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Comp. by: AbdulMalik Stage: Proof Chapter No.: FrontMatter Title Name: ASHERandMULLER
Date:23/5/12 Time:20:01:09 Page Number: 1

From Clone to Bone

The Synergy of Morphological and Molecular Tools
in Palaeobiology

Since the 1980s, a renewed understanding of molecular development has

afforded an unprecedented level of knowledge of the mechanisms by which
phenotype in animals and plants has evolved. In this volume, top scientists in
these fields provide perspectives on how molecular data in biology help to
elucidate key questions in estimating palaeontological divergence and in
understanding the mechanisms behind phenotypic evolution. Palaeobiological
questions such as genome size, digit homologies, genetic control cascades behind
phenotype, estimates of vertebrate divergence dates, and rates of morphological
evolution are addressed, with a special emphasis on how molecular biology can
inform palaeontology, directly and indirectly, to better understand life’s past.
Highlighting a significant shift towards interdisciplinary collaboration, this is a
valuable resource for students and researchers interested in the integration of
organismal and molecular biology.

Robert J. Asher is a Lecturer and Curator of Vertebrates in the University

Museum of Zoology, Cambridge, UK. He is a vertebrate palaeontologist,
specializing in mammals, with interests in phylogenetics and development.

Johannes Müller is Professor of Palaeozoology at the Natural History

Museum, Humboldt University, Berlin, Germany. He is a palaeobiologist,
focusing on the evolutionary diversification of fossil and recent reptiles
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Cambridge Studies in Morphology and Molecules:

New Paradigms in Evolutionary Biology

SERIES EDITORS

Professor Russell L. CiochonUniversity of Iowa, USA

Dr Gregg F. Gunnell Duke University, USA

E D I T O R I A L B OA R D

Dr Robert J. Asher University of Cambridge, UK

Professor Charles Delwiche University of Maryland, College Park, USA
Professor Todd Disotell New York University, USA
Professor S. Blair Hedges Pennsylvania State University, USA
Dr Michael Hofreiter Max Planck Institute, Leipzig, Germany
Professor Ivan Horáček Charles University, Czech Republic
Dr Zerina Johanson Natural History Museum, London, UK
Professor Jukka Jernvall University of Helsinki, Finland
Dr Shigeru Kuratani Riken Center for Developmental Biology, Japan
Dr John M. Logsdon University of Iowa, USA
Dr Johannes Müller Humboldt University of Berlin, Germany
Dr Patrick O’Connor Ohio University, USA
Dr P. David Polly Indiana University, USA
Dr Miriam Zelditch University of Michigan, USA

This new Cambridge series addresses the interface between morphological

and molecular studies in living and extinct organisms. Areas of coverage
include evolutionary development, systematic biology, evolutionary patterns
and diversity, molecular systematics, evolutionary genetics, rates of evolution,
new approaches in vertebrate palaeontology, invertebrate palaeontology,
palaeobotany, and studies of evolutionary functional morphology. The series
invites proposals demonstrating innovative evolutionary approaches to the
study of extant and extinct organisms that include some aspect of both
morphological and molecular information. In recent years the conflict
between ‘molecules vs. morphology’ has given way to more open consideration
of both sources of data from each side, making this eries especially timely.
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Carnivoran Evolution: New Views on Phylogeny, Form and Function

Edited by Anjali Goswami and Anthony Friscia
Evolutionary History of Bats: Fossils, Molecules and Morphology
Edited by Gregg F. Gunnell and Nancy B. Simmons
Evolution of the House Mouse
Edited by Miloš Macholán, Stuart J. E. Baird, Pavel Munclinger and
Jaroslav Piálek
From Clone to Bone: The Synergy of Morphological and Molecular Tools
in Palaeobiology
Edited by Robert J. Asher and Johannes Müller
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Date:23/5/12 Time:20:01:09 Page Number: 4
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From Clone
to Bone
The Synergy of
Morphological and
Molecular Tools in
Palaeobiology

edited by

Robert J. Asher
Museum of Zoology,
University of Cambridge, UK

Johannes Müller
Museum für Naturkunde/Humboldt
University of Berlin, Germany
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cambridge university press

