutionary Biology of Extinct and Extant Organisms

Why and how DNA has found to be more competent than RNA to drive up evolutionary dynamics, as well as expedite biological evolution? This part of the story of progress in the history of the biological evolution of an advanced group of metazoan animals such as birds, reptiles, and mammals would be remained partially conceivable unless the major transitional shift of functional identity of the nucleic acids from RNA to DNA has not properly been elucidated. This functional switch over genetic material from RNA to DNA has driven the biological evolution to the doorstep of Cretaceous Radiation, when a surge of a diversity of multicellular organisms has been witnessed, to create an ambiance of mammals dominated animal kingdom in the post-Cretaceous climatic regime on Earth. The main concern regarding DNA evolution is integrated to its unimodal action of storage and processing of genetic information in respect to bimodal functional traits of RNA when RNA has been considered to be evolved as the original nucleic acid and it is capable of storage of genetic information and enzymatic function. Then, it raises concern further what is the advantage of the emergence of DNA as it only concerned with the storage of genetic information? The molecular biologists assumed that the division of labor like separation of the function of nucleic acid and proteins, which has been witnessed in the transitional shift of DNA and enzyme protein from RNA, has supposedly reduced the mutational load, which helped to carry out a flawless translation as well as error-free replication of genetic material in the concerned organisms for one generation after generation and it helped to maintain homogeneity of a species with a certain genetic profile for a long period of time (Maynard Smith and Szathmary, 1995). As a result, a consistent inheritance of genotypic traits would have been observed in the organisms that carry DNA as nucleic acids, rather than possessing RNA. As we know that in molecular level, DNA comprises Deoxyribose sugar and four nitrogen bases like Adenine, Guanine, Thymine, and Cytosine and the RNA comprises Ribose sugar and four nitrogen base: Adenine, Guanine, Cytosine, and Uracil. Thus, instead of having Deoxyribose sugar, a ribose sugar, possessing the nitrogen base Thymine and Uracil in RNA, DNA has been found to be biochemically more stable in the background of the current oxidizing atmosphere of the Earth, which has been covered with a thick blanket of oxygen and the earth’s surface covered with 3/4th of the water bodies (Maynard Smith and Szathmary, 1995). The last major evolutionary transitions, integrated into the genetic transformation of the organisms at the molecular level from RNA to DNA, paved the biological evolution of life in full swing to attribute an evolutionary edge toward metazoan lineages over protozoan lineage. A diverse group of multicellular organisms would evolve to occupy the ecological niche, which existed in this biosphere to ensure that this blue planet would have been recognized as the planet Earth with full of living organisms, preferentially be recognized as “living planet” in our planetary system. Apparently it seems that there are two distinct categories of all entities or materials on Earth: living organisms and nonliving materials. The evolutionary biologists observed that the borderline between living and nonliving entities is not necessarily

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very distinct as long as the existence of a virus is concerned in our biosphere. Seemingly, the virus has been found to exist in the gray area of evolutionary transition between living and nonliving entities as it shared the composite characteristic features of both ends. The microbiologists and virologists have put their earnest effort to classify these diverse groups of entities (diversity in the virus has generally been observed in terms of shape, size of its structure, and nucleic acid configuration) to locate its position in the conventional model of the tree of life. Incongruous to most of the biological entities, a number of the virus such as SARS virus, hepatitis C virus, poliovirus, and measles virus have RNA genome, whereas adenovirus, papillomavirus, poxvirus, and herpes virus have DNA genome presence in their possession (Timbury, 1983). Even in the RNA virus category, most of the RNA viruses are found to possess a single-stranded RNA (e.g., Rabies, Influenza, etc.), while some members found to carry double-stranded RNA (e.g., Rotavirus, Bluetongue virus, etc.) (Timbury, 1983). Likewise, in the category of DNA virus, double-stranded DNA viruses are predominant (e.g., Poxvirus, Herpes virus, etc.), though single-stranded DNA viruses have also been found (e.g., Tornovirus, Volvovirus, etc.) (Timbury, 1983). Even in the life cycle of some virus-like Retrovirus (e.g., HIV-1, HIV-2), the predominant genetic material is RNA with DNA intermediate in it, whereas, in the life cycle of Hepadnavirus, the predominant genetic material is DNA with RNA intermediate in it (Timbury, 1983). The sketch of the HIV virus has been presented herewith (Fig. 12.1). There is a great deal of controversy about whether the virus is a living or nonliving entity as it shows characteristic features of both types of entity and the contemporary classification system did not assign a virus in any distinct category between living or nonliving. Whenever it stayed outside of the hosts, its mode of nutrition does not comply with the mode of nutrition of living things. Outside of the hosts, it remained in an inert state until it gets in touch with any new one, which has a striking resemblance to the viroid and prions. The only difference with those two is viroid, those are made of only naked DNA, but prion is constituted with only protein. However, outside of the host bodies, it does not perform any metabolic functions, no indication of homeostasis and it does not replicate and refrained to respond to any stimulus. Consequently from a typical perception about living things, it is easy to consider it as nonliving; though getting in touch with living hosts it acts as a living entity that led the opposing group of scientists to recognize as a living entity. The virologists observed that the structure of the virus is very simple as its genetic material like fragments of DNA or RNA has normally been wrapped up by the protective blanket of protein, called a capsid. The virus inserts their fragment of nucleic acid into the host body, then they multiply inside the host body (they do not reproduce) by means of the lytic or lysogenic cycle and come out of the host body, which has a close resemblance to the life of parasites (Timbury, 1983).

The Evolutionary Biology of Extinct and Extant Organisms

FIGURE 12.1 The diagrammatic sketch of the HIV virus has been presented here. Courtesy Goutam Saha.

Nevertheless, a number of evolutionary biologists and virologists considered it as the living organism, and in support of their argument, they advocated that viruses multiply inside the hosts after entered into the hosts and set up organelles by altering the genomic functions of the hosts. The critical observation on the mode of virus action in the hosts has resembled the mode of actions of obligate parasites in their hosts. The way a tree needs soil, or a human being needs this planet, it is the identical way virus needs hosts to survive. There is a rational analogy between the inert, seemingly lifeless state of virus particles outside of host bodies like the dried seeds inside the pods. Therefore, if someone tried to define life from a visual perspective, a dried seed in a pod is apparently looking like a lifeless or nonliving object, unless we sow it to expedite its germination (as long as the seed remains viable) in the same way whenever nonliving virus particle gets in its host, it acts as a living object. It is true that it does not reproduce, but multiplicities and that has been referred to as one of the strongest reasons to consider it as nonliving. We need to keep in mind that it does

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not only keep on producing multiple copies intermittently inside the host in each cycle of multiplication. It produces multiple variants successfully in a short span of time to cope with any unforeseeable changes in its microenvironment. In this regard, the newly emerged virus particles or the members of new generations have better adaptive potential as well as better survival potential in comparison to its parental generation and it should be considered as the key feature to take into consideration if anyone tries to distinguish between living and nonliving entities. Apparently, the viruses are ultramicroscopic structures, very small particles (around 200 nm diameter), found to be characterized as nonliving things whenever they stay outside of any host and found to be in a living state whenever they found in the host as they started replicating in it (Wessner, 2010). Although they possess nucleic acid like DNA and RNA as genetic materials of living organisms, viruses are devoid of ribosomes, the cellular organisms of living organisms responsible for the production of protein during the translational process. All these unique characteristics, instigate the virologists, cell biologists, and evolutionary biologists to contemplate that in the prehistoric time (most likely millions of years ago) the viruses existed as free-living organisms, gradually metamorphosed to parasites (might be due to acting of regressive evolution, such as loss of certain organelles). They supposedly possess the unique genetic elements that acquired the potential to move between cellular entities, transcending their own genetic material in the hosts and took over the control of the host’s genetic set-up to increase its population cycle to emerge in huge numbers and kill the hosts in the long run (Wessner, 2010). Hence, the logical assumption of scientists, specifically evolutionary biologists portrayed the viruses as the precursors of life, which supposedly stretched out the terminal end of organic evolution and initiated the penultimate phase of the biological evolution journey to build an evolutionary bridge between the nonliving and living entities on this Earth. However, the next and most important concern is how did these hemi-nonliving or quasi-living organisms have been evolved? As there is no direct evidence to decipher the origin and evolution of viruses on Earth, the evolutionary biologists resorted to a number of hypotheses, some of the important ones need to be mentioned herewith (Wessner, 2010): A. Progressive hypothesis: It states that the virus evolves out of unique genetic elements and having the potential to move between cells. Precisely, the virologists construed that the part of genes or mobile genetic elements would have the potential to split-out of a genome and able to be attached to a new genome so the new genome would be able to come out of a cell or enter into a new cell. To substantiate their hypothesis, the scientists have conceptualized the replication process of retrovirus. Retrovirus, which is predominantly the single-stranded or ss-RNA virus, getting transformed to double-stranded of ds-DNA under the influence of viral enzyme reverse transcriptase after invading the hosts and migrate to the host’s nucleus. Under the influence of the viral enzyme integrase, the viral ds-DNA got integrated into the host genome. The integrated viral gene

The Evolutionary Biology of Extinct and Extant Organisms

inside the viral genome would have been transcribed and translated further and the RNA polymerase enzyme of the host cells led to making a number of copies of the ss-RNA genomes of virus invaded in the host. A number of new progeny of RNA viruses came out of the cell and begin a new cycle of life again. A number of genome biologists observed that the eukaryotic genomes possess retrotransposons (the eukaryotic mobile genetic elements), which possess around 42% of the human genome has been found to able to move genome to the genome, via RNA intermediate that has a functional resemblance to the retroviruses (Lander et al., 2001). The scientists have assumed further that the acquisition of a unique form of proteins would allow the newly formed viral entities or retroposons to come out of the cell to get into a new cell to start over its life cycle (Wessner, 2010). B. Regressive hypothesis: It contemplates that the viruses are the ultimate remnants of cellular organisms, yielded as a result of regressive evolutions. According to the microbiologists, like the intracellular bacteria such as Chlamydia and Rickettsia, those behaved like obligate parasites, evolved from free-living cellular ancestral lineages and the genomic investigations revealed that mitochondria and Rickettsia prowazekii, supposedly evolve from a common evolutionary lineage (Anderson et al., 1998). The virologists further hypothesized that the virus was supposedly evolved out of the most complex, cellular organism, and their loss of genetic information in the course of regressive evolution and resorted to the parasitic replication pattern of life. A group of virologists has referred the “nucleocytoplasmic large DNA viruses” or NCLDVs, which have possessed a large genome, and supposedly descended out of autonomous complex ancestral evolutionary stock (Wessner, 2010). According to this hypothesis, the autonomous ancestral root-stock of the virus has been made up of the composite organisms, maintained a symbiotic relationship, and in the course of evolutionary transitions, one part of such symbiotic organisms gradually depends on another organism and became parasitic. It settles a new equation of relationship resulting emergence of a parasitic organism after losing its genetic potential (the erstwhile free-living one, involved in symbiotic association), which depends on the hosts (the erstwhile second organism, engaged in a symbiotic relationship) and it is likely to happen as a result of regressive evolution. The evolutionary biologists further construed that after losing the essential genes or expressing the potential of genes, the newly emerged organism, having a parasitic mode of nutrition, struggled to survive as an obligate intracellular parasite inside the host and remained inert like nonliving things outside of the hosts and it is recognized as a virus (Wessner, 2010). The virologists observed furthermore, that Mirnivirus possess a number of ancestral genes involved in its translation process, those are assumed to have existed in some organism, remnants of its genetic profile were capable in the translation process (Wessner, 2010). The microbiologists also observed in their critical

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review that the mode of function of Mirnivirus and Rickettsia prowazekii genomes, the parasitic bacteria has a striking functional similarity (Anderson et al., 1998; Raoult et al., 2004). C. First Virus hypothesis: Whether it is a progressive or regressive hypothesis, it has been presented as two different types of explanations and there is a common theme of background between these two opposing hypotheses, that is cellular entities, as both hypotheses have been postulated on the basis of an assumption that the cellular entities are the ancestral lineage from which the virus has emerged out (Wessner, 2010). According to the progressive and regressive evolution of viruses, cells are considered to be the maiden living, replicating entity on Earth. On the contrary, to the “maiden cellular replicating organism” on Earth, a number of evolutionary biologists have promulgated that viruses might have existed in the precellular world as a maiden replicating body on this Earth, that might have existed even prior the existence of archaea and bacteria (Koonin and Martin, 2006; Prangishvili et al., 2006). According to the RNA World hypothesis of Alexander Rich in 1962 (Neveu et al., 2013), the maiden replicating molecule was RNA and the ancient RNA molecule, which has been recognized as Ribozyme (Zimmer, 2014) found to be able in catalyzing biochemical reactions like enzymes. The virologists construed that as the replicating body, the virus evolved before the evolution of cell on Earth; thus, the ancient RNA has the potential to infect the first cell and it has further been postulated that single-stranded RNA virus was the precellular entity of this Earth, which kick off the journey of cellular evolution on Earth (Wessner, 2010). The existence of virus outside of the living organism as nonliving things, possession of genetic footprint of life, the nucleic acids, both RNA and DNA and the changing of one to another like Retrovirus with the predominant genetic material is RNA with DNA intermediate in it or Hepadnavirus, with the predominant genetic material is DNA with RNA intermediate in it, supposedly paved the way of origin, evolution, and diversification of a derived group of DNA genome possessing virus out of ancestral RNA genome possessing virus. With the passage of time and in the backdrop of environmental changes, further extrapolation of this hypothetical evolution of DNA virus would indicate the further evolution of multicellular organisms, possessing DNA genome in it. It has been discussed earlier that evolution of DNA, in place of prehistoric nucleic acid and RNA, ensured division of labor like the storage of genetic information has been dealt with it, whereas the enzymatic functions have been passed on to the protein formation system, integrated to the translation process of eukaryotes. The evolution of the enzymatic functional system in the organisms found to be a major evolutionary transition as an evolution of the functional molecular trinity of life, such as carbohydrates, proteins, and fats, evolved in the eukaryotic cellular organism along with the appearance of cell walls, membranes, and different organelles that streamlined the biological evolution to a new shift in the paradigm unicellular simple form of life to the multicellular complex form of life (Wessner, 2010).

The Evolutionary Biology of Extinct and Extant Organisms

However, another group of scientists, promulgated that the progenitors of NCLDVs rendered the formation of metazoan eukaryotes. They further hypothesized that the nucleus of the eukaryotic cells as a result of the occurrence of secondary endosymbiotic events, where an enveloped DNA virus emerged as the earliest form of the eukaryotic cell (Villarreall and DeFilippis, 2000; Bell, 2001). However, each hypothesis has its uniqueness and demerits, so it is difficult to consider any particular hypothesis as the absolutely right one to define origin and evolution of the virus, the unique transitional stepping stone between living and nonliving world, but it requires further critical reviews and studies in the interdisciplinary fields of microbiology, virology, molecular genetics, molecular phylogenetics, genomics, developmental genetics, and developmental biology to decipher the identity and evolution of replicating bodies on this Earth (Wessner, 2010).

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Once there was an ancestor between humans and apes: in the quest for the enigmatic missing link

13

“‘Lesser’ apes like the gibbons offered a window into the anatomy of our earliest ape ancestors. Meanwhile the ‘great’ apes e gorillas, chimpanzees, and orangutans e showed the anatomical features our ancestors possessed at the moment they split away from the other apes and began to develop a uniquely human appearance. Gorillas and chimps were not simply our sister species: they were also a lot like the LCA [Last Common Ancestor].” Colin Barras

The terms like “Evolution” and “Natural selection” have mostly been used as a label for a perception that is either poorly defined or understood. However, the point of view or the “misnomers” are ignored by us most often. And the matter of fact is that our stereotypic misconception, “Evolution” does not work like a factory to yield finished products like “species in higher state” to pass the quality control screening process of “natural selection.” So if we would try to comprehend that our evolution has happened yesterday so we, humans are the most powerful, dominating organism in the biosphere, and today “RNA-virus is the most dominating one” that does not mean we are less evolved than the RNA virus. We could have a hypothetical example of a nectar-feeding bird, species out of 100 species, that manage its subsistence by collecting the nectar of honeysuckle flower that does not mean that particular honeysuckle flowering plant acts as a natural selection; the nature and composition of the nectar of honeysuckle flowering plants might get changed with the changes in the environmental conditions. From a survival perspective, most of the nectarfeeding birds close to honey-sucking birds of the identical clan are supposed to be supported by the earlier honeysuckle flowering plants, so any sort of changes either in the honeysuckle or in the nectar-feeding birds are random by nature, where the ultimate goal in the game of “survival of the fittest” is to be alive. So, in the game of swinging of “survival of the fittest,” the pendulum of the evolutionary clock does not follow any directional pathway of evolution as it has no destination and swung by the occurrence of random changes of external conditions, synced with responsive changes of internal conditions of any biological entity. So it is convincible that the unfavorable changes are selected against, whereas the favorable changes have always been favored. Hence, the evolutionary engine has always been steered The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00017-9 Copyright © 2021 Elsevier Inc. All rights reserved.

