Evolutionary analysis PDF
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GLOBAL EDITION For these Global Editions, the editorial team at Pearson has Evolutionary Analysis collaborated with educators across the world to address a wide range of subjects and requirements, equipping students with the best possible learning tools. This Global Edition preserves the cutting-edge approach FIFTH EDITION and pedagogy of the original, but also features alterations, customization, and adaptation from the North American version. Jon C. Herron • Scott Freeman H e r r o n • F r e e m a n This is a special edition of an established title widely used by colleges and universities throughout the world. Pearson published this exclusive edition for the benefit of students outside the United States and Canada. If you purchased this book within the United States or Canada you should be aware that it has been imported without the approval of the Publisher or Author. Evolutionary Analysis FIFTH EDITION GLOBAL EDITION Jon C. Herron University of Washington Scott Freeman University of Washington With contributions by Jason Hodin Hopkins Marine Station of Stanford University and University of Washington Brooks Miner Cornell University Christian Sidor University of Washington Boston Columbus Indianapolis New York San Francisco Hoboken Amsterdam Cape Town Dubai London Madrid Milan Munich Paris Montreal Toronto Delhi Mexico City Sao Paulo Sydney Hong Kong Seoul Singapore Taipei Tokyo Editor-in-Chief: Beth Wilbur Production Management Services: Cenveo Publisher Services Senior Acquisitions Editor: Michael Gillespie Copyeditor: Chris Thillen Head of Learning Asset Acquisition, Global Editions: Laura Dent Design Manager: Mark Ong Acquisitions Editor, Global Editions: Jasmine Singh Cover and Interior Designer: Mark Ong Executive Director of Development: Deborah Gale Art Developer, Illustrator: Robin Green Project Editor: Laura Murray Senior Photo Editor: Travis Amos Project Editor, Global Editions: K.K. Neelakantan Photo Research and Permissions Management: Assistant Editor: Eddie Lee Bill Smith Group Manager, Text Permissions: Tim Nicholls Content Producer: Daniel Ross Text Permissions Specialist: Kim Schmidt, S4Carlisle Media Project Manager: Shannon Kong Publishing Services Media Production Manager, Global Editions: Vikram Kumar Director of Production: Erin Gregg Director of Marketing: Christy Lesko Managing Editor: Michael Early Executive Marketing Manager: Lauren Harp Production Project Manager: Lori Newman Manufacturing Buyer: Christy Hall Senior Production Manufacturing Controller, Global Editions: Cover and Text Printer: Courier Kendalville Trudy Kimber Cover Photo Credit: © Jubal Harshaw / Shutterstock Credits and acknowledgments for materials borrowed from other sources and reproduced, with permission, in this textbook appear on the appropriate page within the text [or on p. 836]. Copyright ©2014, 2007, 2004, 2001, 1998 by Jon C. Herron and Scott Freeman. Published by Pearson Pearson Education Limited Edinburgh Gate Harlow Essex CM20 2JE England and Associated Companies throughout the world Visit us on the World Wide Web at: www.pearsonglobaleditions.com © Pearson Education Limited 2015 The rights of Jon C. Herron and Scott Freeman to be identified as the authors of this work have been asserted by them in accordance with the Copyright, Designs and Patents Act 1988. Authorized adaptation from the United States edition, entitled Evolutionary Analysis,5th edition, ISBN 978-0-321-61667-8, by Jon C. Herron and Scott Freeman, published by Pearson Education © 2015. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without either the prior written permission of the publisher or a license permitting restricted copying in the United Kingdom issued by the Copyright Licensing Agency Ltd, Saffron House, 6–10 Kirby Street, London EC1N 8TS. All trademarks used herein are the property of their respective owners. The use of any trademark in this text does not vest in the author or publisher any trademark ownership rights in such trademarks, nor does the use of such trademarks imply any affiliation with or en- dorsement of this book by such owners. British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library 10 9 8 7 6 5 4 3 2 1 ISBN 10: 1-292-06127-8 ISBN 13: 978-1-292-06127-6 Typeset by Cenveo Publisher Services www.pearsonglobaleditions.com Printed and bound in Slovakia by Neografia Brief Contents PART 1 PART 3 INTRODUCTION 15 ADAPTATION 383 CHAPTER 1 A Case for Evolutionary CHAPTER 10 Studying Adaptation: Thinking: Understanding HIV 15 Evolutionary Analysis of Form and Function 383 CHAPTER 2 The Pattern of Evolution 51 CHAPTER 11 Sexual Selection 421 CHAPTER 3 Evolution by Natural Selection 87 CHAPTER 12 The Evolution of Social Behavior 469 CHAPTER 4 Estimating Evolutionary Trees 123 CHAPTER 13 Aging and Other Life-History Characters 505 CHAPTER 14 Evolution and Human Health 549 PART 2 MECHANISMS OF CHAPTER 15 Genome Evolution and the EVOLUTIONARY CHANGE 161 Molecular Basis of Adaptation 595 CHAPTER 5 Variation Among Individuals 161 CHAPTER 6 Mendelian Genetics in PART 4 Populations I: Selection and THE HISTORY OF LIFE 623 Mutation 193 CHAPTER 7 Mendelian Genetics in CHAPTER 16 Mechanisms of Speciation 623 Populations II: Migration, Drift, CHAPTER 17 The Origins of Life and Nonrandom Mating 247 and Precambrian Evolution 659 CHAPTER 8 Evolution at Multiple Loci: CHAPTER 18 Evolution and the Fossil Record 705 Linkage and Sex 305 CHAPTER 19 Development and Evolution 749 CHAPTER 9 Evolution at Multiple Loci: Quantitative Genetics 343 CHAPTER 20 Human Evolution 783 3 Contents Preface 9 PART 1 INTRODUCTION 15 CHAPTER 1 A Case for Evolutionary Thinking: Understanding HIV 15 CHAPTER 3 1.1 The Natural History of the HIV Epidemic 16 Evolution by Natural Selection 87 1.2 Why Does HIV Therapy Using Just 3.1 Artificial Selection: Domestic Animals One Drug Ultimately Fail? 23 and Plants 88 1.3 Are Human Populations Evolving as a 3.2 Evolution by Natural Selection 91 Result of the HIV Pandemic? 29 3.3 The Evolution of Flower Color in an 1.4 Where Did HIV Come From? 32 Experimental Snapdragon Population 93 1.5 Why Is HIV Lethal? 37 3.4 The Evolution of Beak Shape in Computing Consequences 1.1 When did Galápagos Finches 95 HIV move from chimpanzees to humans? 38 Computing Consequences 3.1 Estimating Summary45•Questions45 heritabilities despite complications 98 ExploringtheLiterature46•Citations47 3.5 The Nature of Natural Selection 104 3.6 The Evolution of Evolutionary Biology 108 3.7 Intelligent Design Creationism 111 CHAPTER 2 Summary118•Questions119 The Pattern of Evolution 51 ExploringtheLiterature120•Citations120 2.1 Evidence of Microevolution: Change through Time 53 CHAPTER 4 2.2 Evidence of Speciation: New Lineages Estimating Evolutionary Trees 123 from Old 58 2.3 Evidence of Macroevolution: 4.1 How to Read an Evolutionary Tree 124 New Forms from Old 63 4.2 The Logic of Inferring Evolutionary 2.4 Evidence of Common Ancestry: Trees 128 All Life-Forms Are Related 69 4.3 Molecular Phylogeny Inference and 2.5 The Age of Earth 76 the Origin of Whales 137 Computing Consequences 2.1 A closer look Computing Consequences 4.1 Calculating at radiometric dating 79 the likelihood of an evolutionary tree 143 Summary80•Questions81 Computing Consequences 4.2 Neighbor ExploringtheLiterature82•Citations83 joining: A distance matrix method 144 4 Contents 5 4.4 Using Phylogenies to Answer Computing Consequences 6.4 Statistical Questions 151 analysis of allele and genotype frequencies Summary155•Questions155 using the χ2(chi-square) test 212 ExploringtheLiterature157•Citations157 Computing Consequences 6.5 Predicting the frequency of the CCR5-∆32 allele in future generations 215 6.3 Patterns of Selection: Testing PART 2 Predictions of Population Genetics MECHANISMS OF Theory 215 EVOLUTIONARY CHANGE 161 Computing Consequences 6.6 An algebraic treatment of selection on recessive