Cambridge, New York, Melbourne, Madrid, Cape Town,
Singapore, São Paulo, Delhi, Mexico City
Cambridge University Press
The Edinburgh Building, Cambridge CB2 8RU, UK

Published in the United States of America by Cambridge University Press, New York

www.cambridge.org
Information on this title: www.cambridge.org/9781107003262

# Cambridge University Press 2012

This publication is in copyright. Subject to statutory exception

and to the provisions of relevant collective licensing agreements,
no reproduction of any part may take place without
the written permission of Cambridge University Press.

First published 2012

Printed in the United Kingdom at the University Press, Cambridge

A catalogue record for this publication is available from the British Library

Library of Congress Cataloging-in-Publication Data

From clone to bone : the synergy of morphological and molecular tools in palaeobiology /
edited by Robert J. Asher, Johannes Müller.
pages cm. – (Cambridge studies in morphology and molecules ; 4)
Includes bibliographical references and index.
ISBN 978-1-107-00326-2 (Hardback) – ISBN 978-0-521-17676-7 (Paperback)
1. Evolutionary paleobiology. 2. Paleobiology–Methodology. 3. Morphology (Animals)
4. Morphogenesis. 5. Molecular biology. I. Asher, Robert J. II. Müller, Johannes, 1973–
QE721.2.E85F76 2012
560–dc23
2012014611
ISBN 978-1-107-00326-2 Hardback
ISBN 978-0-521-17676-7 Paperback

Cambridge University Press has no responsibility for the persistence or

accuracy of URLs for external or third-party internet websites referred to
in this publication, and does not guarantee that any content on such
websites is, or will remain, accurate or appropriate.
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Contents

List of contributors page ix

1 Molecular tools in palaeobiology: divergence and mechanisms 1

robert j. asher and johannes müller

PART I Divergence
2 Genomics and the Lost World: palaeontological insights into
genome evolution 16
chris organ

3 Rocking clocks and clocking rocks: a critical look at divergence

time estimation in mammals 38
olaf r. p. bininda-emonds, robin m. d. beck and
ross d. e. macphee

4 Morphological largess: can morphology offer more and be

modelled as a stochastic evolutionary process? 83
hans c. e. larsson, t. alexander dececchi and luke
b. harrison

5 Species selection in the molecular age 116

carl simpson and johannes müller

PART II Mechanisms
6 Reconstructing the molecular underpinnings of morphological
diversification. A case study of the Triassic fish Saurichthys 135
leonhard schmid

7 A molecular guide to regulation of morphological pattern in the

vertebrate dentition and the evolution of dental development 166
moya smith and zerina johanson

8 Molecular biology of the mammalian dentary: insights into how

complex skeletal elements can be shaped during development
and evolution 207
neal anthwal and abigail s. tucker
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viii Contents

9 Flexibility and constraint: patterning the axial skeleton

in mammals 230
emily a. buchholtz

10 Molecular determinants of marsupial limb integration

and constraint 257
karen e. sears, carolyn k. doroba, xiaoyi cao,
dan xie and sheng zhong

11 A developmental basis for innovative evolution of the

turtle shell 279
shigeru kuratani and hiroshi nagashima

12 A molecular–morphological study of a peculiar limb morphology:

the development and evolution of the mole’s ‘thumb’ 301
christian mitgutsch, michael k. richardson,
merijn a. g. de bakker, rafael jiménez, josé ezequiel
martı́n, peter kondrashov and marcelo
r. sánchez-villagra

13 Manus horribilis: the chicken wing skeleton 328

michael k. richardson

Index 363

The colour plates are situated between pages 000 and 000
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Contributors

Neal Anthwal, Department of Craniofacial Development, King’s College

London, UK

Robert J. Asher, Department of Zoology, University of Cambridge, UK

Robin Beck, Department of Mammalogy, American Museum of Natural History,
New York, USA