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by the selective pressure of natural selection to face the changes to interact with it and adjust with it most of the time to move on. Hence, it is plausible that being human species if we found that in a unique habitat, survival advantage has been enjoyed for having certain traits of an organism like apes, we might have been evolved with similar traits that would help us to dominate in the same habitat and outcompete the apes in the game of “survival of the fittest.” So acquiring such ape-like traits or better traits (convenient for enjoying better survival opportunities) might change our morphological, physiological, or genetic profile to appear as either a simple or ancestral form of appearance. But we could not undoubtedly claim that it is our futuristic program that could determine our evolution; rather it is the zeal of survival among the human species to outcompete other species, to survive as the ultimate winner over all other species on this Earth would supposedly make it happen. According to a well-written script of science fiction, the reversal swing of evolution from human species to ape is a remote possibility. However, from a logical perspective, the identical look of the ape is not so disgraceful as “survival of the fittest” is the thumb rule for every organism not only to ensure its contemporary survival but continue its journey of life on Earth for the future. C. Darwin (1871) in his famous book, The Descent of Man, which has been published around 150 years ago, had put the human species in the same family tree with the other animals, which appeared in the process of biological evolution on the Earth. Hence, the Darwinian doctrine has rendered a clear indication of the origin and evolution of human species from an ancestral stock of living animals; naturally, it contradicts the orthodox belief of creationists. So, it gives two alternative aspects of the origin and evolution of human species on this blue planet (Barras, 2017): 1. Human species has a long-lost parent and anthropologists hypothesized that the human species have one or more than one phylogenetic sister. Hence, those siblings supposed to have a common point of beginning should be recognized as “Last Common Ancestor” or LCA. 2. Humans are not the only sole branching species of a phylogenetic tree rather it has a phylogenetically close related “Sister Species” in this biosphere. Before the Darwinian regime of natural selection, the human species has been categorized as primates, which has little evolutionary significance as a perception. Even Darwinian doctrine itself was not very scientifically proactive in deciphering the holy grail of anthropogenesis, and it had been mentioned in his Origin of Species by Means of Natural Selection. In 1863, Darwin’s colleague, Thomas Henry Huxley, had expressed his hunch in his famous literature “Man’s Place in Nature” that anatomically, the human species looks identical to some extent to gorillas or chimpanzees and Huxley had expressed his concern either one of these must be the phylogenetic sister species of humans. During the glorified regime of creationists in the late 19th century and the beginning of the 20th century, such radical evolutionary perception of origin and evolution of human species by Huxley made him recognized as an enemy among the creationists group, whereas the Darwinian

The Evolutionary Biology of Extinct and Extant Organisms

evolutionists strongly supported his perception. The evolutionary history of primates have a direct relation to the evolutionary history of mammals on the Earth and the evolutionary biologists have referred further to Cotylosaurs of Synapsid reptiles, those have also been recognized as Cynodont reptiles, as well as the ancestral stock of mammals, supposedly evolved around 210 MYA, around Jurassic Period. The old-school paleoanthropologists referred that these prehistoric ancestors related to the extant primates had diverged from an ancient primate species: Elephant Shrew, found in Africa and this kind of primitive mammal has supposedly diversified itself around 145 MYA, in the Cretaceous Period of Mesozoic Era to capture the ecological niches, laid vacant due to the extinction of reptiles (Martin, 1990; Gupta, 2008). Huxley (1863) has propounded to the world of science with “lesser apes” like Gibbons (Hylobates sp.) to share an idea about the anatomical overview of ancestral apes. But molecular investigations and the comparative investigations of the anatomical profile of Gorillas (Gorilla sp.), Chimpanzees (Pan sp.), and Orangutans (Pongo sp.) have appeared as a breakaway lineage of other apes and sister of human species (having unique anatomical resemblance) and both siblings have supposedly emerged out from LCA root-stock. The preliminary level of investigations of Huxley has also been appreciated by the recent anthropogenic investigations made by the famous Paleoanthropologist, Dr. Tim D. White of University of Berkley, USA. Dr. White has recognized chimpanzees as the LCA at the end of his investigations. As per the stereotypic perception of the old-school paleoanthropologists, the primates (smaller sized monkeys) used to scurry and jump around the bushes and canopies of the trees. But it has been found quite different for the apes having bigger bodies with long arms and they prefer to dangle around the tree branches rather than scurrying and jumping over canopies. So the evolutionary biologists have recognized such unique locomotory movements of the big apes as “Brachiation” and which has been considered as the characteristic features of the long-armed apes, and it has further been recognized as the LCA by molecular and evolutionary anthropologists (Smith, 1958; Barass, 2017). One of the eminent primatologist Professor Sherwood Washburn, University of California, Berkley, USA has carefully noticed the walking pattern of the two big apes, Gorillas and Chimpanzees, during his investigations on the comparative biobehavioral features between these big apes in 1960 and he has carefully noticed that they flexed their fingers to get the bodyweight on knuckles, which has further been recognized as “Knuckle walk of LCA” (Smith, 1958). Professor Washburn has further tried to promote it as an early or transitional state of a bipedal mode of walking that “The behavior could even be seen as a stepping-stone on the way to walking upright on two legs” (Barass, 2017). But some anthropologists were there who did not agree with the scientific observation of Professor Washburn and some scientists like Frederic Wood Jones of St. George Mivart argued in favor of different hypothesis as they started promoting the ideas that human species emerged from the lesser apes like lemurs, monkeys, and tarsiers rather than greater apes like chimpanzees or gorillas (Kundu, 2020).

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In 1940, during his investigations on the developmental biology of apes in its relation to evolution, Professor William Straus, the eminent scientist in cellular and developmental biology, John Hopkins University, USA has argued that all those lesser apes evolved independently around tens of millions of years ago whereas human species has evolved very recently so anthropogenesis has not likely to have emerged from primates (Barras, 2017). Professor Straus has further noticed that the locomotory organs like legs, hands, and feet of human species are not so specialized like greater apes and distinct from gorillas, chimpanzees, or orangutans, so he contended further “In these characters man finds his counterparts, not in anthropoid apes [gorillas, chimpanzees, and orangutans] but in animals that are regarded . as more primitive” (Diamond, 1991; Barras, 2017). From the eloquent observation of Professor Straus’s argument that human phylogenetically emerged from a different primate, before greater apes evolved with their “Knuckle walk” the evolutionary path of modern human species has been turned around to a different direction. According to the ideas and argument of Professor Straus, though the identity of the so-called “sister species” of humanity has not found to be very clear yet the shape of the LCA seems to be much larger than that of the monkeys however much lesser than the greater apes and those prefer running through the branches of the bushes rather than dangling beneath the crowns of the tree canopies (Barras, 2017). In the middle of arguments and counter arguments of the different schools of anthropologists about the origin and evolution of human species, scientists have been able to establish the virtual identity of LCA till 1988e90. Meanwhile, Dr. Nathan Young of the University of California, San Francisco, USA has observed and shared further that till the middle of 1990, humans have phylogenetically been considered to the proximity of primates in the contemporary molecular phylogenetic tree of anthropogenesis. Till the middle half of 1990, the evolutionary biologists, molecular biologists, and molecular anthropologists have successfully established the true identity of the phylogenetic sister of human species in the backdrop of their interdisciplinary research works on anthropogenic paleontology in combination with the genomics and molecular genetics carried out in the different time interval on the ancestral lineages of human species. The contemporary, unanimous resolution of the anthropological perception and molecular investigations on the origin and evolution of human species on Earth, chimpanzees, and its close phylogenetically bonobos have been recognized as the phylogenetic sister of humans (Barras, 2017). So the scientists have traversed a long evolutionary trail of anthropogenesis in the labyrinth of hypotheses, and notoriously patchy evolutionary history of palaeontological evidence, evolutionary biologists and molecular anthropologists have got success to catch the glimpse of sunshine at the end of the tunnel to narrate the brief of history or origin and evolution of humans to figure out its phylogenetic history in the reference to the virtual reference of the molecular clock (Gray, 2010). It should be mentioned here that the concept pf molecular clock has jointly been developed in 1960, by the worldfamous chemist Linus Pauling, in collaboration with Dr. Emile Zuckerkandl and they have adopted an experimental protocol where they have logically assumed

The Evolutionary Biology of Extinct and Extant Organisms

“that molecules are constantly changing, and the more ancient the divergence between species, the more time those species have had to accumulate their molecular differences” (Barras, 2017). Based on this principle of “molecular clock,” Pauling and Zuckerkandl have analyzed the proteins of human and gorilla blood to determine the molecular changes they went through, and the scientists’ duo has estimated that the rate of changes those molecules have accumulated in the prehistoric time. Based on their analysis, Pauling and Zuckerkandl have revealed that humans and gorillas have shared a common ancestral phylogenetic lineage around 11 MYA (Zimmer, 2001; Barras, 2017). Such experimental observation has disheartened the paleontologists from old-school as they have typically relied on the fossil evidence but evolutionary biologists (molecular geneticists and genome biologists) have expressed their solidarity toward Pauling and Zuckerkandl as the evolutionary studies opted for an alternative trail to yield feasible results to the contemporary world of science. In support to the contemporary works of molecular biologists, the famous anthropologist Dr. Owen Lovejoy, Kent University, Ohio, USA has made an intriguing observation about the identity of LCA “The gorilla held out as a pretty good candidate . But eventually, the chimpanzee won out” (Diamond, 1991; Barras, 2017). The availability of huge numbers and diverse kind of fossil pieces of evidence of apes from Africa, Asia, and Europe and the molecular age-dating process of those fossils pointed out that around 20 MYA, the planet Earth should be recognized as the “Planet Apes,” However, such metaphoric “Planet Apes” had supposedly collapsed around 7e6 MYA when most of the apes got extinct in the European and Asian continent (Barras, 2017). Nonetheless, the molecular phylogeneticists have affirmed that anatomically modern human species have construed to be diverged out of the ancestral primate lineage most likely from Chimpanzee around 7 MYA (Diamond, 1991; Barras, 2017). Hence, the compilation of traditional paleontological pieces of evidence with contemporary molecular implications of phylogenetic data of primates has helped the evolutionists and evolutionary biologists to conclude that Chimpanzees and anatomically modern humans have likely to be emerged out of LCA root-stock and they have existed or coexisted in Africa at the tentative time of evolution of emergence of modern human species on Earth. In 1997, at the end of a tedious search of the true identity of LCA, the identical molecular phylogenetic verdict in favor of “Chimpanzee and Bonobos” not only helped the researchers to conclude their claims and but helped them to come out of the counter claims, brewed between paleontologists and the molecular geneticists for a time being (Kundu, 2020). But, the evolutionary journey of modern human species on the Earth has not been unanimously accepted, as the renowned anthropologists like Dr. Tracy Kivell of University of Kent, UK, and Dr. Daniel Schmitt of Duke University, USA have stuck to their arguments that “Knuckle Walking LCA” should not be recognized as the human ancestors. Based on backtracking of the molecular clock, Dr. Tim White and Dr. Owen Lovejoy have critically examined the well-preserved fossil specimen of the prehistoric “hominin: Ardipithecus ramidus” alias “Ardi” in 2009 and they

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concluded that this “Ardi” has supposedly evolved around 4.4 MYA, and it should further be shared that the fossil of Ardi has been collected from Ethiopia (White et al., 1994; Barras, 2017). It helped the evolutionists to conduct a better gap analysis to determine the tentative time of emergence between LCA and the penultimate point of time of modern humans became narrowed down further. The anatomical and molecular review of the Ardi’s skeleton had indicated further that it was neither knuckle walker nor brachiating ape, rather its anatomical profile had given an impression to the scientists that its movement seems to be more close to the bipedal movements of modern humans. From a developmental biological perspective, Ardi seems to maintain a transitional bridge between hominoid and hominid groups of primates. So it incited Dr. Tracy Kivell further to opine “Their model means that there is a lot of parallel evolution across all apes. I still think the comparative studies with chimps and other African apes can provide a lot of insight into our evolution” (Barras, 2017). The technological advancement in the field of molecular biology with the advent of nano-technology intrigued the molecular geneticists and evolutionary biologists to take a challenge to testify the genetical profiles of apes and its related descendants among prehistorical primates so that helped the molecular evolutionists and genomicists to define and redefine the complicated phylogenetic implications to reveal an evolutionary history of modern humans in a convincible way. The evolutionary changes among the members of the primates, evolved during the Cretaceous Period, have been featured due to the major pattern of structural changes, possibly due to the changes of climate regime they went through to emerge in a distinct shape in the Tertiary Period and able to retain it further (Kundu, 2020). One distinguished paleoanthropologist Dr. David Begun, University of Toronto, Canada has critically studied the fossil specimen of Dryopithecus in 2015, and his backtracking of the molecular clock has revealed further that Dryopihecus has supposedly evolved around 12.5 MYA. Dr. Begun has further shared his investigations that Dryopithecus has supposedly originated and evolved in Africa and Europe and based on the analysis of molecular data and paleontological observations of Dryopithecus and other identical hominoid apes, he concluded that phylogenetically, Dryopithecus has found to be the close relative to the gorilla. Hence, it is a strong contender to be recognized as one of the LCA of modern humans. The intensive molecular studies of Dr. David Begun has to lead the contemporary evolutionary biologists to comprehend that particularly this prehistoric species and the chimpanzees used to coexist till 10 MYA (Pilbeam, 1996; Barras, 2017). The preponderance of the prehistoric fossil remnants of ancient hominid and hominoid skeletons of the ancestral lineages (of different geological age) of humans and apes have been found scattered over different fossil sites of the different part of the continents such as Africa, Asia, Europe, and Australia. Such dispersed remnants of archaic human fossils have made issues like the origin and evolution of humans complicated in determining the particular space and time of its emergence difficult. The compilation of a series of interdisciplinary, composite investigations like stereotypic analysis of paleontological pieces of evidence, along with conventional, comparative studies of anatomical, morphological, embryological, developmental biology

The Evolutionary Biology of Extinct and Extant Organisms

(like the development of the brain), supplemented with studies on the biobehavioral pattern of humans with other primates has helped the evolutionary biologists to focus on the anthropogenesis in preliminary level. Tremendous advancement of research works on molecular genetics and molecular anthropology has helped the evolutionary biologists to comprehend that around 24e35 MYA, the ancestor of humans, which has also been considered as LCA, most likely evolved in a certain location of Central Africa (Diamond, 1991; Zimmer, 2001). It has further been supported by the analysis of the data available from the mitochondrial DNA of paleontological remnants of the extinct primates and the DNA samples extracted from extant primates including humans (Prothero, 2007). The contemporary progress of advancement in the field of anthropological research works at the molecular level has helped the evolutionary scientists that tree-canopy dwelling elephant shrews (Elephantulus sp.) or jumping shrews had likely gone through evolutionary changes to be evolved as structurally unique mammals like Tarsier and Lemur, the lesser apes (Zimmer, 2001; Prothero, 2007). The evolutionary biologists have tried to accommodate lemurs phylogenetically to the other order and suborder of Primates Prosimii, which has considered to be the ancestral lineages of lesser apes and it had rendered the evolutionists to contemplate the hypothetical origin of Prosimian ancestors of humans. However, the evolutionary progress of modern human species, as well as the brief anthropological history of origin and evolution of anatomically modern human species from its archaic hominoid ancestor, have further been studied in three stages (Kundu, 2020): Primary Stage (Evolution of Pre-Ape-man): There are many paleontological shreds of evidence of pre-ape-man status, which might have also been considered a penultimate status of the human species have frequently been collected from different parts of Africa, and Asia, Europe, and a few numbers of such paleontological pieces of evidence are shared here: i. Aegyptopithecus and Propliopithecus: The conspicuous primate fossil of 40 cm long of gibbon-like (lesser ape) ape of 35 million years old (evolved in Oligocene) fossil has been found in Jebel Qatrani formation of Egypt, Northeast Africa. From the dentine, it seems that it has developed an omnivorous habit (Palmer, 1999). ii. Dryopithecus: It is an extinct primate, of 4 feet high, having close look to a monkey rather than modern apes, gracile jaw having incisors and molar teeth, having a pair of frontal arm and a pair of back legs of the same length, etc. The identical structural pattern of its wrists and suspended limbs has resembled chimpanzees that help scientists to predict its identical locomotion with chimpanzees. Palaeontological evidence of It has been reported from Europe, Africa, and Asia, and the molecular age-dating confirmed that it has evolved around 25e23 MYA, during Miocene (Palmer, 1999; Begun, 2004) iii. Parapithecus or Proconsul: This extinct primate has phylogenetically been considered as basal anthropoids, evolved between 40 and 33 MYA in Egypt

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during the early Oligocene. This extinct primate has been characterized by prognathous facial structure, sharp and pointed canine teeth, blunt nose, and the wide-open forehead like humans (Beard, 2002). iv. Pliopithecus: The molecular clock backtracking has indicated that this extinct primate of Miocene has supposedly evolved between 17 and 13 MYA, which has been discovered by famous anthropologist Edward Lartel from France. Later, it has been reported from Slovakia, Spain. It has morphological similarity to the gibbons, characterized by long limbs, hands, feet, and having brachiate locomotion (Palmer, 1999; Harisson, 2013). v. Sivapithecus or Ramapithecus: The backtracking of the molecular clock of the fossil remnant of this extinct apes have helped the scientist to disclose that it has been evolved around 12.2 MYA, during Late MiocenedEarly Pliocene, from the Siwalik Hills of the Indian subcontinent. It has been reported by Edward Lewis in 1932 but it has also been reported after a few years interval by LBS Leaky from Kenya in 1962. This ancestral predecessor of the humans had close structural similarity to the Orangutan. This extinct primate has been characterized by the monkey-like forehead and identical brain development but the chin, teeth and facial profile resembled the apes. From the structural similarity and supporting molecular analysis, it has been considered as early Hominidae, which is considered to be very close to modern humans. Secondary Stage (Evolution of Ape-man and Prehistoric man): There are a few numbers of paleontological evidence of Ape-man and the Prehistoric archaic humans, which has been considered as the most trustworthy evolutionary trail to touch the base of origin and evolutionary history of the human species that had been collected during many anthropological investigations from dispersed locations of Africa, Asia, and Europe and a few numbers of the major paleontological footprints have further been shared herewith: i. Australopithecus or First Ape-man: Australopithecus has referred to be the first ape-man, which has been reported from the Eastern part of Africa, which has reportedly been evolved around 4e3.3 MYA, and disappeared around two MYA in Pliocene and Pleistocene (Gray, 2010). The 1.5 m high fossil of Australopithecus has found to be possessed with the composite characters of prehistoric Ape in one end and the modern humans like robust and gracile body stature, absence of chin, the bigger-sized brain contained in the brain cavity of 800cc space, along with the possession of SRGAP2 genes, the developing neuron functions in the brain has been assumed and it has further been contemplated that the first modern human species has reportedly diverged out of the Australopithecus lineage around 3 MYA (Toth and Schick, 2005; Reardon, 2012). A few numbers of the famous fossil pieces of evidence of Australopithecus are as follows: a. Lucy: The complete fossil of an Australopithecus afarensis, a woman, has been discovered from Hadar, Ethiopia in 1974.

