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Embryos in Deep Time

Embryos in Deep Time

The Rock Record

of Biological Development

Marcelo Sánchez

University of California Press, one of the most distinguished university presses in the United States, enriches lives around the world by advancing scholarship in the humanities, social sciences, and natural sciences. Its activities are supported by the UC Press Foundation and by philanthropic contributions from individuals and institutions. For more information, visit www.ucpress.edu.

University of California Press

Berkeley and Los Angeles, California

University of California Press, Ltd.

London, England

© 2012 by The Regents of the University of California

Library of Congress Cataloging-in-Publication Data

Sánchez, Marcelo R.

    Embryos in deep time : the rock record of biological development / Marcelo R. Sánchez.

        p.  cm.

    Includes bibliographical references and index.

ISBN 978-0-520-27193-7 (cloth : alk. paper)

    1. Paleobiology.  2. Embryos.  3. Developmental genetics.  I. Title.

QE719.8.S26     2012



Manufactured in the United States of America

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The paper used in this publication meets the minimum requirements of ANSI/NISO Z39.48–1992 (R 1997) (Permanence of Paper).




1. Fossils, Ontogeny, and Phylogeny

2. Evo-Devo, Plasticity, and Modules

3. Fossilized Vertebrate Ontogenies

4. Bones and Teeth under the Microscope

5. Proportions, Growth, and Taxonomy

6. Growth and Diversification Patterns

7. Fossils and Developmental Genetics

8. Missing Links and the Evolution of Development

9. Mammalian and Human Development

10. On Trilobites, Shells, and Bugs

Epilogue: Is There a Moral to Developmental Paleontology?





I would like to thank the University of Zürich and its Faculty of Science, as well as the Institute of Paleontology, for providing an inspiring, challenging, and supportive environment in which I could write this book.

I thank current and past members of my lab and close colleagues for everything I learned from them: Ingmar Werneburg, Laura Wilson, Torsten Scheyer, Christian Mitgutsch, Massimo Delfino, Jasi Hugi, Christian Kolb, Dai Koyabu, James Neenan, Fredy Carlini, Sandrine Ladevèze, Corinne Wimmer, Jan Prochel, Peter Menke, Madeleine Geiger, Katja Polachowski, Fiona Straehl, Patricia Meier, Vera Weisbecker, Fernando Galliari, Lisa Rager, Thomas Schmelzle, and Anjali Goswami. I also thank several colleagues in Zürich and abroad for discussion of ideas and for kindly providing information: Lennart Olsson, Shigeru Kuratani, Mike Richardson, Hiroshi Nagashima, Hugo Bucher, Tom Kemp, John Spice, Norberto Giannini, Johannes Müller, Rainer Schoch, Shige Kuraku, Andreas Wagner, Inés Horovitz, Orangel Aguilera, Lionel Hautier, Renaud Lebrun, Anjali Goswami, Norm MacLeod, Rick Madden, Martin Sander, Kathleen Smith, Paul Taylor, Rafael Jiménez, Nico Goudemand, Claude Monet, Michael Hautmann, Christian Klug, Heinz Furrer, Richard Hoffmann, Kenneth de Baets, Thomas Martin, Alexander Nützel, Claudia Hoffmann, Fredy Carlini, Karin Niffeler, and Séverine Urdy. I thank the contributors to the issue of Seminars in Cell and Developmental Biology that I edited in 2010, for helping to inspire this book: Richard Cloutier, Zerina Johanson, Moya Smith and colleagues, Louise Humphrey, Christoph Zollikofer, Marcia Ponce de León, Martin Sander, Nicole Klein, Nadia Fröbisch, Florian Witzmann, Rainer Schoch, Jennifer Olori, Torsten Scheyer, and Massimo Delfino.

Rob Asher in Cambridge, England, Laura Wilson and Torsten Scheyer in Zürich, and Ann-Christin Honnen in Berlin kindly and critically read early drafts and made very useful suggestions. Three anonymous reviewers and especially Michel Laurin very generously provided critiques and suggestions that improved the clarity of this work and helped me to avoid mistakes. Torsten Scheyer, Christian Mitgutsch, James Neenan, Lisa Rager, Kevin de-Carli (Zürich) and Nigel Hughes (Riverside) kindly revised parts of the text. Torsten Scheyer and Jasi Hugi provided much-needed advice on the paleohistology chapter; Christian Mitgutsch, on ontogeny and historical matters. Zhe-Xi Luo shared information on early mammals with his usual collegiality and good humor. Séverine Urdy (Zürich) generously provided extensive comments and insights relevant to bugs and shells. Any infelicities or inaccuracies that remain are entirely my responsibility.

