The Princeton Guide to Evolution

877 Pages·2013·37.38 MB·English

by  Jonathan B. Losos, David A. Baum, Cahterine L. Peichel, Dolph Schluter, Michael C. Whitlock

The Princeton Guide to
Evolution
The Princeton Guide to
Evolution
editor in chief Jonathan B. Losos
Harvard University
editors David A. Baum advisors Michael J. Donoghue
University of Wisconsin, Madison
Simon A. Levin
Douglas J. Futuyma
Stony Brook University Trudy F. C. Mackay
Hopi E. Hoekstra Loren Rieseberg
Harvard University
Joseph Travis
Richard E. Lenski
Michigan State University Gregory A. Wray
Allen J. Moore
University of Georgia
Catherine L. Peichel
Fred Hutchinson Cancer 3esearch
Center
Dolph Schluter
University of British Columbia
Michael J. Whitlock princeton university pre ss
University of British Columbia Princeton & Oxford
Copyright # 2014 by Princeton University Press
Published by Princeton University Press, 41 William Street,
Princeton, New Jersey 08540
In the United Kingdom: Princeton University Press, 6 Oxford Street,
Woodstock, Oxfordshire OX20 1TW
press.princeton.edu
All Rights Reserved
Library of Congress Cataloging-in-Publication Data
The Princeton guide to evolution / Jonathan B. Losos, Harvard
University, editor in chief ; David A. Baum, University of Wisconsin,
Madison, Douglas J. Futuyma, Stony Brook University, Hopi E.
Hoekstra, Harvard University, Richard E. Lenski, Michigan State
University, Allen J. Moore, University of Georgia, Catherine L.
Peichel, Hutchinson Cancer Institute, Seattle, Dolph Schluter,
University of British Columbia, Michael C. Whitlock, University
of British Columbia, editors.
pages cm
Includes bibliographical references and index.
ISBN 978-0-691-14977-6 (hardcover)
1. Evolution (Biology) I. Losos, Jonathan B.
QH367.P85 2014
576.8—dc23
2013022360
British Library Cataloging-in-Publication Data is available
This book has been composed in Sabon and Din
Printed on acid-free paper.
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
Contents
Preface vii III.3 Theory of Selection in Populations 206
Contributors ix III.4 Kin Selection and Inclusive Fitness 215
III.5 Phenotypic Selection on Quantitative
Section I Introduction 1 Traits 221
III.6 Responses to Selection: Experimental
I.1 What Is Evolution? 3 Populations 230
I.2 The History of Evolutionary Thought 10 III.7 Responses to Selection:
I.3 The Evidence for Evolution 28 Natural Populations 238
I.4 From DNA to Phenotypes 40 III.8 Evolutionary Limits and Constraints 247
III.9 Evolution of Modifier Genes and
Biological Systems 253
Section II Phylogenetics and the III.10 Evolution of Reaction Norms 261
History of Life 47 III.11 Evolution of Life Histories 268
II.1 Interpretation of Phylogenetic Trees 51 III.12 Evolution of Form and Function 276
II.2 Phylogenetic Inference 60 III.13 Biochemical and Physiological Adaptations 282
II.3 Molecular Clock Dating 67 III.14 Evolution of the Ecological Niche 288
II.4 Historical Biogeography 75 III.15 Adaptation to the Biotic Environment 298
II.5 Phylogeography 82
II.6 Concepts in Character Macroevolution:
Adaptation, Homology, and Evolvability 89 Section IV Evolutionary Processes 305
II.7 Using Phylogenies to Study Phenotypic IV.1 Genetic Drift 307
Evolution: Comparative Methods IV.2 Mutation 315
and Tests of Adaptation 100
II.8 Taxonomy in a Phylogenetic Framework 106 IV.3 GSteruocgtruarpeh,icanVdaMriaitgiorant,ioPnopulation 321
II.9 The Fossil Record 112 IV.4 Recombination and Sex 328
II.10 The Origin of Life 120 IV.5 Genetic Load 334
II.11 Evolution in the Prokaryotic Grade 127 IV.6 Inbreeding 340
II.12 Origin and Diversification of Eukaryotes 136 IV.7 Selfish Genetic Elements and Genetic
II.13 Major Events in the Evolution Conflict 347
of Land Plants 143 IV.8 Evolution of Mating Systems: Outcrossing
II.14 Major Events in the Evolution of Fungi 152 versus Selfing 356
II.15 Origin and Early Evolution of Animals 159
II.16 Major Events in the Evolution of
Arthropods 167 Section V Genes, Genomes, Phenotypes 363
II.17 Major Features of Tetrapod Evolution 174 V.1 Molecular Evolution 367
II.18 Human Evolution 183 V.2 Genome Evolution 374
V.3 Comparative Genomics 380
Section III Natural Selection V.4 Evolution of Sex Chromosomes 387