The Evolutionary Biology of Extinct and Extant Organisms

b. Taung child: The fossil remnant of the A.africanus, a young aged primate, has been discovered from Taung, South Africa in 1924. c. STS-71: The fossil remnant of A. africanus has been discovered from Sterkfontein, South Africa in 1947. ii. Homo habilis (Handy-man/first Toolmaker): The scientists have recognized the social cave-dwelling, one of the prehistoric Homo species recognized as Homo habilis which has reportedly been evolved between 1.8 and 1.6 MYA. H. habilis has been reported from East Africa by the famous paleoanthropologist Dr. Richard Leaky and his colleagues in 1961 for the first time, followed by its next level of appearence, rediscovered by Dr. Mary Leaky in 1971. Structurally, the first handy-man was 1.3e1.5 m tall, robust in stature, having characterized with bipedal movement, carnivorous in food habit, and able to hunt the animal for its prey. Scientists have considered that it has a biobehavioral ability to communicate by using sound and supposedly had a distinct division of work according to their sexual/gender orientation. Its brain cavity is covering a space of around 800 ccs. to contain the brain matter. The contemporary anthropological findings of Toth and Schick (2005) have contended that Homo habilis has reportedly been diverted out of an Australopithecus lineage, around 2.5e2 MYA and it has contemplated being traversed a long evolutionary trail of anthropogenesis in course of its origin and evolution to be evolved as phylogenetically close to the anatomically modern species of humans as well as scientifically recognized as Homo sapiens (Gray, 2010). Later paleoanthropologists have further reported that the members of Homo habilis had likely used the primitive form of stone tools to get the meat from the carcass (Jones et al., 1994). iii. Homo erectus erectus or Pithecanthropus erectus: Java man alias Homo erectus erectus has been reported to be evolved around 5 MYA and survived till 1 MYA, during the Pleistocene, and which has been discovered by the eminent paleoanthropologist Eugene Dubois from Indonesia (Java) in 1891. The erstwhile paleontological evidence of Java man revealed that it has evolved as the very close relative of modern human species with a robust stature and a height of around 5 ft with straight robust legs, used to have stout jaw but no chin, brow-ridges sticking out on retreating forehead, presence of large canine teeth had also been noticed, predominantly carnivorous and indulged in cannibalism. Supposedly, Java man had acquired the knowledge about the use of stone tools that were used to cut fleshes and it was contemplated to be used for lightning fire and cooking food, its brain cavity enlarged up to 950 ccs (supposedly having less space for cranial nerves, in comparison to modern human species). The most intriguing fact was that the Java man started forming small communities to get a closer step toward the modern human species. Paleoanthropologists assumed from their investigations that they might not know the usage of wood, bones, and language to communicate properly with each other (Swisher III et al., 2000; Choi and Driwantoro, 2007). iv. Homo erectus pekinensis or Pithecanthropus pekinensis: The prehistoric Peking man (Homo erectus pekinensis) from China has reportedly been evolved during

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780,000e680,000 years ago and its fossil remnants have been recovered from the fossil site of Zhoukoudian, near Beijing in China in the Pleistocene. Peking man has been discovered by the eminent paleoanthropologist, Dr. Davidson Black. The fossil specimen of the Peking man has been characterized by the prehistoric man of 1.6 m height, characterized by a tiny forehead with sticking brow-ridges, predominantly carnivorous and cannibal in food habit. The brain cavity of the Peking man is exceptionally big, which is around 1100cc, and this indicates that they got very close to the modern human species. So it is convincible that in course of development of the brain to acquire a high level of intelligence and unique form of brain function to move further ahead of other animals in terms of comparative evolutionary progress in the animal kingdom Peking man was a true transitional milestone between archaic hominids and anatomically modern human species. The Peking man was supposedly familiar with using bones, stones, wood as tools for hunting, familiar in using animal hides to make a dress, and communicate with each other by using some noise and sound (a preliminary form of language) (Shang et al., 2007; Schmalzer, 2008; Yen, 2014) and based on the investigation of fossil evidence and molecular evidence. Scientists have considered that “Peking Man” has been considered as the nearest ancestor of the modern human species (H. sapiens). v. Homo erectus heidelbergensis or Heidelberg man: Heidelberg man is found to be the archaic hominid of recent one and supposedly the youngest, the phylogenetic predecessor of Homo sapiens sapiens, evolved around 400,000 years ago, during Middle Pleistocene. The fossil specimen of the “Heidelberg Man” has been discovered by Professor Otto Schoetensack from the fossil sites in Heidelberg, Germany in 1908. Later some fossil remnants of “Heidelberg Man” had been found from East and Southern Africa and Europe. It has been characterized by the presence of identical dentine of Homo sapiens sapiens, bigger and stout jaw and largest cavity of the brain of almost 1300 cc space and this led to full-fledged growth of the brain in this prehistoric human predecessor to push. Hence, the “Homo” lineage has emerged as a unique form of modern human species. Some of the paleontologists are skeptical to address the Heidelberg man as the immediate phylogenetic ancestor of Homo sapiens sapiens due to the wide gap of the availability of satisfactory paleontological evidence in the span of 400,000 years (the tentative time of emergence of Heidelberg man) and 40,000 years ago which has been recognized as the period of the emergence of the modern human species (H. sapiens sapiens). Based on the contemporary phylogenetic analysis on molecular genetics and by examining the sample collected from fossil specimen of Heidelberg man from the fossil site of Sima de Los Huesos in Spain, the group of evolutionary biologists, under the leadership of Dr. Matthias Meyer, have tried to draw a convincible observation that “Heidelberg man” should better be categorized in the same phylogenetic rank under immediate ancestor of Modern mandas “Neanderthal lineage” or “Pre-Neanderthals” or “Archaic Neanderthals” rather than recognized under the prehistoric man (Meyer et al., 2016).

The Evolutionary Biology of Extinct and Extant Organisms

Tertiary Stage (Evolution of the true-man including modern human): A big number of contemporary palaeontological evidence of anatomically modern human species, which has been considered an ultimate status of the Homo sapiens sapiens have been collected from scattered fossil sites in the different parts of Africa, Asia, and Europe and some of the archaic hominid representatives of such paleontological evidence are shared herewith: i. Homo sapiens neandarthalensis (Neanderthal man): The Neanderthal Man had reportedly been evolved around 150,000 years ago and became extinct around 25,000 years ago. In 1856, Professor Johann Carl Fuhlrott had discovered the fossil of Neanderthal man from the Neander valley after Dusseldorf, Germany. The fossil specimen of the Neanderthal man has been characterized by the dome-shaped head with a prognathous facial structure. The cranial cavity of its head was around 1600 cc and the skull bone was very thick. It has been examined to be predominantly carnivores by nature and it supposedly practiced cannibalism. Scientists predicted from their investigations that Neanderthal man seems to attack his prey and animals with weapons made up of stone crafted weapons. It has been assumed further that these prehistoric humans used to live in groups; most likely to know the use of fire and cooking their foods, able to used dresses made up of leather hide of animals, and believed in performing some rituals. Their shorter legs with large body size (the males were around 164e168 cm high and the females were 152e156 cm high) and shape indicate that this group of immediate ancestors of modern humans was acclimatized to conserve heat energy. The contemporary molecular investigations revealed that there was genetic admixture in between Neanderthal man and the modern humans (20% of genetic molecular of the Neanderthal genome has been found in the modern human species) as it has been observed in its Asian and European populations rather than its African populations (Helmuth, 1998; Sanchez-Quinto et al., 2012). It helped the anthropologists to hypothesize that an instance of prehistoric interbreeding (or interspecific breeding) has naturally been occurred between the H. neanderthalensis and H. sapiens, the anatomically modern humans around 40,000 -60,000 years ago, and it most likely been taken place before the occurrence of prehistoric and maiden exodus of the archaic human beings out of the african continent, anthropologically recognized as “Out of Africa migration1” (Stringer, 2003; Liu et al., 2006). The Neanderthal man and the anatomically modern human species had supposedly evolved from Homo erectus ancestral lineage between 300,000 and 200,000 years ago (Sanchez-Quinto et al., 2012).

1

Out of Africa hypothesis: According to this hypothesis, the anatomically modern human species around 50,000 years ago and replaced Neanderthal with or without interbreeding.

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ii. Homo sapiens fossilis (Cro-magnon man): The Cro-Magnon Man or “fossil man” has also been recognized as “European Early Modern Human” or EEHM has supposedly evolved around 28,000 to 25,000 years ago and being pushed in the extinction in the Paleolithic age around 10,000 years ago (Reich, 2018). The famous British geologist William King has discovered it from Germany in 1856 and misidentified it as Neanderthal 1. Later on, Anthropologist Louis Lartet re-identified it as Homo sapiens fossils in 1869. The Cro-magnon man has been characterized by the key features like upright body shape and size with a 1.8 m high gracile skeleton with a big carinal cavity of 1600 cc, sharp nose, and wide forehead. The paleoanthropologists have contemplated from their investigations that Cro-magnon people were supposed to be hardworking; they were culturally advanced (as they crafted excellent cave paintings, made different hand-made jewelry like pendants and necklaces). Hence, they could be regarded as the intelligent predecessor of modern humans or Homo sapiens sapiens. From its size of the brain cavity (carinal space), evolutionists have tried to construe that the development of the brain of Heidelberg man seems to be the highest level among the Homo species or anatomically modern human species (Reich, 2018). iii. Homo sapiens sapiens (Modern man): Although conventional ideas of evolution tried to promote, that anatomically modern human species emerged from the ancestral phylogenetic lineage of Homo erectus between 300,000 and 200,000 years ago, although a group of contemporary molecular anthropologists has considered that it had been emerged out of another ancestral lineage, most likely from Neanderthals around 800,000 to 500,000 years ago (Reich, 2018). Regarding backtracking the evolutionary pathways of anatomically modern human beings, there are two opposing hypotheses: 1. “Multiregional Population”: According to this hypothetical model that has supported the survival of dispersed, regional populations of archaic humans and convergence of all of these archaic forms led to evolving “anatomically modern humans” utilizing a variation of clines,2 supported by the favorable action of natural selection, gene flow and genetic drift, etc., in Pleistocene (Wolpoff et al., 1994, 2000). 2. “Recent African Origin”: According to this hypothetical postulation, the idea of evolution of the anatomically Modern Human population of a single lineage has supposedly originated in Africa and drifted away as well as migrated further in other parts of the world pushed other archaic populations of primitive human species (Liu et al., 2006). It was difficult to determine the point time of origin and evolution of modern humans as the calibration

2

Clines: Cline is the measureable gradient of a biological trait of a species in its geographical range. The cline has referred to be as the genetic constituent (e.g., Allele) or phenotypic trait (skin color) of a species. So it may exhibit continuous gradation of character or sudden changes of the trait from one geographic area to the next one.

The Evolutionary Biology of Extinct and Extant Organisms

of the molecular clock as well it’s backtracking to standardize the tentative time of evolution for a specific biological entity involves further consideration of a standard deviation, that yields a period of time having a span of time of a few million years rather than pointing a prehistoric point of time. Naturally, it is quite challenging for the evolutionary biologists to backtrack the origin and evolution of any biological entity that can fit in that specific span of evolutionary time-scale (as the calibration has been set of few million years rather than undertaking a conventional calibration of time scale of few hours or few minutes), indicated by the molecular clock. However, in 1909, a unique effort of collecting and analyzing paleontological evidence from a fossil site of “Roc de Combe-Capelle,” France, from where the oldest but complete fossil of modern human species (Homo sapiens) has been initiated by a renowned German anthropologist. The molecular age-dating process has revealed that it was likely to be evolved around 12,000e10,000 years ago. The contemporary anthropological findings ascertained that the anatomically modern human species, Homo sapiens sapiens has likely to be evolved around 10,000 years ago from a place adjacent to the Mediterranean and the Caspian Sea in the Mesolithic period, having key features like the presence of a slender, gracile skeleton with a big head with the carinal cavity of the brain of 1450 cc space with the small-sized protruding chin, shorter anterior arms than the posterior legs, seems to have better ability to think and working potential; more social and cognitive potential in micromanagement and potential of executing the highest level of command/dominance on all living organisms. The accumulation followed by critical analysis of a huge volume of data collected and compiled by archaeogenetics and population geneticists promulgated that “Out of Africa” is one of the best convincible hypothesis that could define the most of the evolutionary history of anatomically modern human species but the inherent factors like the random occurrence of genetic admixture events have also been supplemented by the “Multiregional population model.” In 2013, Dr. Fernando Mendez and his colleagues had put forth a unique hypothesis based on their archaeogenetic studies to focus on the evolutionary history of anatomically modern humans. Dr. Mendez and his associates have revealed that the occurrence of prehistoric admixture of genetic molecules made it difficult to assume the evolutionary age of matrilineal and patrilineal representative of modern populations of human species. Nonetheless, from the contemporary perspective of molecular phylogenetics and genomics, the anatomically modern human species have logically been recognized as a distinct entity of LCA as well in the unique identity of “Mitochondrial Eve and Y-Chromosomal Adam,” respectively. The molecular depiction of ancestral evidence of Y-chromosomal lineage has found to be around 300,000 years old but no evidence of mitochondrial DNA or Y-chromosomal DNA has been found

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so far in the prehistoric humans beyond 500,000 years ago; naturally, it has indicated the tentative time of evolution of modern human species on Earth (Krings et al., 1997; Mendez et al., 2013). According to the literary expression as well as Shakespearean analogy to define the beauty of a rose flower a poetic expression has uttered with a phrase “a rose by any other name would smell as sweet” and such subtle expression is true in every walk of life even in the world of science. The logical practices of theoretical and conceptual considerations, followed by a review of some practical observations, it is possible to step out of a stereotypic vision of evolution to categorically discard its gradual upgrading unidirectional model and grasping a new perception that just considers that evolution has no directional goal to transform a species to get back its erstwhile, ancestral state (simplified) by traversing through the trail of regressive evolution or to achieve a better-derived state (advance) by traversing through the trail of progressive evolution. The consideration of the concept of progressive or regressive course of evolution is absolutely a judgmental perception that relies on the way of the mindset that incited us to consider it. Hence, a group of contemporary evolutionists has urged to narrate that evolutionary progress is an integral part of the adaptive process, where each biological organism including the intelligent primates like human species adapts to an environment, interacts externally and internally, and holds a niche to attain its sustainability. The external factors, as well as our environment, have intermittently gone through changes in the ambiance of our niche and we, as well as any organisms in that niche, try to readapt and that might lead the organisms and us acquiring some new traits (apparently looking like loosing of existing traits) to get back to a primitive, simple form (or similar form like erstwhile ancestors) to be alive. This kind of evolutionary progress has been referred to by the contemporary group of evolutionists as forwarding evolution as it is immaterial to them whether such process is regressive or progressive they judge the occurrence of such evolutionary process in terms of progress of time and space. When a brief account of comparative structural/anatomical analyses has been taken into consideration, then the structural development of the brain has been considered as one of the important factors that supposedly triggered the origin and evolution of modern human species on Earth. The irreversible structural changes of the brain have normally been witnessed with its size-wise gradual growth of brain (in terms of a carinal cavity) and functional complexities have been witnessed in every stage through the hominoid stages of the primates and it would certainly help in attaining the highest level in the hominid level of primates. As we have witnessed the highest level of development of the brain among modern human species, which has been found in the Cro-Magnon man with a carinal cavity of 1600 cc, has been found to be remarkably lesser in Homo sapiens sapiens (1450 cc), and it raised a valid question in the world of science whether we lost our most intelligent ancestor in this course of the evolutionary journey of human species or not. The anthropologists further noticed that the skulls of the Cro-Magnon Man fossils sustained fatal injuries, which pointed out to a possibility that they might

The Evolutionary Biology of Extinct and Extant Organisms

have been disappeared during the Paleolithic period due to an immense level of intraspecific or interspecific struggle. So little backtracking to the reversal of the development process of evolution that deals with controlling the size of the brain of Cro-Magnon Man to keep continue the journey of evolution of the Homo species with little lesser brain size, perhaps less brain function or little less intelligent form of Homo sapiens sapiens is the ultimate evolutionary swing of natural selection. Harry Lionel Shapiro, the renowned adjunct professor in the Department of Anthropology, Columbia University, has promoted the idea that was based on his predictive analysis of the disappearance and emergence of the new species of the genus Homo in the future to keep the evolutionary progress of Hominid progress. According to his predictive forecast in 1933, Professor Shapiro has proposed the name of Homo futurus or “Future man,” which would be supposed to be gracile, tall, more intelligent, less hairy, and the lifespan would be longer than Homo sapiens sapiens. But the entire consideration is based on prediction as we could not see the future being in present; only we could predict it. Naturally, we do not know whether Homo futuris would come up with a bigger skull with a larger carinal cavity and gracile or not. Rather, we should look at factors like reproduction ability versus greater intelligence; where the rate of reproduction has directly been favored or selected by nature as the primary factor of survival potential of any organism, and it is directly or indirectly related to the existence of the concerned animal. At the same time, the glimmering aura of intelligence, which is directly related to the overall development of the brain, is attributed to the better functional ability of any animal to be alive in a better way. If a trend of brain development is already there in the regressive mode (as we have studied the brain development of the brain of Cro-Magnon Man to its successor Anatomical modern human), the trend might not favor for better survival opportunity to our successor with more intelligence and a series of interfering factors like overall gene drifting, environmental pollution, climatic changes, gradual shrinkage of food chains, shortage of food, and the intraspecific struggle would less likely helping our successors to achieve better sustainability. In some exceptional situations, our perceptional view on somethings stalled our interpretations; if we would look at the morphological and anatomical stature of our phylogenetic ancestors, nobody would disagree about the gracile, stout stature of our prehistoric predecessor and they are looking stout, more powerful in comparison to the modern humans and our empirical analysis would help us to understand that the anatomically modern human species are looking smaller, conceivably having less stamina and seems to be less powerful in comparison to our ancestral hominoid and hominid counterparts. As long as the structural formation of the modern human is concerned, it seems to be in a regressive form as we are getting smaller down the evolutionary trail in comparison to our archaic, prehistoric predecessors. Now it comes in our mind that such evolutionary transformation must be steered under congenial patronage of natural selection, which has influenced such formation of shape and size of the concerned biological entity. Developmental biologists have contemplated that it is an act of compensation of investing more energy in