For help with graphics and formatting issues, I thank Morana Mihaljevic, Kevin De-Carli, Rosi Roth, Fiona Straehl, and Torsten Scheyer. Madeleine Geiger, Katja Polachowski, and Claudia Joehl skillfully prepared some of the figures. John A. Long (Los Angeles), Matt Friedman (Oxford), Jasmina Hugi (Zürich), Joachim Haug (New Haven), Pancho Goin (La Plata), Zhe-Xi Luo (Pittsburgh), Torsten Scheyer (Zürich), Christian Klug (Zürich), Christoph Zollikofer and Marcia Ponce de León (Zürich), Loïc Costeur (Basel), and Rainer Schoch (Stuttgart) very generously made figures available.

For crucial and superb assistance, I thank Heike Götzmann for administrative matters and Heini Walter for IT matters. I also thank my Institute’s director, Hugo Bucher, for his support.

Lynn Meinhardt, Kate Warne, and Chuck Crumly of the University of California Press promptly answered my many questions during the editorial process and kindly provided much advice on a variety of matters, and Sheila Berg provided very useful and comprehensive editorial and stylistic remarks on the manuscript.

Wolfgang Maier in Tübingen has inspired my interest in ontogeny over the years and has been a much-appreciated mentor.

Peter Holzwarth in Zürich, Rob Asher in Cambridge, AnnChristin Honnen in Kiel and Berlin, and my mother, Gloria Villagra, in Puerto La Cruz/Buenos Aires provided moral support.

In the past few years I have been supported primarily by the Swiss Research Council (SNF) and by the University of Zürich.


The diversity of life is usually presented in evolutionary trees: A branching pattern culminates in figures of animals and plants. This is good, as trees convey the common history that organisms, including ourselves, share. But there is a limitation in this kind of representation. The organisms portrayed are static entities, usually adults with the recognizable features of their species. In reality, organisms change throughout their lives. If we wanted to portray the biology of biodiversity, we could show for each organism a high-speed film of the different phases of its life history—for a multicellular organism, from fertilization to death. The kinds and number of changes that occur over the life course are so numerous and complex that different scientific disciplines are devoted to each phase of the process. The first steps of cell division and formation of an embryo are associated with embryology. Much research in this area concerns, for example, gastrulation, the phase in which the germ layers are formed and the body plan of the mature organism is established. Developmental biologists tend to study the point of occurrence or origin of tissues and organs. Comparative anatomists and zoologists are usually concerned with changes occurring after birth, which some biologists like to call growth, as opposed to development. For all these disciplines, molecular biology has offered methods and concepts to address a whole new set of questions concerning the mechanistic bases of life history evolution, also reviving old ones posed by morphologists.

Individual development is a rich subject of investigation in biology. But what about the fact that most species represented on the tree of life are extinct? Some may think that developmental biology needs paleontology like a fish needs a bicycle. They might also claim that the fossil record appears to be totally silent about many aspects of developmental evolution and genetics. I do not think this is the case, and I have written this book to explain why. Of course, paleontology remains largely silent about major topics such as gastrulation. Defining the limits of what paleontology can achieve is thus important. In this context, I am reminded of the contributions of a famous fish anatomist to the discussions in the 1980s about the role of fossils versus molecules in reconstructing the tree of life. Colin Patterson (1933–98), a major figure in the study of fossils who was based for decades in the paleontology department of the Natural History Museum in London, strongly advocated the primacy of information on living species over fossils when investigating evolutionary relationships. He was severely criticized by most fellow paleontologists. Several years later his ideas became much appreciated, and in 1996 he was awarded the Romer-Simpson Medal, the highest recognition of the Society of Vertebrate Palaeontology. The role of paleontology in reconstructing the tree of life is largely recognized by most biologists, in spite of the limitations of working with fragmentary data, which contrasts greatly with the large database of information (e.g., genomic) now known for an increasing number of living species.

