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S E C O N D ED
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DOUGLAS J. FUTUYMA
THE evolution SECOND E D I T I O N
COMPANION WEBSITE www.sinauer.com/evolution
The evolution Companion Website is a valuable companion to the textbook that can help you master the material you will be studying in your evolution course. Available to you free of charge, the site is designed to help you learn the concepts and terminology introduced in each chapter, and to use that knowledge to analyze real-world research.
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Using Fossil Evidence to Make Inferences about the Evolution of Cetaceans
Introduction
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Features of the Companion Website Data Analysis Exercises: These inquiry-based exercises chal
lenge you to think as a scientist and to analyze and interpret experimental data. Based on real papers and experiments, these exercises involve answering questions by analyzing the data from the experiment.
Simulation Exercises: These exercises include interactive modules that allow you to explore some of the dynamic processes of evolution. Each exercise poses questions answered by running the simulation and observing and analyzing the outcomes.
Online Quizzes: For each chapter of the textbook, the companion website includes a multiple-choice quiz that covers all the main topics presented in the chapter Your instructor may assign these quizzes, or they may be made avail
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Flashcards & Key Terms: Flashcard activities help you master the many new terms introduced in the evolution course. Each chapter's set of flashcards includes all of the key terms introduced in the chapter.
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Glossary: A complete online version of the glossary, for quick access to definitions of Important terms.
evolution SECOND EOniON
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evolution SECOND EDIT ION
DOUGLAS J. FUTUYMA Stony Brook University
Chapter 20, "Evolution of Genes and Genomes' by Scott V. Edwards, Harvard University
Chapter 21, ''Evolution and Development by John R. True, Stony Brook University
VA SINAUER ASSOCIATES, INC. • Publishers Sunderland, Massachusetts U.S.A.
On the Cover Wallace's flying frog (Rhacophorus nigropalmatus), an inhabitant of the rain forest canopy in southeastern Asia, glides from tree to tree with the aid of its toe webbing, which is much more extensive than in most other tree frog species. Such modification of ancestral characteristics to serve new functions is a common theme in evolution, and is often associated with adaptation to new ways of life. This species was named in 1869 by the naturalist Alfred Russel Wallace, who conceived of evolution by natural selection independently of Darwin. (Photograph © Stephen Dalton/Minden Pictures, Inc.)
evolution SECOND EDITION
Copyright © 2009 by Sinauer Associates, Inc. All rights reserved. This book may not be reproduced in whole or in part without permission from the publisher.
Sinauer Associates, Inc., 23 Plumtree Road, Sunderland, MA 01375 USA
FAX: 413-549-4300
Email: [email protected], [email protected]
Website: www.sinauer.com
Sources of the scientists' photographs appearing in Chapter 1 are gratefully acknowledged: C. Darwin and A. R. Wallace courtesy of The American Philosophical Library R. A. Fisher courtesy of Joan Fisher Box J. B. S. Haldane courtesy of Dr. K. Patau S. Wright courtesy of Doris Marie Provine , E. Mayr courtesy of Har\'ard News Ser\-ice and E. Mayr G. L. Stebbins, G. G. Simpson, and Th. Dobzhansky courtesy of G. L. Stebbins M. Kimura courtesy of Wilham Prov^ine
Library of Congress Cataloging-in-Publication Data
Futuyma, Douglas J., 1942-Evolution / Douglas J. Futuyma. — 2nd ed.
p. cm. Includes index. ISBN 978-0-87893-223-8 (hardco\-er) 1. Evolution (Biolog)-) I. Title.
QH366.2.F87 2009 576.8—dc22 2009010142
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To my teachers
Larry Slobodkin, Dick Lewontin, Bill Brown
Brief Contents
CHAPTER 1 Evolutionary Biology 1
CHAPTER 2 The Tree of Life: Classification and Phylogeny 17
CHAPTER 3
CHAPTER 4
CHAPTER 5
CHAPTER 6
CHAPTER 7
CHAPTER 8
CHAPTER 9
CHAPTER 10
CHAPTER 1 1
CHAPTER 12
Patterns of Evolution 45
Evolution in the Fossil Record 73
A History of Life on Earth 101
The Geography of Evolution 133
The Evolution of Biodiversity 161
The Origin of Genetic Variation 187
Variation 215
Genetic Drift: Evolution at Random 255
Natural Selection and Adaptation 279
The Genetical Theory of Natural Selection 303
CHAPTER 13 Phenotypic Evolution 337
CHAPTER 14 The Evolution of Life Histories 369
CHAPTER 15 Sex and Reproductive Success 387
CHAPTER 16 Conflict and Cooperation 413
CHAPTER 17 Species 445
CHAPTER
CHAPTER
CHAPTER
18
19
20
CHAPTER 21
CHAPTER
CHAPTER
22
23
Speciation 471
Coevolution: Evolving Interactions among Species 499
Evolution of Genes and Genomes 523
Evolution and Development 553
Macroevolution: Evolution above the Species Level 585
Evolutionary Science, Creationism, and Society 609
Contents