Olaf Bininda-Emonds, AG Systematics and Evolutionary Biology, Carl von

Ossietzky University of Oldenburg, Germany

Emily A. Buchholtz, Wellesley College, MA, USA

Xiaoyi Cao, Center for Biophysics and Computational Biology, University of
Illinois, Urbana, IL, USA

Merijn A. G. de Bakker, Institute of Biology, Leiden University, The Netherlands

T. Alexander Dececchi, Redpath Museum, McGill University, Montreal, Canada
Carolyn K. Doroba, Department of Animal Biology, University of Illinois,
Urbana, IL, USA
Luke B. Harrison, Redpath Museum, McGill University, Montreal, Canada

Rafael Jiménez, Departamento de Genética, University of Granada, Spain

Zerina Johanson, Department of Palaeontology, Natural History Museum,

London, UK

Peter Kondrashov, Anatomy Department, Kirksville College of Osteopathic

Medicine, A.T. Still University of Health Sciences, Kirksville, MO, USA

Shigeru Kuratani, Laboratory for Evolutionary Morphology, RIKEN Center for

Developmental Biology, Kobe, Japan

Hans C. E. Larsson, Redpath Museum, McGill University, Montreal, Canada

Ross D. E. MacPhee, Department of Mammalogy, American Museum of Natural

History, New York, USA
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x List of contributors

José Ezequiel Martı́n, Instituto de Parasitologı́a y Biomedicina López-Neyra,

CSIC, Granada, Spain

Christian Mitgutsch, RIKEN Center for Developmental Biology, Laboratory for

Evolutionary Morphology, Kobe, Japan

Johannes Müller, Museum für Naturkunde, Leibniz-Institut für Evolutions- und

Biodiversitätsforschung an der Humboldt Universität zu Berlin, Germany

Hiroshi Nagashima, Laboratory for Evolutionary Morphology, RIKEN Center

for Developmental Biology, Kobe, Japan

Chris Organ, Department of Organismic and Evolutionary Biology, Harvard

University, Cambridge, MA, USA
Michael K. Richardson, Institute of Biology, Leiden University, The Netherlands
Marcelo R. Sánchez-Villagra, Paläontologisches Institut und Museum,
University of Zürich, Switzerland

Leonhard Schmid, Paläontologisches Institut und Museum, University of Zürich,

Switzerland

Karen E. Sears, Department of Animal Biology and Institute for Genomic

Biology, University of Illinois, Urbana, IL, USA

Carl Simpson, Museum für Naturkunde, Leibniz-Institut für Evolutions- und

Biodiversitätsforschung, Humboldt University of Berlin, Germany

Moya Smith, Dental Institute, King’s College London, UK

Abigail S. Tucker, Department of Craniofacial Development, King’s College
London, UK
Dan Xie, Department of Bioengineering, University of Illinois, Urbana, IL, USA

Sheng Zhong, Department of Animal Biology, Institute for Genomic Biology, and
Department of Statistics, University of Illinois, USA
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1
Molecular tools in palaeobiology:
divergence and mechanisms
r o b e r t j . a s h e r a n d j o h a n n e s m ü l l e r