and Adaptation 189 V.5 Gene Duplication 397
III.1 Natural Selection, Adaptation, and Fitness: V.6 Evolution of New Genes 406
Overview 193 V.7 Evolution of Gene Expression 413
III.2 Units and Levels of Selection 200 V.8 Epigenetics 420
vi Contents
V.9 Evolution of Molecular Networks 428 VII.5 Sexual Selection: Male-Male Competition 641
V.10 Evolution and Development: Organisms 436 VII.6 Sexual Selection: Mate Choice 647
V.11 Evolution and Development: Molecules 444 VII.7 Evolution of Communication 655
V.12 Genetics of Phenotypic Evolution 452 VII.8 Evolution of Parental Care 663
V.13 Dissection of Complex Trait Evolution 458 VII.9 Cooperation and Conflict: Microbes
to Humans 671
V.14 Searching for Adaptation in the Genome 466
VII.10 Cooperative Breeding 677
V.15 Ancient DNA 475
VII.11 Human Behavioral Ecology 683
VII.12 Evolutionary Psychology 690
Section VI Speciation and Macroevolution 483 VII.13 Evolution of Eusociality 697
VII.14 Cognition: Phylogeny, Adaptation,
VI.1 Species and Speciation 489
and By-Products 703
VI.2 Speciation Patterns 496
VII.15 Evolution of Apparently Nonadaptive
VI.3 Geography, Range Evolution, and
Behavior 710
Speciation 504
VII.16 Aging and Menopause 718
VI.4 Speciation and Natural Selection 512
VI.5 Speciation and Sexual Selection 520
Section VIII Evolution and Modern Society 727
VI.6 Gene Flow, Hybridization, and Speciation 529
VI.7 Coevolution and Speciation 535 VIII.1 Evolutionary Medicine 733
VI.8 Genetics of Speciation 543 VIII.2 Evolution of Parasite Virulence 741
VI.9 Speciation and Genome Evolution 549 VIII.3 Evolution of Antibiotic Resistance 747
VI.10 Adaptive Radiation 559 VIII.4 Evolution and Microbial Forensics 754
VI.11 Macroevolutionary Rates 567 VIII.5 Domestication and the Evolution of
Agriculture 760
VI.12 Macroevolutionary Trends 573
VIII.6 Evolution and Conservation 766
VI.13 Causes and Consequences of Extinction 579
VIII.7 Directed Evolution 774
V1.14 Species Selection 586
VIII.8 Evolution and Computing 780
VI.15 Key Evolutionary Innovations 592
VIII.9 Linguistics and the Evolution
VI.16 Evolution of Communities 599
of Human Language 786
VIII.10 Cultural Evolution 795
VIII.11 Evolution and Notions of Human Race 801
Section VII Evolution of Behavior, Society,
and Humans 605 VIII.12 The Future of Human Evolution 809
VIII.13 Evolution and Religion 817
VII.1 Genes, Brains, and Behavior 609
VIII.14 Creationism and Intelligent Design 825
VII.2 Evolution of Hormones and Behavior 616
VIII.15 Evolution and the Media 832
VII.3 Game Theory and Behavior 624
VII.4 Sexual Selection and Its Impact on Mating
Systems 632 Index 837
Preface
Formore than 150 years, since the publication of On the range of readers, from professional ecologists and
Origin of Species, biologists have focused on under- graduate students to land planners, economists, and
standing the evolutionary chronicle of diversification and social scientists. With this model in mind, we set out to
extinction, and the underlying evolutionary processes produce a guide that would be accessible and useful to
that have produced it. Although progress in evolutionary students and scientists in evolutionary biology and re-
biology has been steady since Darwin’s time, develop- lated disciplines, as well as to anyone with a serious in-
ments in the last 20 years have ushered in a golden era of terest in evolution.What makes this volume stand out is
evolutionary study inwhich biologists are on the brink of the breadth and depth of our 107 chapters, each written
answeringmanyof the fundamentalquestions in thefield. by authorities in their respective field. In addition, the
These advances have come from a confluence of tech- articles balance accessibility with depth of analysis,
nological and conceptual innovations. In the laboratory, making the Guide a valuable reference for a broad au-
the rapid and inexpensive sequencing of large amounts dience. Certainly, some articles are more technical than
of DNA is producing a wealth of data on the genomes others, but readers can easily select chapters appropriate
of many species; comparisons of these genomes are al- for their interests and expertise.