The integration of information from paleontology and embryology has a long tradition. During the Victorian era, for example, Thomas Huxley made major contributions in both fields; he was the first to suggest that birds are related to dinosaurs, for example, and he discovered major aspects of the early life history of cnidarians, the group to which corals and jellyfish belong. In fact, many researchers are continuing to make major contributions in these diverse fields. For example, Phil Donoghue, in Bristol, studies conodonts, basal vertebrate animals that have been extinct for about 200 million years, and also has a research program concerning micro RNAs and their role in morphologic diversification. Brought together, his paleontological, developmental, and molecular studies are leading to a better understanding of the history of life.

In this book I examine what we may learn about development directly from the fossil record. Fossils are not just the static objects of defunct animals. With a discerning eye and the appropriate information and conceptual background we can learn much about the reproduction and development of the extinct animal. It would seem that the snapshot of some stage of development that a fossil provides is surrounded by so many unknowns that the interpretation of the often incomplete anatomy remains speculative at best. But there is a method in the study of incomplete fossils, and the inferences drawn by most paleontologists are evidence based.

This book is intended for people with a general knowledge of biology and an interest in fossils and evolution. The notes and references at the back of the book may help to clarify and elaborate the diverse matters I treat here. I beg to be excused for the somewhat haphazard nature of the references cited, as some of the topics treated here are very encompassing and have had a long history of investigation and thoughtful contributions. Many examples are taken from my own work and that of my closest collaborators, as these are the ones I know best. Ultimately, each book presents a personal take on a matter, and this is no exception.


Fossils, Ontogeny, and Phylogeny

Human history is a brief spot in space, and its first lesson is modesty.

Will Durant and Ariel Durant,

The Lessons of History

I remember as a child being very impressed by a statement, attributed erroneously to Thomas Huxley, that claimed that if monkeys were left alone in front of typewriters, they would type by chance and, given enough time, would indeed type the entire Encyclopaedia Britannica. I had an abridged version of the Encyclopaedia in Spanish, fifteen thick volumes, so I had an idea of the extent of text involved. I read the statement for the first time in a creationism booklet, which pointed out the absurdity of the statement.¹ But it made sense to me: unlikely, and yet, given infinite time, it could happen. While writing this book, I decided to investigate the matter a little and found out that this thought experiment about monkeys and typewriters has been seriously treated from philosophical and statistical perspectives and has been used in various popular accounts. In fact, this is one of the best-known thought experiments, dating to a 1913 essay by the French mathematician Émile Borel. Since then it has become a popular illustration of the mathematics of probability. Apparently the likelihood of monkeys typing the Encyclopaedia Britannica or Shakespeare’s works is infinitesimally small. What is the relevance of this to a discussion about evolution and development?² There are two points to discuss: the length of time and the probability of evolutionary change occurring during it.

Geologic time is not infinite, but it is long, very long, or deep—a good descriptor considering that it is in the depth of rocks that we can learn much about this distant past. The term deep time originated with the American writer John MacPhee’s popular account of geology titled Basin and Range. There he discussed how geologists develop a sense of the vastness of time intellectually and emotionally.³ Consideration also of the vastness of the extinct biodiversity raises a transcendent perspective, and it may be the most fundamental contribution to human understanding of the universe that geologists and paleontologists can provide.

Thanks to dated fossils placed in evolutionary trees and to molecular estimates, we know that life originated at least 3.5 to 3.2 billion years ago and that multicellular life is at the very least 700 million years old.⁴ In the twentieth century one of the major achievements in geochemistry was the development of several methods of rock dating, based on isotopes of different chemical elements, leading to the secure establishment of an absolute time dimension of the vast history of earth and life. The evolution of biodiversity is said to have needed long periods of time. For Darwin, it was important to gather information about the antiquity of the earth and of life. He was concerned that there was enough time for truly complex structures, such as the eye, to have evolved. The later discovery of mutations and their randomness would at first glance seem to have made Darwin’s worries justified.