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the development of the brain instead of the body so strategically this world has two possibilities that would steer the evolutionary history of the human species in the future. Either evolution of humans would be initiated with a new human species with smaller body size but more intelligent or the future human species would likely have emerged with bigger body size but appeared to be less intelligent. It is a hypothetical situation, where the extinction of anatomically modern human species or the possibility of a regressive mode of microevolutionary progress depends on various factors, such as alteration of climatic changes, the preponderance of pollutants or its absence in the ecosphere, etc. It should be mentioned that the CO2 level of the atmosphere in the preindustrial revolution era has been recorded between 0.028% and it has increased exponentially due to reliance on the usage of fossil fuel in the era of the industrial revolution and the early half of the post-Industrial Revolution era and the concentration of CO2 has gradually gone down due to lesser reliance on fossil fuel in post-Industrial revolution era. So, hyper emission of carbon in the atmosphere had been raised to 25% in the late eighties and it would surge up to 100% during the middle of the 21st Century and the trend has continued until the invention of eco-friendly technological advancement would have taken place since the beginning of 1990s. Such a trend has further been coming under the consideration of contemporary atmospheric scientists as the recent investigations on emission level of greenhouse gases in the atmosphere between 1979 and 2004 have found to be still in the upsurged mode (Hoffman and Wells, 1987; Hofmann et al., 2006). Biological scientists have observed in their investigation that hemoglobin (Hb) in the bloodstream of modern humans is showing around 245% more affinity to absorb CO (Hb forms CO-Hb or carbaminohemoglobin) rather than absorbing O2 (whereas Hb reacts with O2 to form HbO2 or oxyhemoglobin). So, it shows that the formation of CO-Hb has remarkably decreased the O2 carrying capacity of blood and that further led to critical complications related to poor functioning of reproductive systems such as infertility, incomplete development of a human embryo, frequent miscarriage, and ectopic pregnancy. Furthermore, the atmospheric scientists have observed that the intensity of climate changes, an excessive level of atmospheric pollution by releasing different atmospheric pollutants like UV radiations, DDT, fluoride, etc., beyond the threshold level would raise serious health issues among humans like carcinogenic diseases, downgrading reproductive potential, the onset of acute neurotic diseases like Parkinson’s, etc. and high level of occurrence of such disease and widespread dispersal of such dreadful ailments among human communities might be found catastrophic to the normal existence of Human species on Earth unless the cause of such effect has not been taken into consideration. In several panel discussions on a science-related topic, particularly on the evolutionary history of humans in most times, the moderator would frequently ask a hypothetical question whether the anatomically modern humans could evolve back to apes in near future or not? Being part of a civilized society, we consider ourselves the rational animal and being a rational individual like us it would certainly difficult to comprehend ourselves as a naked ape with more hair and muscular body

The Evolutionary Biology of Extinct and Extant Organisms

as our future generation. However, the matter of fact is that it is not our discussion that would direct the mode of anthropogenesis to a certain direction; if our nature and environment prefer such form to ensure our survival it would certainly allow us to continue our journey of life we may need to take it to be alive. From a theoretical point of view, the derived species could be supplanted by its ancestral predecessor if such ancestral traits would are beneficial or suitable in the new or changed environmental conditions. The example of a microevolutionary journey of a parasitic organism like tapeworms (Taenia solium) needs to be referred here, which has been reported being diverted out of free-living basal species and eventually lost its digestive system in course of evolution. The parasitic tapeworm has taken shelter inside the gastrointestinal tract of a vertebrate organism, they became used to absorb the digested food from the host species. Hence, instead of spending energy on the digestive system and metabolism, parasitic tapeworm started diverting energy investment on reproduction system and that rendered its survival by relying upon simplified traits (without digestive functions or having the system as well) preferred over the ancestral traits to ensure its survival in changed scenario (environment). As long as a theoretical biologist accepts it conceptually, that anatomically modern human species could turn into a gorilla, chimpanzee, or ape-man like primates in course of regressive evolution, the next stage of the impediment of our understanding is whether there is any genetic theories or perception that would help to accept such unique ideas or it is just a utopian thought. If we nurture the stereotypic concept of the genome, it is clear to us that for any species, its unique identity is witnessed through the expression of its unique traits and that has been determined by unique genetic code, retrieved by its typical genome (bearing the unique identity of chromosomal architecture and inside the chromosome, the unique structural pattern of DNA helix). If we contemplate a hypothetical species X, contained a unique genetic code Z in its genome A, that indirectly shows that genome A is unique for the organism X. In course of evolution, Species X would go through the changes under influence of the external factors and all sort of little genetic alterations put together in its genome and after the accumulation of enough changes in its archetypical Genome A, species X would evolve into another unique species Y with modified structured Genome B. According to the conventional perception of speciesdspecies X and species B could never be able to breed (intergeneric breeding) to generate any viable offspring. However, the adaptive radiation of the tree finches in the Floreana island of the Galapagos, the archipelago has proven that interbreeding between the allopatric species is possible as we witnessed that large tree finch Camarynchus psittacula become extinct after it had gone through introgressive breeding with medium tree finches, Camarhynchus pauper. Such evolutionary incidents have indicated further that introgression of genomic constituents is a reality where a species could pass its genetic constituents to another species before getting disappeared. When we would look at the genome profile of apes and modern humans, we can notice a cytogenetic uniqueness of anatomically modern human species where it has a distinct Chromosome number 2, which is also been found in apes like gorilla or chimpanzee in a slightly different orientation. The molecular geneticists have

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considered chromosome number 2 as a fused structure of two separate chromosomes, existing in the ape cells (Rejon, 2017). It is convincible that the fusion of such two pieces of chromosomes in apes led to the evolution of the modern human species. It has further been interpolated that the fusion of two chromosomes has led to the fusion of two centromeres and that likely dissolves to give a unique form of Chromosome number 2 (Rejon, 2017). Though, it is convincible that hypothetical changes of external factors and internal factors like mutations could trigger the splitting of chromosome number 2 to split in half. If such genetical changes of the profile of the human genome has been assisted by the adaptive radiations, the possibility of expecting ape-like organism in the future is most likely to be a reality. We could argue whether such changes of chromosomal architecture are possible or not; we need to look at the occurrence of genetic disorder like “Wolf-Hirschhorn syndrome,” which has been triggered by the deletion (aberration) of a part of the chromosome number 4 of modern human species and that might slow down the growth and IQ development of it. Likewise, another genetic disorder, which has been popularly known as “triple X syndrome” in females, where instead of 2x chromosomes in females, a set of 3x chromosomes have been noticed in their chromosome, leading to poor development of communication skills (like delayed speech). Any chromosomal abnormalities that have normally been found in the embryonic stages of humans could end up in the miscarriage of a fetus. As long as the chromosomal anomalies would have been transferred from one generation to the next one, the aberration or deletion or duplication of chromosomes or the modified genetical profile would have altered the phenotypic traits of the concerned animal, there is a chance of missing a chunk of genetic message or piling up of new genetic messages and either way an ambiguous situation might have emerged that would deter the organism to get back the ancestral or basal state of the genetic configuration, that the ancestral species likely to inherit. We consider mutation is a kind of random process. Hypothetically, if the species X emerged out of the species Y after going through the stepwise mutations down the trail would be 6-4-1. It is theoretically convincible that species Y needs to go through the evolutionary pathway in the reverse direction from 1-4-6 and it might have helped the emergence of species X out of the species Y. There is a stereotypic mode of a mutational shift of nucleotides that has been witnessed in the molecular level when pyrimidine (nitrogen base) Cytosine(C) mutate into pyrimidine (nitrogen base). In another way, Thymine (T) during the transcription process, at the time of formation of RNA or RiboNucleic Acid from DNA or DeoxyriboNucleic Acid, happened to be mutated in a short period. So, the natural evolution or laboratory-based reconstruction of the DNA thread of Ape has not an easy task as point mutation (where a single nucleotide would change the sequential configuration of DNA and RNA thread) could render it difficult to judge, which particular Thymine base needs to be corrected to Cytosine bases to get closer the right DNA thread of the ancestral successor of the modern human species as random nature of mutation of molecular sequencing messed up the original sequence of DNA of the human predecessor.

The Evolutionary Biology of Extinct and Extant Organisms

To have a feasible explanation of the genetic admixture or interbreeding issues, the preliminary effort of DNA hybridization between anatomically modern human species. The Neanderthals have been found unique when a part of nuclear DNA would have been linked to extinct Neanderthal yield no sign of mitochondrial DNA of Neanderthal concerning its origin and evolution that has been detected and that is supposed to be maternally inherited in mammals, specifically in primates (Krings et al., 1997). It led the molecular biologists as well as evolutionary biologists to comprehend that a male Neanderthal would like to meet its counterpart mate with a female anatomically modern human partner to yield fertile offspring whereas the mating of a female Neanderthal to a male partner of anatomically modern human species would rarely yield any offspring (Mason and Short, 2011). Anthropologists figured out that anatomically modern humans arrived Mediterranean region around 45,000e43,000 years ago and before going to extinction Neanderthals used to live there so cultural and biological interactions between these two populations might not be ignored (Higham et al., 2014). Though there were some hypotheses regarding the extinction of Neanderthals like out committed by the anatomically modern human, catastrophic activities like volcanism or climatic changes tried to give some ideas to justify the extinction of Neanderthals on earth but the interbreeding hypothesis seems to be most plausible as it stated that Neanderthals interbreed with anatomically modern human species and as a result of introgressive hybridization, Neanderthals become extinct. The presence of 20% of the Neanderthal genome in the gene pool of modern human species indicated it. A minority group of scientists having expertise in physical anthropology has contemplated that Neanderthals have been genetically absorbed in the genome of Cro-Magnon in course of interbreeding. Yet such observation has sharply contradicted the “African origin hypothesis” but it indicated that the European descendants must have an anthropological link to the Neanderthals. Dr. Hans Peder Steensby, one of the renowned anthropologist from Denmark, has studied a comparative account of the Cranial data of prehistoric humans and strongly supported the inbreeding theory and argued furthermore that Danes, Dutch inherit a part of Neanderthaloid characteristics to pronounce that Neanderthals “. are among our ancestors” (Steensby, 1907). In another example, identical perceptions have been upheld when the paleoanthropologists have referred that the ancient, and well-preserved mummy in Europe has borne a substantial percentage of Neanderthal ancestry (Hawks, 2012). There would be another analogy in support of genetic introgression of the Neanderthaloid genome by referring to the dream of a motorist who desired about driving a vehicle in top gear to move forward and overtaking other cars, it would not happen all the time even on the highway sometimes when the motorist needs to shift from the first track to the next one. Eventually, that motorist needs to slow down sometimes depending on the traffic on the road. Most often, that person needs to go on reverse gear, especially when there is bottle-neck traffic on the road. Hence every unique situation led him/her to make such a decision, particularly when dealing with traffic flow on the narrow or one-way road. The matter of fact is that in reverse gear nobody could drive on a long way but it is necessary sometimes, to avert an

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accident or to move on. Hence, consideration of the present situation and stepping back accordingly has rewarded us often to move forward further in the future and the evolutionary journey of any biological entity is no exception. Hence, possession of a high level of developmental and functionally potential brain structure (or functions perhaps), Cro-Magnon Man, which has supposedly evolved out of Neanderthal root-stock, might not be able to survive for a long time but the emergence of modern anatomically human species has ensured a level of sustainability even being bestowed with lesser brain development. However, evolutionary biologists and anthropologists should consider such “Neanderthal Consequence” of the prehistoric human species, as the combined effect of selection, gene flow, and genetic drift would alter the genetic frequency to form a new species out of the shadows of the founder effect. The natural occurrence of the founder effect among “anatomically modern human species” could have yielded a new Homo species in the future and hypothetically that unique entity should be recognized as “Future man” or Homo futurus. The ultimate challenge of survival of us Homo sapiens is there if Homo futurus evolved shortly as nobody knows whether another “Neanderthal Consequence” might drag the Homo sapiens in the future to be disappeared as a consequence of introgressive breeding with Homo futurus or not and that might push this anatomically modern human species Homo sapiens to be absorbed in the genome of Future man. And we do not know whether the end of this evolutionary journey of anthropogenesis, whether Homo sapiens might gladly share its precious genome to Homo futurus, which encrypts with our history of cultural, social, and scientific development, before being disappeared from this blue planet forever.

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Mitochondrial Eve and Y-chromosomal Adam on planet Earth: Humanity’s metaphoric missing-link between prehistoric past and contemporary present

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“We are looking at the beginning of what we would call Homo sapiens .. What I have found astounding is that it clearly shows we are all one human family. The phylogeny in Africa goes back to the origins of our species, but the fingers of L3 are touching Europe and Asia, saying that we are all closely related” Douglas C. Wallace

To decipher the history of origin and evolution of the modern human species, molecular geneticists, genomicists, and evolutionary geneticists had started their investigations on human DNA since the 1980s. It is quite thrilling to witness that scientists have concentrated their primary focus of investigations on the genes, contained by mitochondria (the ultimate powerhouse of the cell), each of these cell organelles carries its unique, circular-shaped, ring-like DNA, called mitochondrial DNA or plasmid DNA. The origin and evolution of the mitochondrial DNA, which has also genetically been recognized as extranuclear DNA, has contemplated being originated and evolved around 2 billion years ago when an act of successful introgression or engulfing of an oxygen-breathing bacteria had accidently been accomplished by the unicellular ancestor of the modern human species. The reproductive biologists have observed that at the time of fertilization of an egg by sperm, the male gamete is found to be successful in injecting its nuclear DNA to the female gamete, but it failed to deliver its mitochondria to its female counterpart. So, in the postfertilization stage, thousands of mitochondria of female gamete or egg remained unaltered and contended by the zygote as well as future offspring. So, the copies of mitochondrial DNA in any offspring are considered being its maternal inheritance, whereas the nuclear DNA of it has normally found to be inherited through an act of fertilization from its paternal side. So, if we would go back to have a clear idea of the consistency of acquiring the maternal inheritance of the offsprings to go back several generations by examining the mitochondrial DNA, possessed by its cell, we could see that every offspring has consistently inherited the mitochondrial DNA from its The Evolutionary Biology of Extinct and Extant Organisms. https://doi.org/10.1016/B978-0-12-822655-1.00019-2 Copyright © 2021 Elsevier Inc. All rights reserved.

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mother, which was found to be descended from mother to offspring and passed on from one generation to the next since its evolutionary emergence and remained uninterrupted, unless it had gone through mutational changes (which is a normal incident) even after traversing few hundred of thousand years (Zimmer, 2004). So, the mutated mitochondria have been found to be passed on from mother to its offspring, and whenever the offspring become a mother over time it passes on its mitochondria to its next and future generation of offsprings in a consecutive way. So, it rendered the molecular geneticists to recognize distinctive mutation of mitochondrial DNA as the molecular foot-print to utilize it as an essential tool to examine modern human species into a single grand genealogy to unfurl the evolutionary history of that primordial woman, from whom we and our predecessors had inherited the mitochondrial DNA, the precious maternal inheritance for generations after generations through ages (Zimmer, 2004). Based on the molecular evidence, the detailed human family trees have successfully been reconstructed by a group of geneticists and evolutionary biologists, led by Douglas C. Wallace, one of the leading evolutionary and molecular geneticists from University of Pennsylvania and Children’s Hospital of Philadelphia in Pennsylvania, USA, who explored using mitochondrial DNA as a molecular marker and was able to reconstruct the human family tree based on human mitochondrial DNA (Wade, 2000). In March 2000, an interesting article had been published in the “American Journal of Human Genetics” where Dr. Wallace and research colleagues have been engaged in exploring the root of the mitochondrial tree and they have identified the Kung San, the African hunter-gatherers of the northwestern Kalahari desert in South Africa as the ancient population, found to be the proximity of the basal end or root of the human mtDNA tree, reconstructed by them (Meyerhoff, 2013). The scientists have recognized the population of Biaka pygmies of Central Africa, considered to be of identical evolutionary age and found to be restricted in distribution in similar isolated geographical regions. Dr. Wallace has contended that relative isolation of such ancestral human populations supposedly rendered its little or no changes in its mtDNAs in respect to its predecessors of these historic human populations and it inspired Dr. Wallace to state “We are looking at the beginning of what we would call Homo sapiens” (Wade, 2000). Janusz Meyerhoff (2013) in his popular nonfiction “The Story of Us” has referred the unique research investigations of Professor Bryan Sykes and the coresearchers, of Oxford University, United Kingdom, who have discovered seven matriarchal human lineages or seven ancestral mother groups, from whom all Europeans supposedly descended out and those seven ancestral evolutionary lineages have popularly been regarded as “Seven European Daughters of Eve.” The key success of this experiment is due to the technical advantage of the scientists to work with mtDNA, as it has been noticed that the rate of mutation in mtDNA is relatively very low (which is around 1 in 10,000 years) in comparison to nuclear DNA. However, Professor Sykes and the coresearchers had extracted the mtDNA sample from the mouth cavity of 6000 samples, randomly collected and analyzed and shared their findings that revealed that all those ancestral, matriarchal lineages lived between 8000 and 45,000 years ago (Meyerhoff, 2013). The most