lowing scientists to pinpoint the specific genetic changes The Guide is divided into eight sections. The intro-
that have occurred over the course of evolution. In par- ductory section includes four chapters covering the basics
allel, spectacular fossil discoveries have filled many of of evolution: what it is, the history of its study, the evi-
the most critical gaps in our documentation of the evo- dence for its occurrence, and a basic primer of genetic and
lutionary pageant, detailing how whales evolved from phenotypic variation. The following seven sections cover
land-living animals, snakes from their four-legged lizard the major areas of evolutionary biology, each beginning
forebears, and humans from our primate ancestors. In with a synoptic overview by the section editor. Section II:
addition, providing the data that Darwin could only Phylogenetics and theHistoryofLife, covers thehistoryof
imagine, field biologists are now tracking populations, life andhow it is studied. It includes chapters on the evolu-
directly documenting natural selection as it occurs, and tion of each of the major forms of life, as well as on the
monitoring the resulting evolutionary changes that oc- studyof life’s history through the examinationof the fossil
cur from one generation to the next. record and the construction of phylogenetic trees that
At the same time, evolutionary biology is making an detail the relationships among species and higher taxa.
impact throughouthumansociety.Manycurrent issues— Section III: Selection and Adaptation, moves to evolu-
such as the rise of newdiseases, the increased resistance of tionary processes, focusing on natural selection, the pre-
pests and microorganisms to efforts to control them, and sumedprimary driver of evolutionary change. Section IV:
the effect of changing environmental conditions on nat- Evolutionary Processes, covers gene flow, genetic drift,
ural populations—revolve around aspects of natural se- andnonrandommating. SectionV:Genes,Genomes,Phe-
lection and evolutionary change.Many disparate areas of notypes, examines the link between genes andphenotypes
modern life—medicine, the legal system, computing— and how they evolve, focusing on the rapid growth of
increasingly employ evolutionary thinking and use meth- knowledge and continuing research in genetics and de-
odsdeveloped inevolutionarybiology.Paradoxically, even velopmental biology and the relationships of these fields
as our understanding of evolution and its importance to to evolutionary biology. Section VI: Speciation andMac-
society has never been greater, substantial proportions of roevolution, moves the focus to the species level and
thepopulation inanumberof countries—mostnotably the above, emphasizing theoriginof species—that is, speciation
UnitedStates andTurkey—dispute the scientificfindingsof —andevolutionary change that drives large-scale changes
evolutionary biologists and resist the teaching of evolution in the history of life through time, such as the rise of
in schools. particular taxa and the extinction of others. Section VII:
This volume follows on the success of The Princeton Evolution of Behavior, Society, and Humans, focuses on
Guide to Ecology, edited by Simon Levin. Published in behavioral and social interactions that occur within spe-
2009, the ecology guide has proven valuable to a wide cies, including competition formating success (referred to
viii Preface
as sexual selection) and the evolution of traits such as TrudyMackay, Loren Rieseberg, Joseph Travis, and Greg
parental care, communication, and altruism. Although Wray. Inaddition, theeditorial staffatPrincetonUniversity
chapters in this section are broad in taxonomic scope, Press was indispensable. The entire project was skillfully
many have particular relevance to human biology. Fi- overseenbyexecutiveeditorAnneSavarese,andday-to-day
nally, Section VIII: Evolution and Modern Society, ad- management moved smoothly and efficiently under the
dresses how evolutionary biology directly affects the watchful eyes of editorial assistants Diana Goovaerts and
health and welfare of humans today. SarahDavid, and production editor KarenCarter.
Wemourn the loss andgratefullyacknowledge thecon-
This volume could not have been possible without the tribution of our distinguished colleague Farish Jenkins,
efforts of the editors and authors, whose work was instru- who died on November 11, 2012.
mental to such a wide-ranging and authoritative work.