and dominant alleles 218 CHAPTER 5 Computing Consequences 6.7 Stable Variation Among Individuals 161 equilibria with heterozygote superiority and unstable equilibria with heterozygote inferiority 222 5.1 Three Kinds of Variation 162 6.4 Mutation 230 Computing Consequences 5.1 Epigenetic Computing Consequences 6.8 inheritance and evolution 168 A mathematical treatment of mutation as 5.2 Where New Alleles Come From 171 an evolutionary mechanism 232 5.3 Where New Genes Come From 175 Computing Consequences 6.9 Allele Computing Consequences 5.2 Measuring frequencies under mutation–selection balance 234 genetic variation in natural populations 176 Computing Consequences 6.10 Estimating 5.4 Chromosome Mutations 180 mutation rates for recessive alleles 236 5.5 Rates and Fitness Effects of Mutations 183 6.5 An Engineering Test of Population Summary188•Questions189 Genetics Theory 238 ExploringtheLiterature190•Citations190 Computing Consequences 6.11 Predicting the frequency of Medea across generations 240 Summary241•Questions241 CHAPTER 6 ExploringtheLiterature243•Citations245 Mendelian Genetics in Populations I: Selection and Mutation 193 CHAPTER 7 6.1 Mendelian Genetics in Populations: Mendelian Genetics in Populations II: Hardy–Weinberg Equilibrium 194 Migration, Drift, and Computing Consequences 6.1 Combining Nonrandom Mating 247 probabilities 199 Computing Consequences 6.2 The Hardy– 7.1 Migration 248 Weinberg equilibrium principle with more Computing Consequences 7.1 An algebraic than two alleles 203 treatment of migration as an evolutionary 6.2 Selection 205 process 250 Computing Consequences 6.3 A general Computing Consequences 7.2 Selection treatment of selection 208 and migration in Lake Erie water snakes 252 7.2 Genetic Drift 254 Computing Consequences 7.3 The probability that a given allele will be the one that drifts to fixation 262 Computing Consequences 7.4 Effective population size 265 Computing Consequences 7.5 The rate of evolutionary substitution under genetic drift 270 6 Contents 7.3 Genetic Drift and Molecular Evolution 274 7.4 Nonrandom Mating 289 Computing Consequences 7.6 Genotype frequencies in an inbred population 293 7.5 Conservation Genetics of the Florida Panther 297 Summary299•Questions299 ExploringtheLiterature301•Citations302 CHAPTER 8 Evolution at Multiple Loci: Linkage and Sex 305 Computing Consequences 9.3 The selection gradient and the selection differential 363 8.1 Evolution at Two Loci: Linkage 9.5 Predicting the Evolutionary Response Equilibrium and Linkage to Selection 364 Disequilibrium 306 9.6 Modes of Selection and the Computing Consequences 8.1 Maintenance of Genetic Variation 370 The coefficient of linkage disequilibrium 309 9.7 The Bell-Curve Fallacy and Other Computing Consequences 8.2 Hardy– Misinterpretations of Heritability 374 Weinberg analysis for two loci 310 Summary379•Questions379 Computing Consequences 8.3 Sexual ExploringtheLiterature381•Citations381 reproduction reduces linkage disequilibrium 315 8.2 Practical Reasons to Study Linkage Disequilibrium 321 Computing Consequences 8.4 Estimating PART 3 the age of the GBA–84GG mutation 323 ADAPTATION 383 8.3 The Adaptive Significance of Sex 328 Computing Consequences 8.5 A demographic model of the maintenance of CHAPTER 10 males in the nematode Caenorhabditiselegans 331 Studying Adaptation: Evolutionary Summary338•Questions339 Analysis of Form and Function 383 ExploringtheLiterature340•Citations341 10.1 All Hypotheses Must Be Tested: Oxpeckers Reconsidered 384 CHAPTER 9 10.2 Experiments 387 Evolution at Multiple Loci: Computing Consequences 10.1 A primer on statistical testing 391 Quantitative Genetics 343 10.3 Observational Studies 392 9.1 The Nature of Quantitative Traits 344 10.4 The Comparative Method 396 9.2 Identifying Loci That Contribute to Computing Consequences 10.2 Calculating Quantitative Traits 348 phylogenetically independent contrasts 398 Computing Consequences 9.1 Genetic 10.5 Phenotypic Plasticity 401 