The Evolutionary Biology of Extinct and Extant Organisms

unique findings of this research investigation have further ascertained that each of “Seven European Daughters of Eve” was found to be emerged out of “Lara clan,” one of the ancestral human clans, existed in the African continent (Meyerhoff, 2013). It is quite interesting to notice that an earnest effort has been made to take this academic research to the next level to check its commercial potential. In April 2000, a unique business venture, called “www.Oxfordancestor.com” had started its operation in the United Kingdom, with the offer to tell its customers, which of the particular lineage of seven daughters of Eve, they have descended from. Dr. Bryan Sykes of the University of Oxford was the founder of this company. It was convenient to work out for European communities as the entire European communities belong to any of the seven mitochondrial lineages (exclusively traced out in Europe) out of nine mitochondrial lineages of mitochondrial Eve (Wade, 2000). For analyzing the DNA sample, www.oxfordancestor.com, the genealogical investigating company had introduced a simple protocol of collection of the sample, from its clients, by simply collecting the saliva sample from the mouth cavity by smearing a cotton swab, technically called buccal swab and they charged $180.00 for each test. To make this genealogical investigation (based on mtDNA analysis) in a mythological framework, pertaining with a determination of evolutionary lineages (that any individual belongs to a particular haplogroup) of any living individual to trace back its genetical and evolutionary inheritance from the particular matriarchal lineage of African Eve, Dr. Sykes has given names to these seven lineages (seven daughters of Eve) and put the necessary information related to their evolutionary time of origin. It has been appeared to be an interesting effort to know our genealogical identity, as well as the evolutionary root of someone, belongs to haplogroup U, has reportedly descended from Ursula, likely to be lived in the northern part of Greece around 45,000 years ago or someone, that belongs to haplogroup X, reportedly descended out of Xenia, lived in Caucasus mountains around 25,000 years ago (Wade, 2000). The most interesting information needs to be shared here that Dr. Sykes has stepped forward later to expand his arena of genealogical investigations as he engaged in examining the evolutionary history of the rest of the haplo-lineages all over the world, specifically the 14 lineages in Africa and 16 lineages in Eurasia and Americas (Wade, 2000). Allan C. Wilson, The professor in the Department of Biochemistry, University of California, Berkley, USA had studied the mtDNA samples, randomly collected from 147 individuals from the geographical regions of Africa, Asia, Australia, Europe, and New Guinea, reviewed the family tree reconstruction, observed that an unusual kind of mutation was possessed by the genomes of four people from different geographical locations and tried to present a feasible explanation to justify it as they had likely been descended out of a common maternal rootstock, rather than a remote possibility of the emergence of that unusual kind of mutation happened in the same location of the gene of those four different individuals, originated in different geographical locations at the same point of time, accidently (Zimmer, 2004). Wilson along with his research associates (Zimmer, 2004) had completed a reconstruction to construe that overlapping of all evolutionary lineages have

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supposedly merged to major five genetical linages, emerged from respective continents coalesced to a common ancestor, but it has also been observed that rest of the seven individuals of African descent have formed a second major evolutionary lineage. Wilson and his research teammates have tried to present a convincible explanation of their experimental observation as they have contended “the African branches of the tree had acquired twice as many mutations as the branches from Asia and Europe” (Zimmer, 2004). Wilson and his research team members have critically reviewed their experimental results and claimed that the origin of humanity had emerged in Africa and over time this main evolutionary lineage of African descent had been spread out in course of (Out of Africa) intercontinental migration of this ancestral human population (Ellis, 2003; Zimmer, 2004). In this regard, it needs to be mentioned here that in 1933, the oldest international burial of 100,000 years old, one of the important archaeological and site has been discovered by R. Neuville in the Qafzeh cave nearby Nazareth, Israel (geographically adjacent to Africa) where the age-dating examination had ascertained that the body, found in the grave found to be around 60,000e80,000 years old, paleo-anthropologically reconciled the tentative time-line of the historical migration of human species, stepped out of Africa first-time (Gugliotta, 2008). According to the paleoanthropological narrative, the anatomically modern man or Homo sapiens had supposedly left Africa to reach Asia first followed by Indonesia and finally arrived at Australia around 50,000 YBP (Meyerhoff, 2013). It has further been observed that the modern men have reached Europe from East Asia first time around 40,000 YBP and on its way they have met Homo neanderthalensis or Neanderthal man, one of the valiant archaic human representative (who had reportedly been survived Ice Age in Europe for 250,000 years), and possibly being pushed to the brink of extinction by our ancestors in less than 10,000 years the evidence of interbreeding and genetic introgression has also proved that our ancestors have gone through an intimate relationship with this archaic human predecessor (Meyerhoff, 2013). So, its genetics as well as evolutionary genetics about accumulation and analyzing the DNA sequencing data either from mtDNA or from the Y chromosome, have been found to play a cardinal role in helping out those scientists who engaged in the genealogical reconstruction of the past of modern human species. It is a matter of fact that the lineage of trees of their family tree, reconstructed are mainly based on the principle of genetic differences, found in the noncoding regions of DNA as well as genes naturally having least effect on the body and it is found to be little chaotic to determine the exact evolutionary age (as it has found to be varied, determined by different investigators, in their unique research models) of any particular ancestral lineage of human species, as the source of DNA, worked with and fine calibration of molecular clock varied in distinct research protocols adopted by the scientists, yet the empirical success of the results from such genealogical investigations, should not be underestimated. However, the key findings of all genealogical investigations have found to have appeared as unique findings, that intends to project that backtracking of all evolutionary lineages empirically coalesced to a starting point, the evolutionary marathon of humanity, once started at “Eden,” the metaphoric

The Evolutionary Biology of Extinct and Extant Organisms

birthplace of humanity and which is supposedly uncharted somewhere in the African continent. It has been resonated from the statement of Dr. Peter A. Underhill of Stanford University, USA, the eminent evolutionary biologist, who has engaged in genealogical reconstructions of humanity based on DNA sequencing from Y chromosome for decades as he claimed further “We are all Africans at the Y chromosome level and we are all brothers” (Wade, 2000). The collaborative studies of palaeontological evidence of ancient human fossils, paleo-anthropological evidence of tools, used in prehistoric time, molecular footprints as well as genealogical pieces of evidence related to the evolutionary history of humanity for the past few decades have made it clear that the extant genealogical lineages of men and women have emerged out of the evolutionary cradle of archaic genetical and genomic root-stock of “hunter-gatherers,” who once roamed around somewhere in Africa before a sect of it stepped out of this continent to explore the rest of the world, around tens of thousands of years ago. Even if we try to introduce ourselves nowadays and try to establish our racial identity based on the variation of melanocytes of our skin or structural orientation, the color of our hair or eyes and several visible traits of the diverse community of 1.6 billion people on planet Earth, this kind of superficial identity is a pseudoscientific approach to trace back our true identity, in the perspective of evolutionary genetics, we could not ignore our genetical identity and denounce or history of origin and evolution to accept the truth that we are all descendants of our African ancestors. Once the scientists have come up with their findings of Africa as the sacred birthplace of our ancestors around tens of thousands of years ago, it started haunting our minds exactly where it happened? In absence of a unanimous observation of paleontologists, evolutionary geneticists, paleoanthropologists, and other interdisciplinary scientists, some hypothetical scenarios have been floated over from time to time, when a group of scientific analysis put their claim for Ethiopia or Kenya of eastern Africa, another group of scientists tried to substantiate their claim in favor of South Africa, and amid such ongoing bickering of claim and counter-claims, the third group of evolutionary scientists is very much optimistic to track down the location of Eden, the lost and sublime abode in the history of humanity, that would end this evolutionary standoff, that we are going through for last few decades. At this point only we could assume that if we would consider the principles of biological evolution, we could assume that such evolutionary birthplace of humanity supposedly visualized like a strange and sublime “stone age paradise,” where the omnipotent primate of Anthropocene, the modern human species as well scientifically recognized Homo sapiens, would have descended out of their archaic human predecessors and gone through fine nurturing the intellects along with trimming of their behavioral and cultural skills to have emerged as the most competent hominin on this planet Earth. It appeared to be as a simple, panoramic picturesque of arcadia when we tried to comprehend about our evolutionary homeland but a serious of an earnest endeavor of the evolutionary scientists found to be remaining unsuccessful till now that rendered shaken the tenacity of the scientists who have engaged for last few decades to track down the location of our birthplace. The lack of tenacity stemmed out the surging of

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skepticism in a group of evolutionary scientists regarding its actual existence and it has been resonated in the words of David Reich, an eminent geneticist from Harvard University, USA as he firmly expressed his skepticism: “When it comes to human ancestry, there was no Garden of Eden” (McKie, 2020). So, whenever the cumulative efforts for the last few decades in quest of the Garden of Eden in the uncharted territory of Africa undertaken by the paleontologists, molecular geneticists, archaeologists, and evolutionary biologists and the interdisciplinary scientists have appeared to end on a dead end, the researchers have taken a less-known path to define the evolution of Homo sapiens and have made an effort for a feasible explanation about our evolutionary homeland in Africa, auspicious birth of our ancestors have supposedly taken place around tens of thousands of years ago. The alternative proposition of evolution of our ancestral lineages was found to be convincible as the researchers have claimed that the anatomically modern human species have unlikely to have emerged as a solitary ancestral group of modern human species in a particular place in a particular period, rather our predecessors have contemplated being evolved for half a million of years, where a discontinuous multitude of Africa has contemplated being the evolutionary cradle of anatomically modern human species on planet Earth. In support of this hypothesis, Professor Chris Stringer one of the eminent paleoanthropologist and the visiting professor of University College London, Archaeology, UK, had firmly stated “the immediate predecessor of modern humans probably arose in Africa about 500,000 years ago and evolved into separate populations” (McKie, 2020). Professor Stringer has elaborated his findings, based on his research investigation, made on this topic for the last 2 decades as he contended that in the adverse time, when the environmental ambiance made the Sahara desert dry and desiccated zone, the fragmented populations of ancestral human species struggled for its existence that supposedly pushed a big number of the human population to the brink of extinctions, whereas a small number of human populations have ensured its sustainability in this adverse environmental regimes, so whenever, the reversal of this adverse environmental conditions took place, the ultimate survivors of those fragmented populations have managed to increase its population size in the backdrop of congenial environmental conditions, and in such condition, the random exchange of genetic materials have been taken place in intraspecific level (McKie, 2020). Furthermore, Prof. Stringer had observed that this type of events happened intermittently in different places of Africa for the next 400,000 years, and it has further been contemplated that the modern version of human species, those are found to be in the well-diversified state all over the world likely to be occupied all inhabitable niches in such way. To move a step forward, Dr. Eleanor Scerri, one of the eminent experts on human evolution, from Max Planck Institute, Jena, Germany has tried to define the evolution of modern human species in her “mix-n-match building blocks evolution” hypothesis where she has claimed that the anatomically modern human species had likely descended out of a genetically interlinked group of people, splitting out and merging of those lineages had likely to have happened, spatiotemporally, in course of its evolutionary journey of human species over time since its maiden

The Evolutionary Biology of Extinct and Extant Organisms

emergence, so the anatomically modern human species had emerged in distinct populations in different regions of the world, with distinct physical features and cultural habits as a result of mix-n-match of ancestral and modern traits, inherited as well as accumulated from their immediate and distant evolutionary cousins (McKie, 2020). Normally, it has been observed that the animal species with a large population with a widespread distribution over a large geographical region like across the continent is usually found to be fragmented into a subspecies over time and in course of microevolution all these subspecies likely to have emerged as new species. The experts involved in different aspects of the evolution of modern human species have contended that it has not happened (fortunately) and the probable reasons that likely to stop happening so for modern human species have been considered the “longrange social networking” spree of modern human species that supposedly slowed down the rate of human evolution but promoted its emergence “en masse across Africa” (McKie, 2020). So, the bottom line is that if we consider long-range social networking is one of our important behavioral traits, it has likely played a cardinal role in our evolution. A feasible extrapolation, that has supported the interpretation, mentioned earlier has further been resonated by the geneticist Professor Mark Thomas of University College London, UK, who strongly argued that its accumulation of a set of interrelated factors like culture, knowledge, belief, and its recognition of social values are found to be most important issues could ensure our sustainability, specifically in the dawn of civilization when it has been found to be initiated with tribal populations (McKie, 2020). Furthermore, Professor Thomas had clearly defined that cultural inheritance has played the most important role that attributed the sustainable evolution of a social animal like anatomically modern human species, so he firmly stated “Without culture, we would be dead .. We know things today that we were worked out by ancestors tens of thousands of years ago and have been passed along over the generations. Culture is our life-support system” (McKie, 2020). Let us go back to square one to find it out whether there is any justified reason to comprehend a hypothetical possibility to a belief that the origin and evolution of modern human species have been taken place from a particular location in Africa and it is quite intriguing that it has been supported in the early research works of the eminent molecular biologists like Dr. Allan Wilson of University of California, Berkley, USA, who along with a bunch of promising molecular biologists have successfully analyzed the molecular footprints of mitochondrial DNA (an important genetical material, that we inherit from our mothers) and compared its variations, the samples collected from individuals, representing global populations (McKie, 2020). The key research findings of Dr. Wilson created a buzz when he referred his reconstruction of the giant family tree of humanity and claim its root in the African continent with affirmation and contended further that it did not only claim to trace back to a large group of historic population of Homo sapiens, it put its legitimate claim based on mitochondrial DNA analysis that the entire population of anatomically modern human species has been emerged out of the matriarch lineage from the African continent, who has popularly been recognized

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as Mitochondrial Eve or African Eve. So the possible extension of such research findings helped to create a notion that African Eve is the universal mother of humanity and the evolutionary birth of the modern human species has taken place somewhere in Africa and it has initiated a perception of single-origin of Homo sapiens, supposedly traced back somewhere in the African continent (perhaps in Botswana) (McKie, 2020). On the other hand, in an analogous concept, the contemporary investigations on the DNA sequences from Y-chromosome helped Dr. Fernando L. Mendez, the eminent population geneticist of Stanford University, USA, and his colleagues primarily noticed that the Y-chromosome determines maleness in humans, published their work in American Journal of Human Genetics and they further contemplated that the Y-chromosomal most recent common ancestor as well as popularly recognized as Y-Chromosomal Adam or African Adam is the most recent common ancestor (MRCA) of all males (Mendez et al., 2013). The published works of Mendez and his colleagues have pointed further that their investigations ascertained that there is a great variation in the DNA molecules of the Y-chromosome and it is getting increased over time, which rendered them suggest that emergence of Y-chromosomal Adam had supposedly taken place in West Africa (Mendez et al., 2013). So an effort of the evolutionary biologists to put together African Eve and African Adam putting them together in the same story to have a bigger family had not found to be happy ending story as African Eve had reported being inhabited in one end of the African continent whereas the African Adam had reported being appeared from a distant location of the same continent and that is not convenient to start planning for a large family. The paleontological shreds of evidence failed to project any paleoanthropological resolution, unequivocally that emergence of humanity happened in a particular location of Africa as the fossil evidence of Lucy (AL288-1), had been discovered in Hadar, Ethiopia, by the eminent paleoanthropologist Donald Johanson of Cleveland Museum of natural history, USA, in 1971 and who claimed that 40% of this female hominin had matched to anthropologically archaic human species Australopithecus afarensis (paleoanthropologically represented by the fossil specimen “Lucy” in the scientific arena), supposedly emerged in around 3.2 mya (Johanson and Wong, 2009). For a number of times, Dr. Johanson has been asked whether it is appropriate to use the term missing link to introduce “Lucy” (the representative of Australopithecus afarensis), the female archaic human fossil specimen as the evolutionary link between African apes and anatomically modern human species, that is, ourselves. In reply, Dr. Johanson has said “Australopithecus afarensis is not the ‘missing link’ between apes and humans, it is one of the important evolutionary intermediaries between more apelike creatures and more recent, more [modern] human-like ancestors” (Johanson and Wong, 2009). On the other side, one of the fossil expedition in the Blombos cave, South Africa in between 1997 and 1998, the paleoanthropologists have analyzed the artifacts and human fossil evidence and came to a conclusion that geologically the archaic human lineages in this geographical location supposedly belong to Middle Stone Age (supposedly emerged between 100,000 and 70,000

The Evolutionary Biology of Extinct and Extant Organisms

YBP) and descended out of Neanderthal rootstock (Grine et al., 2009). From the palaeontological review, it is difficult to establish that emergence of ancestral human lineages had emerged from any particular location of Africa in a particular period. Although preliminary analysis of the DNA sequences of Y-chromosomal DNA has tried to project that African Eve and African Adam had lived around the same period (Cann, 2013), the investigations on the archaic Y haplogroup by Dr. Eran Elhaik of University of Sheffield, UK, and his coresearchers had shaken the foundation of conventional biological models of mitochondrial Eve and Y-chromosomal Adam, once it has been published in the European Journal of Human Genetics in 2014, as it pushed back the evolutionary age of African Adam 8300 years older than the conventional model revealed with and it challenged the earlier observation that claimed that origin of Y-chromosome has likely to have happened in a different species (through interbreeding) that projected the age of Adam almost double of its original evolutionary age (Elhaik et al., 2014). Furthermore, Dr. Elhaik had tried to present his narrative of the existence of more than one African Adam and African Eve, which has indirectly invalidated the earlier perception of the emergence of humanity from any particular geographical location in a particular period as he claimed “It is obvious that modern humans did not interbreed with hominins living over 500,000 years ago. It is also clear that there was no single Adam and Eve but rather groups of Adams and Eves living side by side and wandering together in our world” (Elhaik et al., 2014). It left the quest for the evolutionary birthplace of humanity in Africa to remain unaccomplished. So, it has emerged as a new perception regarding the origin and emergence of humanity that the slow evolutionary attribution of modern human species on planet Earth is just not a matter of coincidence it is the inevitable process of the successful emergence of modern humanity with its diverse format of the multitude as modern human species has not emerged with all its genetical, biological, and cultural traits that might help to distinguish a population from another one it supposedly developed, accumulated, and emerged. As the social networks of the modern human species broadened, related to its integral history of migration to explore a new inhabitable niche, invasion to preexisting habitats, occupied by the different colony and merging with them, extinction of archaic lineages, genetic introgression with archaic lineages to inherit the unique genetic principles, etc., rather than it could be defined in the conventional model of family trees or evolutionary trees, that tried to give an impression that the branches of the tree usually come out of its main trunk, so coalescing of the diverged branches would help out to track down its root. It is difficult to ignore that cultural inheritance, which has descended from the ancestral lineage to the contemporary derived lineages of modern human species, has rendered our evolutionary journey to shape so we could not ignore the reality that culture is the evolutionary support system of our history of emergence, without which we are just like other primates, the conventional outcome of biological evolution on Earth. So, whenever Chris Stringer claimed “There is no evidence at all that one single part of Africa produced all this modern behavior,” it makes sense (McKie, 2020).