In 1987, Cambridge University Press published a volume entitled Molecules and

Morphology in Evolution: Conflict or Compromise? edited by the esteemed British
palaeobiologist Colin Patterson. Since the 1980s, we have witnessed a great deal
of incorporation of the tools and data of molecular biology into palaeonto-
logical hypothesis building and testing. The degree of integration is substantial
enough so as to rule out the rather pejorative subtitle of the 1987 volume,
‘conflict or compromise’. We believe a new designation is appropriate: ‘synergy’.
Stated differently, our ability to address major questions in biological history
requires the integration of molecular methods and data into the palaeobiolo-
gist’s toolkit. The antagonism implicit in the notion of ‘conflict or compromise’
is more an artifact of disciplinary boundaries and analytical traditions, and is
not firmly rooted in the data of biology. Palaeobiologists today routinely
consider data from molecular biology in their research on the shape and
antiquity of the tree of life (‘divergence’), and in understanding the genetic
and developmental mechanisms behind morphological change (‘mechanisms’).
This book documents aspects of this synergy, focusing on these two general
categories: divergence and mechanisms. It derives from the symposium
‘molecular tools in palaeobiology’ that took place during the 2009 meetings
of the Society of Vertebrate Paleontology in Bristol, UK. In retrospect, we
realize that the ‘vertebrate’ orientation of that conference has resulted in a level
of taxonomic focus in this book that excludes many important contributions
regarding evolutionary divergence and mechanisms. Nevertheless, this is no
small taxonomic category, and there has been much to say about it since 1987.
The unifying theme of that symposium, as in this edited volume,
is general: how have molecular methods become critical in particular sub-
fields of palaeobiology, and how does this constitute interdisciplinary syn-
ergy to understand life history?

From Clone to Bone: The Synergy of Morphological and Molecular Tools in Palaeobiology,
ed. Robert J. Asher and Johannes Müller. Published by Cambridge University Press.
# Cambridge University Press 2012.
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Date:23/5/12 Time:15:27:41 Page Number: 2

2 Asher and Müller

Divergence
Many aspects of the synergy we would like to emphasize in this book
were evident to the authors of Patterson (1987). For example, on its cover,
Patterson’s volume depicted Ernst Haeckel’s artistically rendered Tree of Life,
published in German in 1874. From our perspective in 2011, careful inspection of
that tree reveals the extraordinary extent to which the comparative anatomists
of the nineteenth century ‘got it right’ in terms of the overall structure of
animal, particularly vertebrate, phylogeny (Figure 1.1). Although biologists of
the 1980s were unable to completely tease apart many issues in systematics –
such as relations near the base of chordates, between birds and mammals, and
among mammalian orders – for the species they had in common, Goodman
et al. (1987) and Bishop and Friday (1987) proposed trees that were not far off
from those outlined over a century before.
Concordance of vertebrate trees generated by molecular data today with
those based on comparative anatomy of the nineteenth century is remarkable:
not much has changed compared with the basic structure deciphered by
naturalists two centuries ago. Haeckel (1874), Gill (1872) and others of their
time considered dozens of major groups and hundreds of species, recognizing
the nested relationships of vertebrates, gnathostomes, bony and cartilaginous
fish, ray- and lobe-finned fish, tetrapods, amphibians and amniotes, diapsids
and synapsids. Since then, there have been a few major questions regarding
this understanding of vertebrate phylogeny, such as the possibility of a bird–
mammal clade (Huxley 1868; Hedges et al. 1990; Gardiner 1993), the placement
of coelacanths with ray-finned fish (Arnason et al. 2004), or the paraphyly of
rodents (D’Erchia et al. 1996). However, subsequent analysis of more compre-
hensive data sets, often by the same investigators, has resolved these issues
beyond any reasonable doubt (Hedges 1994; Murphy et al. 2001; Hallström and
Janke 2009) and has left the Tree of Haeckel and Gill relatively unscathed.
Changes within groups have occurred (particularly mammals), but perhaps the
only substantial change among major vertebrate groups has been the recogni-
tion that tunicates are closer to vertebrates than Branchiostoma (Delsuc et al.
2008), switching two branches that Haeckel had already placed immediately
adjacent to one another (Figure 1.1).
It’s worth comparing, for example, the 88-taxa study by Hugall et al. (2007)
with Haeckel’s tree as displayed on the cover of Patterson (1987). The former
(Hugall et al. 2007: figs. 1, 2) places hagfish and lamprey at the base of verte-
brates, followed by a monophyletic frog–salamander–caecilian clade (they did
not sample Chondrichthyes or Actinopterygia), followed by amniotes, which
consist in turn of Mammalia as the sister taxon to an archosaur–squamate clade.
 humans
gorillas orangs
chimpanzees gibbons
hominoids
bats
ungulates anthropoids
rodents I. TELEOST SERIES (XIV.–XXII.).