mapping and LOD scores 352 10.6 Trade-Offs and Constraints 403 9.3 Measuring Heritable Variation 357 10.7 Selection Operates on Different Computing Consequences 9.2 Additive Levels 411 genetic variation versus dominance genetic 10.8 Strategies for Asking Interesting variation 359 Questions 415 9.4 Measuring Differences in Survival Summary416•Questions416 and Reproductive Success 362 ExploringtheLiterature418•Citations419 Contents 7 CHAPTER 11 Computing Consequences 13.1 Late-acting deleterious mutations are weakly selected 515 Sexual Selection 421 Computing Consequences 13.2 Alleles 11.1 Sexual Dimorphism and Sex 422 conferring early benefits and late costs can 11.2 Sexual Selection on Males: be adaptive 518 Competition 431 13.3 How Many Offspring Should an 11.3 Sexual Selection on Males: Individual Produce in a Given Year? 527 Female Choice 437 13.4 How Big Should Each Offspring Be? 531 Computing Consequences 11.1 Runaway 13.5 Conflicts of Interest between Life sexual selection 444 Histories 536 11.4 Sexual Selection on Females 452 13.6 Life Histories in a Broader 11.5 Sexual Selection in Plants 455 Evolutionary Context 539 11.6 Sexual Dimorphism in Humans 458 Summary 544•Questions544 Summary 462•Questions462 ExploringtheLiterature546•Citations546 ExploringtheLiterature464•Citations465 CHAPTER 14 CHAPTER 12 Evolution and Human Health 549 The Evolution of Social Behavior 469 14.1 Evolving Pathogens: Evasion of the 12.1 Four Kinds of Social Behavior 470 Host’s Immune Response 551 12.2 Kin Selection and Costly Behavior 473 14.2 Evolving Pathogens: Antibiotic Computing Consequences 12.1 Calculating Resistance 559 relatedness as the probability of identity 14.3 Evolving Pathogens: Virulence 562 by descent 475 14.4 Tissues as Evolving Populations 12.3 Multilevel Selection and Cooperation 485 of Cells 567 Computing Consequences 12.2 Different 14.5 Selection Thinking Applied to Humans 570 perspectives on the same evolutionary process 487 14.6 Adaptation and Medical Physiology: 12.4 Cooperation and Conflict 491 Fever 578 12.5 The Evolution of Eusociality 497 14.7 Adaptation and Human Behavior: Summary 500•Questions501 Parenting 581 ExploringtheLiterature502•Citations503 Computing Consequences 14.1 Is cultural evolution Darwinian? 583 CHAPTER 13 Summary 589•Questions589 ExploringtheLiterature591•Citations591 Aging and Other Life-History Characters 505 13.1 Basic Issues in Life-History Analysis 507 CHAPTER 15 13.2 Why Do Organisms Age and Die? 509 Genome Evolution and the Molecular Basis of Adaptation 595 15.1 Diversity among Genomes 596 15.2 Mobile Genetic Elements 600 15.3 The Evolution of Mutation Rates 605 15.4 Gene Duplication and Gene Families 608 15.5 The Locus of Adaptation in Natural Populations 615 Summary 620•Questions620 ExploringtheLiterature621•Citations622 8 Contents Computing Consequences 18.1 Evolutionary trends 720 18.3 Taxonomic and Morphological Diversity over Time 721 18.4 Mass and Background Extinctions 723 18.5 Macroevolution 733 18.6 Fossil and Molecular Divergence Timing 741 Summary 744•Questions745 ExploringtheLiterature746•Citations746 PART 4 CHAPTER 19 THE HISTORY OF LIFE 623 Development and Evolution 749 19.1 The Divorce and Reconciliation of CHAPTER 16 Development and Evolution 750 19.2 Hox Genes and the Birth of Evo-Devo 752 Mechanisms of Speciation 623 19.3 Post Hox: Evo-Devo 2.0 758 16.1 Species Concepts 624 19.4 Hox Redux: Homology or Homoplasy? 777 16.2 Mechanisms of Isolation 630 19.5 The Future of Evo-Devo 778 16.3 Mechanisms of Divergence 637 Summary 779•Questions780 16.4 Hybridization and Gene Flow ExploringtheLiterature780•Citations781 between Species 643 16.5 What Drives Diversification? 651 CHAPTER 20 Summary 654•Questions655 ExploringtheLiterature656•Citations657 Human Evolution 783 20.1 Relationships among Humans CHAPTER 17 and Extant Apes 784 20.2 The Recent Ancestry of Humans 794 The Origins of Life and 20.3 Origin of the Species Homo sapiens 804 Precambrian Evolution 659 Computing Consequences 20.1 Using allele frequencies and linkage disequilibrium to date 17.1 What Was the First Living Thing? 