Developmentoftheguidealsobenefitedimmenselyfromthe
wisdomof our advisors,Michael Donoghue, SimonLevin, Jonathan B. Losos
Contributors
Aneil F. Agrawal, Department of Ecology and Evolutionary Graham Bell, Department of Biology, McGill University
Biology, University of Toronto III.6 RESPONSES TO SELECTION: EXPERIMENTAL
IV.5 GENETIC LOAD POPULATIONS
Michael E. Alfaro, Department of Ecology and Evolutionary Yehuda Ben-Shahar, Department of Biology, Washington
Biology, University of California, Los Angeles University in St. Louis
VI.15 KEY EVOLUTIONARY INNOVATIONS VII.1 GENES, BRAINS, AND BEHAVIOR
Garland E. Allen, Department of Biology, Washington Michael J. Benton, School of Earth Sciences, University of
University in St. Louis Bristol
I.2 THE HISTORY OF EVOLUTIONARY THOUGHT VI.13 CAUSES AND CONSEQUENCES OF EXTINCTION
Dan I. Andersson, Department of Medical Biochemistry and Janette W. Boughman, Department of Zoology, Michigan
Microbiology, Uppsala University State University
VIII.3 EVOLUTION OF ANTIBIOTIC RESISTANCE VI.5 SPECIATION AND SEXUAL SELECTION
Michael J. Angilletta Jr., School of Life Sciences, Arizona Paul M. Brakefield, Department of Zoology, University of
State University Cambridge
III.13 BIOCHEMICAL AND PHYSIOLOGICAL ADAPTATIONS V.10 EVOLUTION AND DEVELOPMENT: ORGANISMS
Charles F. Aquadro, Department of Molecular Biology and Edmund D. Brodie III, Department of Biology, University of
Genetics, Cornell University Virginia
V.1 MOLECULAR EVOLUTION III.5 PHENOTYPIC SELECTION ON QUANTITATIVE
Jonathan W. Atwell, Department of Biology, Indiana TRAITS
University C. Alex Buerkle, Department of Botany and Program in
VII.2 EVOLUTION OF HORMONES AND BEHAVIOR Ecology, University of Wyoming
BFriaonlocgisyc,oUJn. iAvyearsliat,yDoefpCaartlmifoernntiao,f IErcvoinloegy and Evolutionary VI.6 SGPEENCEIAFTLIOWN, HYBRIDIZATION, AND
VIII.13 EVOLUTION AND RELIGION Michael A. Cant, Biosciences, University of Exeter
Doris Bachtrog, Department of Integrative Biology, VII.10 COOPERATIVE BREEDING
University of California, Berkeley Paulyn Cartwright, Department of Ecology and Evolutionary
V.4 EVOLUTION OF SEX CHROMOSOMES Biology, University of Kansas
Charles F. Baer, Department of Biology, University of Florida II.15 ORIGIN AND EARLY EVOLUTION OF ANIMALS
IV.2 MUTATION Amy Cavanaugh, Department of Biological Sciences,
Nathan W. Bailey, School of Biology, University of St. University of Wisconsin, Rock County
Andrews VIII.5 DOMESTICATION AND THE EVOLUTION OF
VII.15 EVOLUTION OF APPARENTLY NONADAPTIVE AGRICULTURE
BEHAVIOR Michel Chapuisat, Department of Ecology and Evolution,
Timothy G. Barraclough, Division of Ecology and Evolution, University of Lausanne
Imperial College London VII.13 EVOLUTION OF EUSOCIALITY
VI.2 SPECIATION PATTERNS Deborah Charlesworth, School of Biological Sciences,
Spencer C. H. Barrett, Department of Ecology and University of Edinburgh
Evolutionary Biology, University of Toronto IV.6 INBREEDING
IV.8 E
VVEORSLUUSTSIOELNFIONFGMATING SYSTEMS: OUTCROSSING JTuelxiaasCalatrAkue,stJianckson School of Geosciences, University of
N. H. Barton, Institute of Science and Technology Austria II.8 TAXONOMY IN A PHYLOGENETIC FRAMEWORK
IV.4 RECOMBINATION AND SEX
Peter R. Crane, School of Forestry and Environmental
David A. Baum, Department of Botany, University of Studies, Yale University
Wisconsin, Madison II.13 MAJOR EVENTS IN THE EVOLUTION OF LAND
II PHYLOGENETICS AND THE HISTORY OF LIFE PLANTS