Mammals
carnivorans
whales sloths lemurs &
lorises
Date:23/5/12 Time:15:27:41 Page Number: 3

marsupials
monotremes CYCLOGANOIDEA (XIII.).
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primitive mammals

MOLLUSCA.
birds RHOMBOGANOIDEA (XII.).

? MOLLUSCOIDEA
teleosts African turtles
reptiles MAMMALIA.
lungfish ? CROSSOPTERYGII (XI.).
garfish amphibians crocodiles GANOID
lizards CHONDROSTEI (VIII.).
SERIES.
lungfish BATRACHIA–REPTILIA.
lamprey snakes DIPNOI (X.).
cartilaginous fish

Vetebrates
jawless animals ACTINISTIA (IX.) A VES.
hagfish
Title Name: ASHERandMULLER

ACANTHODEI (VII.).
skull-less animals lancelet
? OSTRACOSTEI and HETEROSTRACI.
insects ascidians

PIS CES.
crustaceans HOLOCEPHALI (VI.).
salps
chordates
arthropods ELASMOBRANCHII. RAIAE (V.).
tunicates
HYPEROARTIA (III.).
molluscs
echinoderms scolecidans
annelids SQUALI (IV.).

primitive worms HYPEROTRETA (II.).

Invertebrate gut-
animals
jellyfish
“plant animals” worms

VERTEBRATA.
MARSIPOBRAN CHII.
sponges
primitive
metazoan LEPTOCARDII–CIRRHOSTOMI (I.).
planaeadans protists
egg-animals

synamoebae

amoebae

monera
Primitive animals

Figure 1.1 Nineteeth-century evolutionary trees of Ernst Haeckel (left) and Theodore Gill (right). Haeckel’s image is from the
1897 English version of Evolution of Man, repeating his previously articulated views (e.g. Haeckel 1874, p. 513). Gill’s phylogeny
was published in 1872. Both show a remarkably high level of agreement with current ideas on vertebrate interrelationships,
including the monophyly of craniate vertebrates, cyclostomes, gnathostomes, cartilaginous and bony fish, actinopterygians,
sarcopterygians, tetrapods, amphibians and amniotes (Hugall et al. 2007; Delsuc et al. 2008). (See also colour plate.)
Comp. by: AbdulMalik Stage: Proof Chapter No.: 1 Title Name: ASHERandMULLER
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4 Asher and Müller

The 179-gene data set of Delsuc et al. (2008: figs. 2 and 3) across deuterostomes
similarly supported vertebrates, gnathostomes, cartilaginous and bony fish,
actinopterygians, tetrapods, amphibians and amniotes. This basic structure, as
inferred by both Hugall et al. (2007) and Delsuc et al. (2008), does not differ
substantially from that proposed by Haeckel (1874) or Gill (1872), extending
even to cyclostomes (i.e. hagfish and lamprey as sister taxa) and turtles within
archosaurs (i.e. birds and crocodiles).
To put this in context, there are approximately 2
10157 ways in which the 88
taxa sampled by Hugall et al. (2007) could be interconnected as rooted, bifur-
cating trees (Felsenstein 1978). Why is it that out of this extraordinary number
of possibilities Hugall et al. (2007) honed in on essentially the same pattern as
that proposed by Haeckel and Gill in the nineteenth century? The answer of
course speaks to the prediction made by Darwin in 1859, that there is a genuine
Tree of Life subject to reconstruction using the evidence left behind by the
mechanism of descent with modification, evidence that manifests itself on a
developmental continuum between genotype and phenotype. Haeckel and Gill
knew about the phenotypic side of this continuum. Hugall et al. (2007) focused
on one small part of genotype: sequences of the nuclear Rag-1 gene; Delsuc
et al. (2008) had a much larger genetic data set with fewer sampled vertebrate
taxa. That each source of data supports such a specific hypothesis out of such an
astronomical number of possibilities is testament to the reality of Darwinian
evolution. A largely consistent topological signal across independent data sets is
what one would expect if animals actually share genealogical history with one
another via the mechanism of descent with modification (Penny et al. 1982).
Phylogenetic consensus has been more elusive for parts of the Tree of Life
other than vertebrates that (1) contain much more ancient branching points,
(2) have not been as thoroughly documented genomically and anatomically,
(3) are more prone to phenomena such as lateral gene transfer, and/or (4) have a
much more limited fossil record (Woese 1987; Doolittle and Bapteste 2007).
Nevertheless, evolutionary biologists who are focused on the most difficult
branches on the Tree of Life should not understate the consensus elsewhere
that has proven robust. Because it is natural for investigators to focus on areas
of controversy and disagreement, uncertainty at one level (e.g. do metazoans
share a single common ancestor?) has, on occasion, been inaccurately portrayed
as an irreconcilable stumbling block for the entire phylogenetic enterprise. For
example, Patterson (1987: p. 4) quoted a particularly pessimistic passage from
Ernst Mayr’s 1982 book The Growth of Biological Thought (p. 218): ‘The futile
attempts to establish the major phyla of animals induced at least one competent
zoologist . . . [to call] common descent . . . a beautiful myth not established by
any factual foundation. . . . Honesty compels us to admit that our ignorance
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Divergence and mechanisms 5