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With due respect to the evolutionary tree model, John Hawks, the renowned anthropologist of the University of WisconsineMadison, USA has gently expressed his concern that as a metaphor, it might be considered as an important model but it might narrate the history of humanity in a wrong way in reality and he stood behind his “braided stream” analogy, where he tried to define the history of humanity as several braided rivers (has resembled the multibraided crane wire rope), those weaved in and out to go through the evolutionary labyrinth of tens of thousands of years before getting emerged as a huge water channel like rivers that presenting a convincible picture of the evolution of humanity (Hawks and Cochran, 2006). Based on the analysis of molecular markers of human species, since last 2 decades, Dr. John Hawks started resonating in favor of mix-n-match hypothetical origin of humanity (i.e., origins and evolution of humanity in more than once in more than one place), postulated by Dr. Chris Stringer, and he further contended with the firm assertion “. evidence began to emerge in 2010, showing that most living humans carry at least a small fraction of Neanderthal genes. Later that year, the Denisovan genome confirmed that some living human populations have genetic ancestry in multiple archaic human populations not yet discovered from archaeological or fossil evidence. But this year, the reality of population mixing blossomed, as ancient genomes themselves were incorporated into a yet deeper network of separating and remixing” (john hawks weblog, 2015). Dr. Vanessa Hayes of Garvan Institute of Medical Research and University of Sydney, Australia, one of the renowned geneticist, along with coresearchers had published an interesting research article in Nature on October 18, 2019, based on the genomic analysis of 1200 indigenous Africans in the southern part of Africa and successfully traced out an ancestral DNA lineage on Earth and observed that the contemporary successors of this ancestral lineage have been inherited with a collection of mitochondrial genes as well as molecular signature, known as L0, maternally inherited through mitochondria and this molecular signature, remained unchanged in some populations possessed it generations after generations for hundreds of thousands of years (Chan et al., 2019). From their meticulous research investigations, Dr. Hayes and her research colleagues were able to track down the tentative time and place, when L0 split out to give rise to sublineages, genetically possessed by some extant, indigenous African populations. The researchers are almost certain that they discovered the identity of the maiden L0 molecular signature carrier, which thrived till date for thousands of years since their time of emergence (Specktor, 2019). Based on her experimental observations, Dr. Hayes and her associates had firmly claimed that “we’ve known for a long time that humans originated in Africa and roughly 200,000 years ago .. But what we hadn’t known until this study was where, exactly this homeland was” (Chan et al., 2019). The critical observation of Dr. Hayes and her research colleagues ascertained that L0 lineage is an important sequence of DNA encoding that has taken place in mitochondria and if someone tries to make an empirical comparison between mitochondrial DNA and nuclear DNA, mitochondrial DNA appeared to be a fraction of the genome of modern human species and

The Evolutionary Biology of Extinct and Extant Organisms

a big reserve of our DNA is stored in our cell nuclei rather than found to be contained by mitochondria in our cell. During inheritance of the nuclear DNA from our both parents, it usually goes through genetic recombinations in each generation and mutational changes are found to be an integral part in the inheritance of nuclear DNAs from ancestors to their offsprings but there is no possibility of recombination as the offsprings inherited mtDNA from their maternal lineage and remained unaltered for thousands of years as the rate of mutation is considerably very slow (rate of mutational changes in mtDNA is around one in 10,000 years, happened in 300e600 generations cycle) so in tracking the genetic history of humanity, mtDNA or mitogen has played a cardinal role indeed (Gibbons, 1998; Secktor, 2019). So, discovering the existence of L0 in the extant representatives of modern human species has intrigued the geneticists to accept the fact the offsprings have inherited the aforesaid mitochondrial gene from their mothers and it has been descended through the matrilineal lineage since it has emerged in the DNA sequence of mitochondrial Eve, the primordial woman or the universal mother of all mothers (Chan et al., 2019). Dr. Hayes and her research team had ascertained that L0 lineage was originally found in a couple of indigenous groups of populations in South Africa, belonging to the Khoisan tribal communities. The research team also examined the sublines (split away lines from L0 over time) of L0, split out of it and found among some indigenous communities, lived across pan Africa and these preliminary findings intrigued Dr. Hayes to compare L0 and derive lineages of L0 to determine the evolutionary age of divergence of L0 in African Eve (Chan et al., 2019). To carry out this experiment, they had sequenced 200 L0 mt-DNAs in indigenous communities lived in South Africa and they compared the database of 1000 L0 sequences, to have a clear idea, how the ancient lineage and its split away derived lines or subgroups of L0 go through the trail of evolution in course of time and possessed by the vast diverse indigenous communities in South Africa, found in dispersed condition across the African continent. This experimental data helped Dr. Hayes and her teammates to contemplate the possible location and the tentative time, whenever the descendants of African Eve had further split out into distinct lineages, leading to the emergence of diverse indigenous groups across pan Africa (Chan et al., 2019). At the end of their genealogical investigations, it appeared that Dr. Hayes and her teammates had found to be successful in tracking down the historical home-land of Mitochondrial Eve as Dr. Hayes firmly claimed: “using that [evolutionary split of L0 subgroups from L0 haplogroup lineage], we could pinpoint what we believe is our human homeland” (Chan et al., 2019). “Makgadikgadi-Okavango,” a vast paleo wetland in South Africa of 120,000 square kilometers in area and Africa’s largest palaeo-lake has recognized as the largest lake in South Africa and the African continent. Dr. Hayes and her colleagues had figured out that Mitochondrial Eve supposedly originated around 200,000 YBP and lived in the same place till 170,000 YBP before stepping out 30,000 years before L0 lineage split into the first L0 subgroup (Specktor, 2019). So it projected a fact that the ancient haplogroup L0 had stayed in “Makgadikgadi-Okavango” paleo-wetland site for 30,000 YBP before stepped

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out in course of the first historic intrazonal migration that raised a valid question in our mind whether there had any convincible reason that rendered that our greatest grandmothers and grandfathers to left behind their homeland to explore uncharted territory (Specktor, 2019). According to the experimental studies of Dr. Hayes and her coworkers, it has been contemplated that even after hunting, raising the families, and other household engagements for 30,000 years, our ancestors would have failed to cope with abrupt climate changes, happening in “MakgadikgadiOkavango” that pushed them forward in intrazonal migration first time (Chan et al., 2019). By analyzing the sediment core samples from this area and running a paleoclimate-proxy and model data, Dr. Hayes and her colleagues have concluded that substantial change of microenvironmental condition of “MakgadikgadiOkavango,” especially the change of rainfall, enhanced the level of humidity in this paleo-wetland area had supposedly opened up green corridors toward northeast and south-west directions, through which the out of homeland migration supposedly took place between 130,000 and 110,000 YBP, leading the L0 and its subgroups dispersed further around “Makgadikgadi-Okavango,” leading the existence of a scattered population of different indigenous groups settled around this paleo-wetland area in South Africa (Chan et al., 2019). Although it has given a feasible explanation about recognition of the historical homeland of Mitochondrial Eve, the genealogical investigation had not given any clue about the geographical location and tentative time of emergence of Y-chromosomal Adam as well as the male lineage counterpart of Mitochondrial Eve. According to Dr. Stringer, the discovery of the historical homeland of African Eve, construed by Dr. Hayes, might not necessarily be considered as the same homeland for African Adam (Specktor, 2019). Rather Dr. Chris Stringer has claimed further “Looking at the male-inherited Y chromosome, the most divergent lineages currently known in extant humans are found in West Africa. Not South Africa, suggesting our Y-chromosome ancestors may have originated from there” (Specktor, 2019). Based on their findings on genealogical investigations, Dr. Stringer and Dr. Hayes had finally advocated in favor of multiple homelands for African Eve and African Adam, over pan Africa instead of considering one specific location, often recognized as “Garden of Eden” (Knapton, 2019; McKie, 2020). Dr. Pontus Skoglund, of Francis Crick Institute, UK, who is one of the leading molecular geneticists, has engaged in studying a comparative account of gene flow between archaic and anatomically modern human species, concerning the evolution of human species in Africa by analyzing the molecular foot-print of ancient DNA, extracted from the palaeontological remnants. Dr. Skoglund had expressed his concern in this experimental protocols regarding interpretation of the experimental findings, as he observed that special attention is inevitable in such phyllogenetic analysis and interpretation during working on such DNA samples, mostly drawn from the human fossils, likely to be hundreds of thousands years old. As the environmental conditions of the archaic humans are mostly unknown, it is considered to be a challenging task for a molecular phyllogeneticist to determine that the extracted DNA samples from the archaic human fossils have structurally

The Evolutionary Biology of Extinct and Extant Organisms

been remained unaltered or damaged , after being entrapped in the fossil specimen for hundreds of thousns years; so decrypting such archaic DNA codes and depiction of the evolutionary history of modern human species from such DNA sample with certainty needs to be made with caution as socio-behavioral and socio-cultural interactions of those archaic human individuals, have found to be mostly unknown to us (McKie, 2020). So it is a time to acknowledge that to understand and depicting the evolutionary history of modern human species we need to integrate cultural inheritance along-with inheritance of genetic history that has been accumulated through social, behavioral, and cultural interactions through maintaining long-distance social networking in intercommunities level and carried it forward from generation to generation for tens of thousands years employing a vertical mode of inheritance from ancestors to its offsprings. According to Edward O.Wilson, who has been regarded as the father of sociobiology and father of biodiversity, “Homo sapiens have had one hell of a history! And I am speaking both of deep historyevolutionary, genetic history- and then, added on to that and interacting with it, the cultural history recorded for the past 10,000 years or so on” (Wade, 2000). So, the contemporary observation of the advancement in the last 2 decades in the domain of molecular genetics and genomics might create confusion about the authenticity of the genealogical analysis, that tries to define the evolutionary progress of life on Earth. To elucidate the problematic part of such genealogical analysis based on the DNA sequencing, collected from the fossil, samples have been found to yield erroneous or inconsistent results as the problem lies in the evolutionary age of the object and the DNA samples have been collected from. The forensic anthropologists had observed that intramolecular bond of the DNA molecule started to loosen over time, which usually started since physical death of any biological object and an exposition of scorching heat has diminished the disappearance of the evolutionary transcripts, embedded in the hard tissues like bones, and teeth of the biological object, exhumed from a grave or procured through the excavation of a fossil site (Latham and Miller, 2018). So it is convincible that the fossil, which was likely to be excavated from a potential fossil site of from a cave of tropical or temperate region of buried fossil under the permafrost of temperate to the subarctic region of Europe and temperate Asia would supposedly yield a precise result (about evolutionary age of the specimen) rather than the result analyzed of the DNA sample, collected from a biological specimen, collected from a fossil site in the equatorial and subtropical region of tropical Asia and Africa, intermittently exposed to the heat waves in its ambiance (Bergfeld et al., 2017; Latham and Miller, 2018). So, more often, our vision has been compared to a historical metaphor of the candlelight era of the 1970s, when people just visualize in the enlightening part of an enlighten candle, as far as its glow could reach out in its vicinity we could see all objects in our ambiance but the bottom part of the candle (that has been remained dark in form of a circle deterred our vision to see whether anything is there in that circle of shadow or not) have found to be beyond our vision so flame itself could not wipe-out all darkness to get it exposed in our vision; likewise, extraction of DNA

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sample could not ensure that an earnest effort of DNA analysis would depict the evolutionary history of humanity with certainty. So the bonafide contenders of Pan-African evolution of humanity like Chris stringer, Eleanor Scerri, John Hawks, Vanessa Hayes, and Pontus Skoglund have further claimed that their perception about the evolution of anatomically modern human species in Africa seems to give a new outlook to define and redefine not only the evolutionary journey of a biological species but exploring the origin and evolution of a species, recognized as modern human species, the story of origin and evolution of human societies are integrated to its unusual trail of biological evolution that should better be recognized as collective and collaborative evolution of humanity. Most probably the modern human species would have not been evolved as modern human species, it would not have gone through the labyrinth of long-range social networking to accumulate and inherit knowledge, beliefs, set of moral values, social practices, intellects, behavioral, morphological, genetical and cultural traits as a result of getting in and out of the labyrinth of genealogical lineages arrayed in a typical fashion of braided river so its not origin, rather be considered as pan-African origins and evolution of modern human species happen, likely to be contemplated in a period (rather than a particular point of time) in a wide matrix of a continent (rather than a specific location of the continent) from the metaphoric cradle of African Adams and African Eves (rather than a primordial couple: Adam and Eve). Although an earnest endeavor for finding out the evolutionary birthplace of modern human species is still unsettled, yet the palaeontological, genealogical investigations for the last few decades made it clear that the evolution of Homo sapiens has taken place in the African continent around 200,000 YBP. The narratives of the history of humanity portrayed by anthropologists ensured that the ancient humans are looking like us but anthropologists did not mention whether their thought process resembled our thought process or not. If we would try to claim that the evolution of the modern human species is an exclusive milestone in the evolutionary history of hominin, as it is integrated with the intellectual breakthroughs like utilizing the multifarious use of fire, making tools to make living under social orientation. But it is a matter of fact that our historic ancestors as well as extant hominin, Homo sapiens had not invented by themselves, rather they inherited it from the archaic hominins, inventing it millions of years ago. The key difference between this modern human species to the archaic humans is the emergence of the modern human species with a special ability to think for the future and learn from the past with an extraordinary sense of creativity, the ultimate evidence of human cognition, which has scientifically considered as “higher order of consciousness.” The expression of intellectual and creative ideas, state of imagination, symbolic thought process, and depiction of our ambiance have often been expressed through our visual representation of arts. According to Benjamin Smith of the University of Western Australia, one of the famous rock art scholars has stated “We couldn’t conceive art or conceive of the value of art until we had higher-order consciousness” (Marchant, 2016; https://www.smithsonianmag.com/history/journey-oldest-cavepaintings-world-180957685/).

The Evolutionary Biology of Extinct and Extant Organisms

In 2014, an interesting research communication had been published in the renowned journal “Nature,” authored by Professor Maxime Aubert of University of Wollongong, Centre of archaeological Science, New South Wales, Australia, who along with six coresearchers from Australia and Indonesia have published a paper, entitled “Pleistocene cave art from Sulawesi, Indonesia,” a stunning discovery of historical cave art on the Maros-Pangkep region of the Indonesian island of South Sulawesi, a unique visual art-work of human and animals inside the cave wall (Aubert et al., 2014). These cave paintings consist of some humanoid figures (one having the bird-like head, and another having a tail), a couple of warty Sulawesi pigs and four dwarf buffaloes and it depicts a myth, a high level of imagination and state of the creation of “Asian indigenes’ rather than a clear format of realistic imagination. The Australian and Indonesian scientists have undertaken the uraniumethorium age dating process that determined that this unique cave artwork has been prepared by our ancestors around 44,000 years ago, which rendered them to contemplate it as one of the historic art-work from the Asian continent, historically comparable to the ancient art-works prepared by the ancestors of modern human species in Europe, like the paintings of Chauvet cave in France (Greshko, 2019). Dr. Peter Veth of the University of Western Australia, Australia, one of the renowned archaeologist has claimed: “As with the early dates of people voyaging across the sea to Australia and engaging in highly complex art, here we have [Southeast] Asian Indigenes showing human-animal relations before sapiens ‘sapiens’ even got to Europe” (Greshko, 2019). The cave artworks of Sulawesi have broken the myth, once considered earlier that Europe was finishing school for humanity as it has firmly resonated by Dr. April Nowell of the University of Victoria, Department of archaeology, Australia, who said: “We have long known this view of Europe as a ‘finishing school’ is no longer tenable, and the richness of the finds from Australia and Indonesia continue to underscore this point” (Greshko, 2019). The magnificent depiction of visual arts in the format of historical cave paintings, murals, etc., of lions, mammoths, rhinos, mammoths, and humanoid figures of Altamira, Chauvet, and Lascaux has pondered the scientists to hypothesize that depiction of the highly creative, imaginative and abstract state of the thought process has been found among the ancient population of modern human species, once they have arrived in Europe from Africa around 40,000 YBP, and the scientists assumed that unlocking the imagination potential as well as accumulation and presentation of creative skills (through the depiction of visual arts), noticed in our ancestors supposedly happened as a result of helpful genetic mutation (Marchant, 2016; https://www. smithsonianmag.com/history/journey-oldest-cave-paintings-world-180957685/). Dr. Elizabeth Culley of Arizona State University, Department of archaeology, USA, who has considered to be the connoisseur in the field of cave art, has expressed her concern about the South Sulawesi cave paintings in a simple manner as she stated: “There’s a huge variation in cultures [between Asian and European], there’s a lot of space dividing these traditions . but they’re also very consistent .. That, to me, is the real take-home: They’re contemporaneous with a very, very similar tradition, which must have some shared origin” (Greshko, 2019). So, Dr. Culley’s observation

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has pondered the scientists to nurture two alternate possibilities to explain the identical creative imaginations and its sophisticated presentation made by the two break-way ancestral lineages of our common predecessor of pan African descent: 1. If the emergence of the power of expression of abstract imagination and sophisticated creation has been related to the favorable genetic mutation in their brains, then such similar kind of genetic mutations happened independently in two distinct genetic lineages, migrated to Europe and migrated to South Sulawesi, and the probability of such identical genetic changes in the evolutionary history of humanity is less likely in real life. 2. The alternative explanation of such identical expression of artistic expressions, expressed by the distinct genetic lineages, follows two distinct tracks of migrations to start from a common point of origin of the African continent to follow the dichotomous track of human migration to arrive at two distinct geographical locations of two separate continents that have pondered the scientists to hypothesize that all these derived lineages from different geographical locations coalesced back to meet at the common root-stock of humanity and most likely our historic ancestor would have that special gene (that we have inherited in course of the evolutionary journey over time), responsible for the expression of the cultural cognition, creative sophistication, and abstract form of imagination, and these genes would have been stored in the genome of our great-great-grandmothers and great-great-grandfathers, once lived in the metaphoric Garden of Eden in Africa around 200,000 YBP.