661 the modern human expansion from Africa 811 17.2 Where Did the First Living Thing 20.4 The Evolution of Distinctive Human Come From? 669 Traits 816 17.3 What Was the Last Common Ancestor Summary821•Questions821 of All Extant Organisms and What Is ExploringtheLiterature823•Citations824 the Shape of the Tree of Life? 677 17.4 How Did LUCA’s Descendants Evolve Glossary 829 into Today’s Organisms? 692 Summary 697•Questions698 IllustrationCredits 836 ExploringtheLiterature700•Citations700 Index 844 CHAPTER 18 Evolution and the Fossil Record 705 18.1 The Nature of the Fossil Record 706 18.2 Evolution in the Fossil Record 710 Preface E volutionary biology has changed dramatically during the 15 years we have worked on Evolutionary Analysis. As one measure of this change, consider that when the first edition went to press, the genomes of just five cellular organisms had been sequenced: three bacteria, one archaean, and one eukaryote. As the fifth edition goes to press, Erica Bree Rosenblum and colleagues reported in the Proceedings of the National Academy of Sciences (110: 9385–9390) that they had sequenced the genomes of 29 strains of a single species, the chytrid fungus Batra- chochytrium dendrobatidis. This work was part of an effort to unravel the evolutionary history of an emerging pathogen that has decimated amphibian populations around the world and driven some species to extinction. The avalanche of sequence data has allowed evolutionary biologists to answer long-standing questions with greatly increased depth and clarity. In Chapter 20, Human Evolution, for example, we dis- cuss a recent analysis of differences among genomic regions in the evolutionary relationships among humans, chimpanzees, and gorillas. For some questions, the answers have changed completely. In the fourth edition we noted that available sequence data provided no support for the hypothesis that modern humans and Neandertals interbred. But in the fifth edition we describe genomic analyses sug- gesting that the two lineages interbred after all. Evolutionary Analysis provides an entry to this dynamic field of study for undergraduates majoring in the life sciences. We assume that readers have com- pleted much or all of their introductory coursework and are beginning to explore in more detail areas of biology relevant to their personal and professional lives. Therefore, throughout the book we attempt to show the relevance of evolution to all of biology and to real-world problems. Since the first edition, our primary goal has been to encourage readers to think like scientists. We present evolutionary biology not as a collection of facts but as an ongoing research effort. When exploring an issue, we begin with questions. Why are untreated HIV infections typically fatal? Why do purebred Florida p anthers show such poor health, and what can be done to save their dwindling population? Why do mutation rates decrease with genome size among some kinds of organisms, but increase with genome size among others? We use such questions to engage stu- dents’ curiosity and to motivate discussions of background information and theory. These discussions enable us to frame alternative hypotheses, consider how they can be tested, and make predictions. We then present and analyze data, consider its implications, and highlight new questions for future research. The analytical and technical skills readers learn from this approach are broadly applicable, and will stay with them long after the details of particular examples have faded. New to This Edition M any of the research areas we cover are advancing at a rate we would not have dreamed possible just a few years ago. We have looked close- ly at every chapter to both improve how we are teaching today’s students and to thoroughly update our coverage. 9
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