concerning these relationships is still great, not to say overwhelming.’ The

zoologist to which Mayr is referring is Fleischmann (1901), hardly representa-
tive of biological thought from Mayr’s perspective in 1982. Broadly speaking,
this passage takes genuine uncertainty regarding pre-Cambrian divergences
and overgeneralizes from this to common descent itself. On the contrary, given
the agreement we now have about vertebrate interrelations (for example) such
hyperbole is inaccurate and misleading for both students and the general public.
The scrutiny of protein sequences starting in the 1960s did indeed overturn
several cherished ideas in systematics, such as an ancient human lineage to the
exclusion of other great apes dating to the early Miocene (see Goodman et al.
1987; Andrews 1987). Zuckerkandl and Pauling’s (1962: table 2) early application
of the molecular clock to divergences within great apes yielded a surprisingly
prescient result. For the differences they observed in human and gorilla alpha
and beta haemoglobin molecules (one and two amino acid substitutions,
respectively), they estimated a common ancestor between the two species to
have existed approximately 11 million years ago. Such an interpretation is much
closer to the view accepted today than to the previous theory that early
Miocene apes, such as ‘Ramapithecus’, shared ancestry with humans to the
exclusion of other great apes (Simons 1972).
Interestingly, the calibration used for Zuckerkandl and Pauling’s estimate
was ‘the common ancestor of man and horse [which] lived in the Cretaceous
or possibly in the Jurassic period, say between 100 and 160 millions of years
ago’ (Zuckerkandl and Pauling 1962: p. 200). In hindsight, it is interesting
to note that while some recent molecular clock studies support ‘common
ancestor of man and horse’ (i.e. the divergence between Laurasiatheria
and Euarchontoglires) just about 100 million years ago in the Cretaceous
(Bininda-Emonds et al. 2007, but see Kitazoe et al. 2007 or Hallström and
Janke 2010), as a calibration this divergence has no palaeontological basis
whatsoever (Wible et al. 2007; Benton et al. 2009). Nevertheless, it yielded a
result for hominine divergence which is not far off from that accepted today
based on our understanding of both the fossil record and a molecular clock
(Lockwood 2007).
To some specialists of the mid/late twentieth century, even one with such a
major influence and apparently broad perspective as Ernst Mayr, it seemed that
after dethroning the idea of an independent human lineage dating to the early
Miocene, all other such cherished ideas were soon to follow. They didn’t.
Again, and with the important qualification that many surprises have occurred
within certain groups (e.g. mammals; see Asher et al. 2009), the genomic work
of the last decade has confirmed the basic vertebrate topology first recognized
in the nineteenth century, not scrambled it (Figure 1.1).
Comp. by: AbdulMalik Stage: Proof Chapter No.: 1 Title Name: ASHERandMULLER
Date:23/5/12 Time:15:27:42 Page Number: 6