Conclusion: Missing link: In search of our distant cousins footprints, a quest for our evolutionary journey to the past CONCLUSION “The puzzle of the eukaryotic cell origin is extremely complicated, as many pieces are still missing. We hoped that Loki would reveal a few more pieces of the puzzle, but when we obtained the first results, we couldn’t believe our eyes e the data simply looked spectacular” Thijis Ettema

Let us try to get in touch with the philosophical introspection of the origin and evolution of life on Earth. Let us follow the footsteps of the evolutionary biologists to understand the main objective of discovering a “missing link” or an evolutionary link between the two distinct life forms on this Earth (Connor, 2015). It is nothing but a sincere effort to walk through the uncharted trail of biological evolution, which helped the discoverer or explorer to unfurl the mystery of the evolutionary journey of life in the backdrop of time and space between the two distinct life forms, the transitional links set in. If we try to look at the conventional system of living organisms classification and try to put an ultra-microscopic, unicellular, simple form of microbes at the bottom and put the multicellular, complex form of animals in one end and the multicellular, complex form of plants in another end, it is apparently difficult to form a tree of life as it is difficult to comprehend who emerged out of whom? The recent advancement in the interdisciplinary field of research works in the field of evolutionary biology, genomics, and molecular phylogenetic helped to discover a new microbial organism, the living successor of the last common ancestor of the two distinct branches of life on Earth emerged as a simple microbial form of life, and a complex form of metazoan life occupied almost all ecological niches of this biosphere in this contemporary regime of Anthropocene (Connor, 2015). When the scientists started exploring the evolutionary history and tried to gauge the evolutionary progress of the current form of a certain animal or plant in respect to their ancestral root-stock, it has not been restricted merely in the limited scope of investigations, rather it always creates an opportunity to drift out of the primary

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focus of investigations to look into a bigger picture on the evolutionary ramification of that organism in terms of its phylogenetic relationship with the immediate and distant allies. Naturally, phylogenetic investigations always create an opportunity to go above and beyond the preset/determined research objective, and at one point it provoked the burning curiosity of research scientists to engage them in the introspective exploration of the ultimate evolutionary mirror, to look for who we are and as a modern human species, how did we evolve? The meticulous research of the cosmologists, geologists, and research scientists in the field of Earth Sciences revealed that planet earth has been originated as dark proto-earth, which has gone through in the course of inorganic and organic evolution for 4e3.5 billion years of time to have appeared as the blue, three-quarter waterfilled elliptical surface of planet Earth, which is the abode of a diverse array of living organisms (Brown, 2019). The evolutionary biologists discovered the primitive cellular form of “proto-life” in the primordial rocky surface that has been evolved around 4e3.5 billion years ago, after which the evolutionary scientists construed the evolution of LUCA (Last Universal Common Ancestor) took place, which gave rise to subsequent forms of living organisms on this Earth (Connor, 2015; Brown, 2019). Later, around 2 billion years ago, from LUCA, two distinct categories of life forms descended out (Connor, 2015; Brown, 2019): a. prokaryotesdlike simple unicellular body of bacteria and b. eukaryotesdthe complex form of multicellular organisms having an organized nucleus and a number of organelles Till 1977, Carl Woese’s discovery of archaea and bacteria has only been considered as a unicellular microbe, which belongs to prokaryote (Woese and Fox, 1977). However, the age-dating process of prehistoric, poorly preserved fossils and the biochemical signature of the prehistoric multicellular organisms with an organized nucleus ascertained that the ancient Eukaryotes evolved around 2.7e2.1 mya (Brown, 2019). The gap of 600 million years provoked the scientists to entangle with each other with a number of unique hypotheses on the origin and evolution of eukaryotes on Earth. A group of scientists postulated that the eukaryotes have supposedly evolved out of “proto-life” root-stock, grown on the primordial rock surface, whereas the second group of scientists promulgated that eukaryotes evolved out of the Archaean lineage of the prokaryotic root-stock (Brown, 2019). However, it has been assumed that the formation of complex structures and the presence of a number of organelles, the emergence of protein-synthesizing, and other metabolic functioning genes evolved among eukaryotes. The most unique findings in the world of biological evolution were that when the evolutionary biologists ascertained that the modern human species has supposedly evolved out of the Archaean lineage, rather than bacteria, which has been evolved around billions of years ago (Brown, 2019). Ultimately, in 2015, a group of an evolutionary biologist, under the leadership of Thijs Ettema in Upsala University, Sweden, discovered the LUCA of prokaryotic and Eukaryotic life form on Earth, which intrigued Thijs Ettema to make a provocative statement, as he said “We’ve identified an organism that seems to

Conclusion: Missing link: In search of our distant cousins footprints

represent a very, very distant cousin of ours and in doing so, it tells us something about our own dark past,” furthermore Dr. Ettema, commented “We are looking at the origin of complex life that occurred sometime after the origin of life itself. This discovery puts the origin of complex life in the spotlight” (Connor, 2015). In 2015, during their studies, Dr. Ettema has discovered a new microbial organism, belonging to archaea, recognized by the research teammates as Lokiarchaeota, which has been retrieved sedimentary sample in the seabed floor around 2352 m deep of the Arctic Ocean, between Norway and Greenland, around 10 km away of the volcanic hydrothermal vent, known as “Loki’s Castle” (Loki is the Norse trickster God) (Connor, 2015; Brown, 2019). The most unique observation of this discovery that amazed Dr. Thijis Ettema and the fellow researchers that the newly discovered microbe has undoubtedly belonged to the prokaryotic division of archaea, but it possessed 100 genes that usually belongs to eukaryotes and those genes were found to be responsible for forming membrane and complex cellular structures in eukaryotes (Brown, 2019). Though the initial reaction of the wonder-struck research scientists of “Lokiarchaeota” or “Loki” was that they must have an error in their analysis and the possibility of their studied sample contaminated by any eukaryotic debris as in that sample, under investigations, there should not be any eukaryotic organism in that sample. The diagrammatic sketch of Lokiarchaeota and its cellular unit has been presented in Figs. 1A and B. They started over, but they got the same result and the genome sequencing of the “Loki” has rendered them to discover a new species; however, the intermittent effort of the scientists to recreate the microbes in the laboratory has not been materialized and they came up with the observation that slow down the cell division process, which took place around one in every 10 years in the deep sea microenvironment, was most likely the main reason of their failure to recreate it (Connor, 2015) Figs. 1A and B.

FIGURE 1A The diagrammatic sketch of Lokiarchaeota. Courtesy Goutam Saha.

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FIGURE 1B The inter-cellular structure of Lokiarchaeota. Courtesy Goutam Saha.

The critical observations of the genomic studies of Dr. Ettema and the fellow scientists ensured that “Loki” holds a position of Missing link that holds an intermediate position between the simple cellular prokaryotes and the complex cellular eukaryotes. It provoked Thijs Ettema to redefine the term “missing link” as Dr. Ettema said “If you look at the term ‘missing link’, it is something that lived back in time and is the last common ancestor of prokaryotic and eukaryotic organisms” and he further said “This is an organism living today, is a descendent of the last common ancestor perhaps e but is has retained characteristics of the last common ancestor. This is interesting because we can say that this ancestor might have been somewhat more complex than we had previously thought” (Connor, 2015). The discovery of “Loki” and the findings of the eukaryotic genes in it put the eminent microbiologist Brett baker, University of Texus, USA in an initial state of jolt, when he worked on a group of archaea, retrieved from the sediment samples of the White Oak River of North Carolina, USA. At the time of genome sequencing, he felt that his Archaean sample must be related to “Loki,” which made him to express his reaction “It completely changed my lab’s research” (Brown, 2019). In 2016, Dr. Baker and his research colleagues published a paper on his newly discovered Archaean species as “Thorarchaeota,” in the name of Norse thunder God (Brown, 2019). Since then, Dr. Baker collaborated with Dr. Ettema to discover a number of phylogenetically related archaea species and name them in the name of different Norse Gods and they named the entire group of newly discovered Archaean species under a group called “Asgard archaeota” (Asgard is known as the home of a tribe of Norse Gods) (Brown, 2019). In 1967, when Lynn Margulis tried to present his hypothesis as an endosymbiotic evolution of eukaryotes, which depicts the emergence of eukaryotes out of the prokaryotic bacterial symbiont and referred mitochondria as the remnants of the erstwhile bacterial symbiont, it might sound like a hypothetical contemplation (Gray, 2017).

Conclusion: Missing link: In search of our distant cousins footprints

However, the discovery of “Asgard archaeota” revealed that the evolutionary occurrence of “endosymbiosis,” which played a key role in the evolution of Evo-link between simple, prokaryotes and complex form of eukaryotes, shown that the presence of a number of genes in archaea is responsible for the formation of internal structures of eukaryotes such as nuclei, Golgi bodies, and microtubules. This made the scientists consider that archaea existed on this Earth prior evolution of eukaryotes took place and all of these so-called “eukaryotic genes,” the eukaryotic molecular tool kits have been transcended from ancestral, simple Archaean lineage to complex, eukaryotic lineage (Brown, 2019). The discovery of “Loki” and its role as a major transitional stepping stone in the origin and evolution of eukaryotes apparently sounds like crossing the finishing line of a marathon race as it helps to elucidate the evolutionary journey of metazoan life as well as the evolution of a diversified group of eukaryotes, a feasible conjecture, which depicts its prehistoric beginning with the evolution of an Archaean prokaryotic living organism, around billions of years ago. Whatever we heard about the evolutionary journey of “Loki,” that is just the beginning of the story and we do not know what is waiting for us at the end. Whatever we know about Archaean evolution that was the contribution to the metagenomic investigations of Dr. Ettema and his colleagues as the DNA sequencing, biochemical investigations, and functional review have been made from the samples collected from the environment and the analysis of DNA samples has not been made after extracting it from its original cellular structure (Brown, 2019). It is a matter of fact that according to the experimental protocol that has been followed in “single-cell genomics,” there is almost no chance of contamination of mixing up DNA samples that would affect the result at the end of the genome sequencing of the species concerned. But then, the “single-cell genomics” is found to be contemporary technology (experimentally practiced for the last couple of decades), applied in the field of applied genomic investigations, so scientists are not very much acquainted with the troubleshooting process to use this technique for a wide array of genomic investigations. As Dr. Ettema and his research colleagues failed to coordinate phylogenomic investigations of “Loki” by using technology known as “single-cell genomic,” they have chosen to coordinate their investigations by adopting “metagenomic investigations” of “Loki,” but to get a clear picture of the evolutionary role of “Loki” in the emergence of eukaryotes, a precise method of genomic investigation is tenable (Brown, 2019). The most interesting thing is that we try to visualize the progress of evolutionary transitions in eukaryotes as well as metazoan lineage, which has conventionally passed through one generation to the next through the vertical transmission of traits and through the germlines, as a result of recombination of unique traits as we are much more biased to the sexual reproduction to consider it as the key biological process of recombination of characters. However, we do not really look around the asexual method of reproductions that have been predominant in Archaea and bacteria. Those prokaryotic, simple organisms employed horizontal gene transfer to share unique traits and exchange genes among their close phylogenetic allies.

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Hence, if we need to adjudge the qualitative progress of the evolution of life, particularly in the higher group of animals like mammals, including modern human species, it is not merely the result of vertical transmission of unique traits accrued through sexual recombination of unique genes, transcended through germ lines, rather it is the unique reticulate combination of vertical gene transfer, which is apparently visible along with the horizontal transfer of genes. Though it’s difficult to recognize the prokaryotes like Archaea as our distant ancestors; however, it’s a matter of fact that we have received the genes from such prokaryotic biological predecessors through horizontal gene transfer. So, the intermittent process of horizontal gene transfer for thousands of thousands of years have not only ensured the passage of genes from prokaryotes to eukaryotes to enrich the gene pool of eukaryotic living entities but has also paved the way for unique genetic recombination and its inheritance, resulting in the expression unique phenotypic expressions among the newly evolved eukaryotic organisms, leading the evolutionary journey of eukaryotes remained uninterrupted, on Earth. Therefore, being a part of the modern human species when we feel proud to be evolved as the most intelligent species on Earth and when we try to find out our evolutionary cousins, we just look around Pan troglodytes (Chimpanzees), Pan paniscus (Bonobos), etc., but we may ignore to recognize our distant evolutionary cousins like Archaea, specifically Lokiarchaeota alias “Loki.” We cannot simply ignore ourselves to stay away from evolutionary introspection, who we are on this Earth, where do we come from and being a forerunner among eukaryotes, what is our inheritance, behind the glorious history of our evolutionary successes as the proud member of Homo sapiens in our micromanaged regime of Anthropocene on this planet we called Earth.

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237

Index Note: ‘Page numbers followed by “f ” indicate figures and “t” indicate tables.’

A Abiogenesis hypothesis, 153e154 Acanthodii, 73 Acer saccharum, 138 Acidocalcisomes, 17 Acoelomorphs, 133 Acorn worms, 83 Actinopterygii, 76 Actinopterygiians, 76 Adenine, 159 Aegyptopithecus, 173 African lungfish (Protopterus annectens), 44e45, 45f African origin hypothesis, 185 Age-dating process, 96 Agnatha, 72e73 Aiolopoda, 103e104 Aistopods, 56 American Journal of Human Genetics, 188e189 Amiiformes, 76 Ammonia (NH3), 42e43 Amphibamus, 49 Amphibians, 41, 54e55. See also Metazoans evolution, 42e43 evolutionary emergence, 48 evolutionary history, 57 maiden, 43e44, 55 terrestrialization of, 56 Amphibious fish, 42 Amphioxus, 83e87, 89e90 Anchiornis, 26 Ancient fossil bird, 23 Animalia, 138e139 Annelids, 95, 98, 103 Anomalocaris, 99 Antennipatus, 102 Apes, 170 Archaeomis siemensi, 23 Archaeopteryx, 2e4, 22e23, 24f, 26, 29 A. lithographica, 23 avian features, 25 fossil specimen of, 23 reptilian features, 25 Archaic Neanderthals, 176 Archionis, 26 Archosaurs, 59 Arctic Canada, 54

Ardipithecus ramidus, 171e172 Arthrodires, 74e75 Arthropoda of organism, 107 Arthropods, 97e98, 104 Articulata hypothesis, 103 Articulins, 143 Asian Peripatid (Cretoperipatus burmiticus), 101 Astasia longa, 147 Auricular operculum, evolution of, 43 Australopithecus, 174e175 A. afarensis, 174, 194e195 A. africanus, 175 Autopodium, 44 Autotrophic prokaryotes, 141

B Bacterivore Euglenids, 146 Bacterivory, 140 Balanoglossus B. misakiensis, 83 B. simodensi, 84e86 Basal Actinopterygiians, 76 Bilateria, 110 Bilaterians, 110e111, 133 Bimodal breathers, 42 Biological entity, 1e2 Biological evolution, 19e20, 109e110, 191e192 Birds, 24e25 Blastaea, 130 BMP4, 91e92 BMP7, 91e92 Bony fishes, 69, 72e76 Bootstrap analysis, 139 “Braided stream” analogy, 196 Branchiosaurus, 49 Buccal swab, 188e189

C Cacops, 49 Camarhynchus pauper, 183 Camarynchus psittacula, 183 Cambrian radiation, 81e82, 96, 113e114, 126 Capitella, 103 Capsid, 160 Captorhinids, 59 Carbaminohemoglobin (CO-Hb), 182 Carbon dioxide (CO2), 42e43

239

240

Index

Cartilaginous fishes, 69, 72e76 a-Catenin, 134 Cathaymyrus, 82 Caudatul autotomy, 63 Cell membrane, 17 Central nervous system (CNS), 88, 106 Cephalodiscidia, 87 Chaetopterus varioedatus, 105 Chelicerata, 97 Chengjiang Lagerstatte, 81e82 Chimeras, 74e75 Chimpanzees (Pan sp.), 168e169 Chlamydia, 163e164 Chlamydomonas, 138, 143 Chlorella vulgaris, 135 Chlroarachniophytes, 141e142 Choanae, 43 Choanocytes, 127, 129e130 Choanoflagellates, 127 Chondrichthyes, 72e76 Chordata, 83, 85e86 evolutionary trail, 83 notochord, 83e87 Chordates, 83e88 Chromosome number 2, 183e184 Cladodontiformes, 73e74 Cladoselachiformes, 73e74 Classical hypothesis, 109e110 Cline, 178e179 Close phylogenetic proximity, 150 Cnidaria, 110 Cnidarians, 133 Coelacanths, 47 Coelophysis, 32e33 Coevolution theories, 14 Colacium, 145 Colonial theory, 129 Comb-jellies, 115 Compsognathus, 23 Confuciusornis, 27 Congenial environmental abode, 126 Connective links, 21e22 Connexin, 115e116 Continental drifting, 56 Creationism, 23e24 Cretaceous Radiation, 102 Cretaceous-Tertiary mega-extinction event, 50 Cro-Magnon Man, 185e186 Crossopterygian fish, 48 Crossopterygians, 55 Crustacea, 97 Cryptoglena, 145