Evolution is far from random, and monkeys in front of typewriters are not a good analogy for evolutionary processes. One of the main points made in recent books on evolution is the non-randomness and predictability of evolution. This is not a theoretical conclusion but rather something shown empirically by the patterns seen in living phenotypes and genotypes and also in fossils. The fact that mutations in some genes have a high probability of being selected repeatedly in independent lineages facing similar environmental conditions is called parallel genotypic adaptation. This makes genetic trajectories of adaptive evolution predictable to some extent, leading to the reconstruction of molecular processes that most likely operated in extinct species in spite of the contingency of evolution. Development in extinct species can also be reconstructed thanks to principles that have been discovered to be shared by huge groups of species, even involving the the same developmental genes. And yet diversity, in terms of both species and breadth of form, is vast, like the deep time in which it evolved.


The theory of evolution provides a rational explanation for the rich biodiversity that surrounds us. Every day across the world more and more people live in cities, but even those who are rarely confronted with nature are aware of at least some of this diversity thanks to television or a visit to a zoo. Approximately 1.5 million species have been described, and 10 million to 100 million species are estimated to inhabit the planet. But this huge number of species is only a small fraction of the total number of species that have existed on the planet; conservative estimates suggest that as much as 99 percent of the entire diversity of life that has existed on earth is extinct.⁵ Most of that past diversity is largely undocumented in spite of the work of paleontologists, as remains of most of those species no longer exist or await discovery and study.

The portion of this large diversity that is most directly obvious to us is vertebrates, the group of backboned animals to which we belong. There are about 59,000 living vertebrate species, but many more species have been described. Some vertebrate groups are better known paleontologically than others. Dinosaurs, for example, are known from some 550 described genera, but it is estimated that approximately 1,850 genera must have existed. Not all new genera and species of fossil organisms that are described are valid, as paleontologists continuously revise their decisions on taxonomy and new studies of variation and anatomy help to refine criteria on which to base decisions. A survey in 2003 determined that the then-valid 4,399 genera of fossil mammals represented 80 percent of the total number of genera ever described. This figure was 67 percent in 1945, as reported by the American paleontologist George Gaylord Simpson in a classic paper. More and more valid fossil genera of mammals and of other vertebrates are being named.

The case of the evolution of our own genus, Homo, illustrates the controversy and diverging opinions on the taxonomy of fossil forms. Yet on many issues there is broad agreement. For example, most anthropologists acknowledge that about two million years ago, at least five different species of humans inhabited the planet. We are the last branch of a once much richer evolutionary tree since our ancestors diverged from chimpanzees some seven million years ago.

The numbers I present here serve simply to illustrate the fact that if we wish to understand the evolution of biodiversity, looking at the past is fundamental. The role of paleontology in describing extinct biodiversity is obvious, but there are many other ways besides mere description in which paleontology contributes to evolutionary biology.


The new fields of inquiry created by the emergence of molecular biology in recent decades brought about much well-founded enthusiasm. It also led in some circles to questioning the justification for continuing older disciplines such as paleontology. In the context of these discussions, many of my colleagues have reflected on the many specific aspects that paleontology alone can address to help other biological disciplines and establish an integrative research agenda. These include the following.

1. Fossils provide a time scale for evolution. The oldest representatives of groups from datable rocks provide numbers in which at least a splitting among groups of organisms must have occurred. If we have the DNA sequences of two living species and thus know how much they differ, and if we know when their forms became distinct in the fossil record, we can establish a rate of DNA change. This rate can then be used to estimate the divergence dates of other, related groups for which fossils are not yet known.

Figure 1. Main geologic eras and periods discussed in the text and their age in millions of years.

2. Fossils provide information on organisms’ historical distribution in space. The young Charles Darwin himself noticed this during his voyage around the world. He recorded fossil marine molluscs in the Andes, with obvious implications for the dramatic changes occurring in geologic time. The discovery of fossil platypus relatives in South America several years ago, among other discoveries, provided hard evidence of presupposed faunal connections with Australia. The distribution across Southern Continents in the Triassic of a dog-sized early mammalian relative, Lystrosaurus, and of extinct marine reptiles called mesosaurs in the Permian provided independent evidence for continental drift. Fossils document the past presence on islands of many forms greatly affected by human presence and driven in many cases to extinction in prehistoric times, as is the case for the many giant lemurs found in caves in Madagascar. The list of examples is indeed very long, and the significance of fossils in solving (and creating) biogeographic puzzles or serving to test