6 Asher and Müller

For mammals, at least, there remains today more uncertainty about divergence
dates than topology among living clades. Bininda-Emonds et al. (this volume)
have made substantial contributions towards understanding mammalian diver-
gences. Building upon a supertree meta-analysis of mammals (Bininda-Emonds
et al. 2007), one which has a far larger taxon sample of mammals than any
previous study, they make the case that ordinal divergences within mammals
substantially predate the Cretaceous–Tertiary (KT) boundary at 65 million years
before present. Palaeontologists have known for some time that the earliest
occurrences of undisputed crown-placental mammals do not predate the KT
boundary (Kielan-Jaworowska 1978; Asher et al. 2005; Wible et al. 2009). Given
the obvious presence of such clades as rodents and carnivorans in the early
Palaeocene, it is reasonable to expect that at least some placental divergences
predate the KT boundary. We know that first appearances in the fossil record are
not synonymous with actual cladistic divergence (Benton et al. 2009). However,
a missing record of crown placentals extending to the early Cretaceous, over
120 million years ago (Kumar and Hedges 1998), seems too much in conflict
with our growing understanding of the Cretaceous fossil record (Foote et al. 1999;
Reisz and Müller 2004; Hunter and Janis 2006), particularly given the limitations
and pitfalls of the molecular clock (Graur and Martin 2004; Kitazoe et al. 2007).
Bininda-Emonds et al. (this volume) offer perspective on this ongoing debate
on the Mesozoic antiquity of crown-placental mammals.
Estimating divergence times from differences in molecular evolution is only
one way of measuring rates of evolutionary change. Evolutionary rates can also
be assessed in terms of morphological evolution, such as phenotypic or taxo-
nomic change (Polly 2001). Simpson’s (1944) classic work Tempo and Mode in
Evolution indicates how palaeontologists have sought for many years to assess
how evolutionary change can be measured and, ideally, quantified from a
morphological perspective. The question remains, however, as to how morpho-
logical change through time can or should be measured, and if it is possible to
use morphological data complementary to molecular methods for assessing
rates of evolution. Larsson et al. (this volume) address this issue from a novel
perspective and present a road map for using morphology not only as a tool to
measure evolutionary rates through time, but also to estimate divergence times
on a similar basis as molecular approaches.
Recent years have seen a tremendous progress in the field of genomics as a
result of major advances in DNA extraction and sequencing. At first glance this
type of research appears unrelated to palaeobiology because of its strictly
genetic nature and necessary focus on living forms. However, not only is it
possible to reveal genomic data from extinct organisms (Paäbo 1989; Noonan
et al. 2005), including some that are truly ancient (Organ et al. 2008), but in
Comp. by: AbdulMalik Stage: Proof Chapter No.: 1 Title Name: ASHERandMULLER
Date:23/5/12 Time:15:27:43 Page Number: 7

Divergence and mechanisms 7

combination with methods from phylogenetic and comparative biology, fossil-

ized structures can be used in conjunction with genomic data to gain insights
into the biology of long extinct taxa (Organ et al. 2007; 2009). A review of this
issue by Organ (this volume), demonstrates the great potential for ‘palaeoge-
nomics’ in biology, and how it can reveal insights into both deep time and the
recent past. He illustrates this potential with recent work on ancient genome
size and sex chromosome reconstruction for species that have been extinct for
tens of millions of years.
Estimating rates of speciation and extinction, and thus diversification, is a
classical theme in macroevolution and for a long time could only be approached
using fossil taxa (Raup 1978; Sepkoski et al. 1981). In recent years, major
advances in bioinformatics and gene sequencing techniques enabled researchers
to also use DNA-derived phylogenetic hypotheses and divergence estimates to
calculate diversification rates (see Ricklefs et al. 2007). This novel approach did
not make the palaeontological method obsolete, however, but instead stimu-
lated and fostered new research on the underlying processes of diversification,
resulting in a wealth of new studies from both neontology and palaeontology.
The progress in this field also made it possible to reconsider a classical question
of evolutionary theory: how does natural selection work, and on how many
levels? Simpson and Müller (this volume) address the concept of species
selection, an issue with a long tradition in palaeontology and often discussed
as a possible evolutionary process. They describe how molecular phylogenies
can be used to measure the extent and impact of species selection, and suggest
that species selection is ubiquitous, providing deeper insights into the causes of
diversification.