Cryptomonads, 141e142 Ctenophora, 110, 114f ctenophora-sister hypothesis, 120e121 Ctenophores, 110e111, 113e114, 131 neuromuscular systems in, 117 neurons, 115 Cultural inheritance, 192e193 Cutaneous respiration in amphibians, evolution of, 43 Cycloneuralians, 103 Cynagonathus crateronotus, 33 Cynodonts, 31, 33f, 40 paleontological evidence, 31e32 reptiles, 168e169 therapsids, 36 Cytosine, 159

D Darwinian doctrine, 168 Descent of Man, The, 168 Deuterostomes, 82e83, 92, 106, 132 Deuterostomians, 81, 88 Diadectes, 59, 61 affinity, 61 reptilian lineage of adaptations, 62 Diadectidae, 62 Diadectomorpha, 62 Dialipina, 67e68 Dictyostelids, 134 Dictyostelium discoideum, 134 Diencephalon, 89e90 Dimetrodon, 58e59 Dinosaurs, 35 Diploblastic tissues, 118e119 Diplocaulus, 56 Dipnoans, 55 Direct development of Deuterosomian organisms, 84 Direct eye contacts, 4e5 Discoplastis, 145 Discosauriscus, 60e61 Dissolved oxygen in water, 41e42 Distal-less (Dll), 104e107 Division of labor, 157 Dix, 91 Dll orthologs genes (Dlx genes), 104, 106e107 DNA, 124, 155e156 analysis, 199e200 hybridization, 185 inception of, 17 molecules, 194e195

Index

samples, 172e173 sequencing, 190e191 application of, 28 Dopamine, 116e117 Dorudon, 11e12 Dragon Birds, 22e23 Drosophila sp., 102e103 Dryopithecus, 173 Duck-billed platypus, 37 Duplication, 124e125 Dwykaselachus oosthuizeni, 74e75, 74f

E E. coli, 15e16 Ecdysozoans, 104 Echidnas, 38 Echinoderms, 83 Ecological niche, 159 Ediacaran Fauna, 126 Elephant Shrew, 168e169 Elongation Factor-1a sequences (EF-1 sequences), 138e139 Embryogenesis, 148 Endogenous fertilization, 57e58 Engrailed gene, 103 Entelognathus, 77e79, 77f Enteropneusts, 83 body parts, 88 proboscis, 83e87 worms, 83 Eoandromeda, 112e113 Eocaecila, 49 Eoconficiusornis, 27 Eogyrinus, 49 Epigenesis, 125, 155 Eryops, 55 Eugenozoa, 150 Euglena sp., 143, 144f, 149 E. longa, 147 E. obtusa, 146 Euglenaceae, 145 Euglenaformis, 145 Euglenaria, 145 Euglenid chloroplasts, 147 Euglenids, 140e141, 150 Eukaryotic cell, 141 Eukaryovore Euglenids, 146 Eukaryovory, 140 Eunotosaurus, 59 Euro-Gondwanan hypothesis, 101e102 “Eurogondwana and Out of India” hypothesis, 102 Eusthenopteron, 55

Evo-links, 21e22, 107 importance, 22 prehistoric existence, 22e23 Seymouria, 60 Evolution, 19e20, 109e110, 167e168 Evolutionary cousin, 6e8 Evolutionary development (Evo-Devo), 102e103 Evolutionary down-gradation, 109e110 Evolutionary functions, 19e20 Evolutionary link, 46 “Evolutionary potential of bounce-back of amphibians” hypothesis, 51 Evolutionary transition, 124 Evolutionary tree, 50 Evolutionary up-gradation of traits, 109e110 Evolutionary-link, 54 Express Sequence Tags (ESTs), 133 External nostrils, evolution of, 43 Extraplastidic apparatus, 147e148 Eyespot, 147e148

F Face-to-face contacts, 4e5 Fedexia, 49 Ferritin H mRNA, 15 “Fin to Limb” hypothesis, 53e54 First Ape-man, 174e175 First virus hypothesis, 164 Fish out of water, sociobehavioral analogy of, 41e42 Fishes, 35, 70e71 Flagellate theory, 129 Fleshy-finned fishes to sarcopterygii, 75e76 Form I-prime rubisco, 5e6 Fossil remnants, 53, 63 Fossilization process, 1e2 Founder Fish, 77 Freshwater Euglenid species (Heteronema scaphurum), 141 Fungi, 137e139

G Gapejunction proteins, 115e116 Gastraea, 130 Gene duplication, 155 Gene soup, 154 Genetic soup, 154 Genome first theories, 13, 16 Geobatrachus, 49 Gibbons (Hylobates sp.), 168e169 Ginkgo, 138 Gnathostomes, 72e76

241

242

Index

Gondwanan Origin of Onychophorans, 100e101 Gorillas (Gorilla sp.), 168e169 Great Chain of Being, 4e5 “Great Dying” event, 31e32 “Great Oxygenation” event, 5e6 Green grasper, 142e145 Ground sharks, 74e75 Group B Sox genes, 89 Guanine, 159 Guiyu, 46 Gyphosaurus, 23

H Hadzi’s hypothesis, 131 Haikkouichtys, 82 Hallucigenia, 99 Hedgehogs gene, 103 Heidelberg man, 176 Helenodora, 102 Hemichordata, 81e83. See also Chordata Hemoglobin (Hb), 182 Hesperonis, 27 Heterotrophic eukaryotes, 141 Higher order of consciousness, 200 Holocephali, 74e75 Hominin fossils, 171e172 Homo erectus erectus, 175 Homo erectus heidelbergensis, 176 Homo erectus pekinensis, 175e176 Homo futuris, 181 Homo futurus, 185e186 Homo habilis, 175 Homo neanderthalensis, 190e191 Homo sapiens, 151, 175, 185e186, 190e192 evolution, 192, 200 perception of single-origin, 193e194 Homo sapiens fossilis, 178 Homo sapiens neandarthalensis, 177 Homo sapiens sapiens, 176, 180e181 Homo sapiens sapiens, 178e179 Horizontal gene transfer, 150 Hox genes, 105, 134 complements, 83 Hox1, 90 Hox3, 90 Hox4, 90 Human evolution, 192e193 Human family trees, 188e189 Human species, 168e169 Hunter-gatherers, 191e192 Hyalophacus, 147 Hybodont sharks, 73e74 Hydroides, 103 Hylonomus, 58

I Ichthyosaurs, 59e60 Ichthyosis, 27 Ichthyostega, 54e55 Indirect development of Deuterosomian organisms, 84 Inorganic evolution, 125 Intermediate form of missing link, 6e8 Invertebrates, 92 Ionotropic Glutame receptors (iGluRs), 115e116

J Janusiscus, 68e70, 77e79 Jawed vertebrates, 72e76 Jeholornis, 27

K Knuckle Walking LCA, 169, 171e172 Knuckles, 169 Koolasuchus, 49

L L-glutamate,

115e116 L0 lineage, 196e197 L0 molecular signature carrier, 196 Labyrinthodonts, 43e44 Lagerstatte, 95 Lamarckism principle, 123 Lampris guttatus, 72 Large Shallow-water fish (Tiktaalik roseae), 10e11 Last Common Ancestor (LCA), 169e170 Last Universal Common Ancestor (LUCA), 16 Latimeria, 47 L. chalumnae, 47 Lepisosteiformes, 76 Lepocinclis, 145 Limnoscelidae, 62 Limpet-looking dorsal shell, 96 Living organisms, 158e159 Lizards, 35 Lobopods, 103e104 Long-beaked Echidna, 37 Lucy, 174 Lungfish, 41e42 Lungs, evolution of, 43 Lystrosaurus, evolutionary history of, 34

M Maiden amphibian, 43e44 Maiden amphibians, 55 Mammalian T-brain genes, 89 Mammals, 32, 34

Index

Marsupials, 31, 36 Maxicircles, 148 Megadiversity of Arthropod, 102e103 Megazostrodon, 36 M. rudnerae, 36 Mesencephalon, 89e90 Mesoglea, 118e119 Mesohyl, 118e119 Mesosaurus, 59, 62e63 Metabolism first theories, 13e14 Metaboly, 143e145 Metazoans, 115, 126. See also Amphibians evolution, 127 multicellularity, 127e128 soft-bodied, 125 Metencephalon, 89e90 Microbrachis, 49 Microraptor, 26 Microsaurs, 56 Microtubule reinforced pockets (Mtr pockets), 146 “Middle America Trench” of Pacific Ocean, 96 Milleretta, 59 Millerettids, 59 Mineralization, 72e76 Minicircles, 148 Missing diary, 1e2 Missing link, 1e2, 10, 19 arguments, 8e9 functional analogy, 2e4 ideas, 8 intermediate and transitional form, 6e8 literary usage, 21 transitional feature, 9e10 Mitochondrial DNA (mtDNA), 187e188, 193e194, 196e197 Mitochondrial Eve, 188e189 “Mix-n-match building blocks evolution” hypothesis, 192e193 Mixotrophy, 142 Mnemiopsis leidyi, 110e111 Molecular clock, 170e171 Molecular missing links, 6 Molecular Timetrees, 101 Molluscs, 96e97, 104 Monera, 137 Monoecious bodies, 98 Monomorphina, 140, 145 Monotremata, 36e38 Monotrematum suderamericanum, 38 Monotremes, 31, 39 Morphostasis, 142

Most recent common ancestor (MRCA), 194e195 Moyeria, 140 mRNA sequences, 14e15 Msx, 91 Multiregional population, 178e180 Mutated mitochondria, 187e188 Myllokunmingia, 82

N National Academy of Science, 44e45 Natural selection, 167e168 Neanderthal Consequence, 185e186 Neanderthal lineage, 176 Neanderthals, 185 Nematodes, 103 Neopilina, 96 Neopilina galatheae, 96 Neopterygiians, 76 Nephridia, 98 Non-Chordates, 88 Nonliving matter, 153, 159e160 Noradrenaline, 116e117 Nucleic acids, 157 Nucleocytoplasmic large DNA viruses (NCLDVs), 163e164

O Obdurodon dicksonii, 38 Obligate parasites, 161 Octameric rubisco, 6 “On the Origin of Species by means of Natural Selection” (Darwin), 21e22 Onychophora, 98 Onychophorans, 97e99, 103e104, 107 Opabinia, 99 Opah, 72 Orangutans (Pongo sp.), 168e169 Organized mucosal-associated lymphoid tissues (O-MALT), 46e47 Origin of Species (Darwin), 2e4, 8 Origin of Species by Means of Natural Selection, 168e169 Osmotrophic euglenas, 145 Osmotrophy, 140 Ossification, 72e76 Osteichthyes, 72e76 Osteolepiformes, 44 Out of Africa hypothesis, 177, 179e180 Owenetta, 60 Oxygen (O2), 42e43 Oxyhemoglobin (HbO2), 182

243

244

Index

P Pakicetus, 11e12 Paleontological evidence, 22e23 Panarthropods, 103e104 ParaHox, 90 Parapithecus, 173e174 Pareiasaurids, 60 Pareiasaurs, 60, 62 Pax3/7, 91 Pedicellate teeth of amphibians, evolution of, 43 Peg-like teeth, 61 Peking man, 175e176 Pellicle, 143, 145 Pelycosaurs, 62 Peripatopsis capensis, 105 Peripatus sp., 98e99, 99f Permeable skin, 43 Permian extinction, 34 PermianeTriassic boundary, 31e32 Petalomonas cantussygni, 148 Phacaceae, 145 Phacus sp., 145e147 Pharyngeal gill pores, 88 Phlegethontia, 49 Photoautotrophic euglenas, 145 Photoautotrophic Euglenids, 142, 146 Photoautrophy, 140 Photosynthesis, 143 Phototaxis, 147 Phototrophic Euglenids, 142, 149 Phylogeneticists, 125 Pilina, 96 Pisces, 71e72, 80 Pithecanthropus P. erectus, 175 P. pekinensis, 175e176 Placental mammals, 31 Placentalia, 36 Placodermi, 73 Placoderms, 68e69 Placozoa, 110 Plantae, 138 Plants, 35 Plasmid DNA, 187e188 Plate skin fishes, 73 Platyhystrix, 49 Platypus (Ornithorhynchus anatinus), 37e39 Plesiosaurs, 59e60 Pleurobrachia sp., 110e111 Pleurosaurus, 64 Pliopithecus, 174 Polyphyletic theory, 131

Porifera, 110 Porifera-sister hypothesis, 112, 120e121 Postosuchus, 32e33 Pre-Cambrian period, 111e112 Pre-Neanderthals, 176 Prebiotic evolution, 16 Presynaptic triad, 115e116 Primitive arthropods, 98 Primitive jawed fish, 73 Primitive jawless fish, 72e73 Primordial soup, 153e154 Pro-Annelids, 95 Proannelids, 98 Prochordates, 91 Procolophonians, 60 Procolopon, 60 Proconsul, 173e174 Progressive hypothesis, 162e163 Propliopithecus, 173 Prosimii, 172e173 Protein, 13e14 Proterospongia, 130 P. haeckeli, 127, 135 Proterrestrial reptiles, 71e72 Protista, 125, 137, 140 Protists, 125 Protophytes, 125 Protopterus, 47 Protostomes, 106, 132 Prototheria, 37e38 Psarolepis, 46 Pteris, 138 Pterobranchs, 83 Ptychodera flava, 83e85

Q Quingmenodus, 46 Quiridium-like limbs, evolution of, 44

R Ramapithecus, 174 Rapaza viridis, 142, 144e145 Ratfishes, 74e75 Ray-finned fishes, 76 Recapitulation theory, 130 Recent African Origin, 178e179 Regressive hypothesis, 163e164 Reptiles, 24e25, 32, 34, 57 fossil experts, 58 herbivorous, 35 Retrovirus, 162e163 Rhabdopleura compacta, 86e87

Index

Rhipidistians, 75e76 Rhynchocephalia, 63 Ribosomal RNA (rRNA), 12e13, 16e17, 138e139 28s ribosomal RNA, 15 Ribosome, 14, 17 biomolecules, 17e18 ribosome-first theory, 12e15 Ribozyme, 157e158 Riccia, 138 Rickettsia, 163e164 R. prowazekii, 163e164 RNA, 13, 15e16, 159 RNA World hypothesis, 155e156 RNA-virus, 167e168 Rodhocetus, 11e12 Rubisco, 5e6

S Saccharomyces cerevisiae, 139 Saccoglossus kowalevskii, 84e85 Santacruzgnathus abdalai, 35e36 Sarcoglossus kowslevskii, 83 Sarcopterygian fish, 46, 48 Sarcopterygii, 75e76 Sarcopterygiians, 75e76 Sauropleurs, 56 Scientific authenticity, 22 Scutosaurus, 60 Sea corals, 20e21 Secondary endosymbiosis, 141, 143 Selfish Gene, The (Dawkins), 17 Serotonin, 116e117 Seven European Daughters of Eve, 188e189 Sex determination factor (SDF), 39 Sex-determining region Y protein (SRY protein), 39 Seymouria, 59e60, 61f S. baylorensis, 60 Shelled-eggs, 58, 60 Short-beaked-Echidna (Tachyglossus aculeatus), 37 Sinornis santensis, 27 Sister species, 170 Sivapithecus, 174 Snail, 91 Spermatogenesis, 148 Sphenodon, 63e65 Spiracles, 100 Splice-site variants, 149e150 Stegosaurus, 24 Stigma, 147e148 Stinging cells, 115 Stone age paradise, 191e192 Strombomonas, 145

STS-71, 175 Stylopodium, 44 Superficial identity, 191e192 Survival of the fittest, 167e168 Symbiosis, 125, 155 Synapsids, 38 Syncytial theory, 130e131

T Tallinn University of Technology, 67e68 Tapeworms (Taenia solium), 182e183 Taung child, 175 Teleosts, 76 Temnospondyls, 55 Terrestrialization of amphibians, 56 of organisms, 126 Tetrapoda, 41 Tetrapods, 45 evolution of, 43e44 lineage, 60 origin and evolution, 46e47 Tetraselmis sp., 142 Theria, 37e38 Theropods, 27 Thrinaxodon, 32 bio-behavioral patterns, 32e33 movement, 32 T. liorhinus, 31e32 Thymine, 159 Tikataalikis, 10e12 Tiktaalik, 54 T. roseae, 43e44, 53 Trachelomonas, 145 Transcriptome, 149e150 Transfer RNAs (tRNAs), 12e13, 15e16 Transitional entity, 26 Transitional form of missing link, 6e8 Transitional fossils collection, 20 evidence, 19e20 forms, 27 Transitional links, 21, 104 Translation, 156 Triachodon, 32 Triceratops, 24 Trichoplax adhaerens, 126 Trilobita, 97 Triple X syndrome, 183e184 Tritylodontidae family, 35 Tritylodontids, 35 Tseajaiidae, 62

245

246

Index

Tuatara, 63 Turtles, 35 Tyrannosaurus, 28 protein sequence, 28e29 T. Rex, 27

U Unicellular plants, 125 Unikonts, 134 Uniramia, 97 University of Chicago Medical Center, 44e45 Uracil, 159 Urceolusts, 148 Urmetazoa, 127 Urochordata, 88

V Velociraptor, 26 Velvet worms, 98e101 Vertebrates, 89e90, 92 embryological developmental stages of, 69e70 evolutionary history of, 34e35 fossils, 67

Virion, 153 Viruses, 162

W Warm-blooded animal, 72 Westlothiana, 58 Wingless gene, 103 Wolf-Hirschhorn syndrome, 183e184

X Xenacoelomorpha, 133 Xenoturbella, 132 Xiaotingia, 26

Y Y chromosomes, 39e40, 194e195 Y-chromosomal Adam, 194e195 Yunnanozoon, 81, 82f phylogenetic allies, 82

Z Zeugopodium, 44