Mechanisms
All of the chapters in Patterson’s 1987 book concerned the Tree of Life,
methods for its reconstruction, and aspects of antiquity as inferred by the fossil
record and molecular clocks. The focus of those authors was very much
on phylogenetics, and virtually nothing was said regarding a field that is now
of considerable importance to palaeontologists: evolutionary development.
During the 1980s ‘Evo-Devo’ was of course a sophisticated discipline (Akam
et al. 1988; Keynes and Stern 1988), but was generally the domain of those
working on model organisms and beyond the practical remit of most
palaeontologists.
This is quite different today, and the disciplinary scopes of palaeobiology and
evolutionary development have become increasingly intertwined (e.g. Smith and
Hall 1990; Hall 2002; Smith 2003; Donoghue and Purnell 2009; Sánchez-Villagra
Comp. by: AbdulMalik Stage: Proof Chapter No.: 1 Title Name: ASHERandMULLER
Date:23/5/12 Time:15:27:43 Page Number: 8

8 Asher and Müller

2010; Schmid and Sánchez-Villagra 2010; Takechi and Kuratani 2010). This
coalescence is reflected in the majority of chapters in this book (summarized
below) in which concepts of ontogeny and developmental genetics are applied
to palaeontological questions, in stark contrast to the virtual absence of devel-
opmental subject matter in the chapters of Patterson (1987). While both
Patterson’s book and this one include too few chapters to comprise an infallible
barometer of the course of palaeobiological thought over three decades; it
is nevertheless tempting to view this difference as an indication of how the
understanding of developmental genetics of model organisms has become a
major springboard for hypothesis generation and testing in palaeobiology.
For example, Anthwal and Tucker (this volume) note the diversity of form
among mammalian mandibles, in particular the variable presence and size of
the condylar, coronoid and angular processes. Certain adult phenotypes such as
the small, un-marsupial-like mandibular angle of the adult koala, are late
occurrences during development (Sánchez-Villagra and Smith 1997); due to
differential growth of other parts of the jaw during ontogeny, the mandibular
angle may become more (or less) apparent. The coronoid process of the dentary
is similarly variable; the mandibular condyle exhibits some variation across
mammals but less than the angular and coronoid processes. Perhaps more
importantly, specific phenotypes of the condylar, coronoid and angular pro-
cesses observed in nature have also been observed within the phenotypic
repertoire documented in past studies of transgenic mice and human genetic
disorders. Anthwal and Tucker review these morphologies and note the compli-
cated, but tractable, roles of several genetic loci among mouse knockout studies
and human pathologies that are likely behind the variation observed in nature.
Buchholtz (this volume) discusses a long history of the study of the verte-
brate axial skeleton, focusing on some of the mechanisms by which mammals in
particular exhibit phenotypic diversity despite an extraordinary level of conser-
vatism throughout the Order. Relative to other chordates, mammals show
relatively little variation in vertebral counts, particularly among more cranial
vertebral segments. The identification of skeletal modules, for example those
patterned in somitic versus lateral plate mesoderm, has gained some support in
the recent literature (Hautier et al. 2010). In the context of recent discoveries
regarding the differential expression of Hox genes in specific mesodermal
tissues (McIntyre et al. 2007), Buchholtz documents phenotypic modules across
species and contributes to the understanding of the means by which mammals
may deviate from a fundamentally conserved skeletal body plan.
One of the greatest enigmas in vertebrate evolution is the origin of turtles
and, relatedly, the turtle shell (Rieppel 2009). Turtles are unique among
chordates by possessing a shoulder girdle inside the ribcage. How this change
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