CHAPTER 1 C H A P T E R 3
Evolutionary Biology 1 What Is Evolution? 2 Before Dan/vin 4 Charles Darwin 6 Darwin's Evolutionary Theory 7 Evolutionary Theories after Darwin 8 The Evolutionary Synthesis 9
Fundamental principles of evolution 9
Evolutionary Biology since the Synthesis 11 Philosophical Issues 12 Ethics, Religion, and Evolution 13 Evolution as Fact and Theory 13
CHAPTER 2
The Tree of Life: Classification and Phylogeny 17 Classification 19 Inferring Phylogenetic History 22
Similarity and common ancestry 22 Complications in inferring phylogeny 25
The method of maximum parsimony 27
An example of phylogenetic analysis 29
Evaluating phylogenetic hypotheses 31
Molecular Clocks 33 Gene Trees 35 Difficulties in Phylogenetic Analysis 37 Hybridization and Horizontal Gene Transfer 42
Patterns of Evolution 45 Evolutionary History and Classification 47
Inferring the History of Character Evolution 48 Some Patterns of Evolutionary Change Inferred
from Systematics 50 Most features of organisms have been modified from
pre-existing features 50
Homoplasy is common 53 Rates of character evolution differ 56 Evolution is often gradual 57
Change in form is often correlated with change in function 58
Similarity among species changes throughout ontogeny 58 Development underlies some common patterns of
morphological evolution 59
Phylogenetic Analysis Documents Evolutionary Trends 63
Many Clades Display Adaptive Radiation 64 Patterns in Genes and Genomes 66
Genome size 66 «
Duplicated genes and genomes 67
C H A P T E R 4
Evolution in the Fossil Record 73 Some Geological Fundamentals 73
Plate tectonics 74 Geological time 74
The geological time scale 75
The Fossil Record 77 Evolutionary changes within species 77
Origins of higher taxa 79
The Hominin Fossil Record 88 Phylogeny and the Fossil Record 91 Evolutionary Trends 92 Punctuated Equilibria 93 Rates of Evolution 96
V I I I CONTENTS
CHAPTER 5 C H A P T E R 7
A History of Life on Earth 101 Before Life Began 102 The Emergence of Life 102 Precambrian Life 104 Paleozoic Life: The Cambrian Explosion 108 Paleozoic Life: Ordovician to Devonian 111
Marine life 111
Terrestrial life 112
Paleozoic Life: Carboniferous and Permian 114 Terrestrial life 114
Aquatic life 115
Mesozoic Life 115 Marine life 115 Terrestrial plants and arthropods 116
Vertebrates 119
The Cenozoic Era 121
Aquatic life 122 Terrestrial life 123 The adaptive radiation of mammals 123 Pleistocene events 126
CHAPTER 6
The Geography of Evolution 133 Biogeographic Evidence for Evolution 134 Major Patterns of Distribution 135 Historical Factors Affecting Geographic
Distributions 137 Testing Hypotheses in Historical Biogeography 140
Examples of historical biogeographic analyses 141
The composition of regional biotas 145
Phylogeography 146 Pleistocene population shifts 146
Modem human origins 147
Geographic Range Limits: Ecology and Evolution 150 Range limits: A n evolutionary problem 152
Evolution of Geographic Patterns of Diversity 153 Commimity convergence 153
Effects of History on Contemporary Diversity Patterns 155
The Evolution of Biodiversity 161 Estimating and Modeling Biological Diversity 162
Estimates of diversity 162
Taxonomic Diversity through the Phanerozoic 163 Rates of origination and extinction 164 Extinction rates have declined over time 165 Do extinction rates change as clades age? 168 Causes of extinction 168 Mass extinctions 169
Diversification 171 Modeling rates of change in diversity 171 Does species diversity reach equilibrium? 174
CHAPTER 8
The Origin of Genetic Variation 187 Genes and Genomes 188 Gene Mutations 190
Kinds of mutations 191 Examples of mutations 195 Rates of mutation 196 Phenotypic effects of mutations 200 Effects of mutations on fitness 202
The limits of mutation 205
Mutation as a Random Process 206 Alterations of the Karyotype 207
Polyploidy 207
Chromosome rearrangements 208
CHAPTER 9
Variation 215 Sources of Phenotypic Variation 217 Fundamental Principles of Genetic Variation in
Populations 220 Frequencies of alleles and genotypes: The Hardy-
Weinberg principle 221 An example: The human MN locus 223 The significance of the Hardy-Weinberg principle:
Factors in evolution 224
CONTENTS IX
Frequencies of alleles, genotypes, and phenotypes 225 Inbreeding 225
Genetic Variation in Natural Populations: Individual Genes 227
Morphology and viability 227 Inbreeding depression 229 Genetic variation at the molecular level 229
Genetic Variation in Natural Populations: Multiple Loci 232
Variation in quantitative traits 236
Variation among Populations 241 Patterns of geographic variation 241 Gene flow 244 Allele frequency differences among populations 246 Human genetic variation 248
C H A P T E R 1 0
Genetic Drift: Evolution at Random 255 The Theory of Genetic Drift 256
Genetic drift as sampling error 256 Coalescence 257
Random fluctuations in allele frequencies 259
Evolution by Genetic Drift 260 Effective population size 261
Founder effects 263 Genetic drift in real populations 263
The Neutral Theory of Molecular Evolution 266 Principles of the neutral theory 267 Variation within and among species 269
Support for the neutral theory 270
Gene Flow and Genetic Drift 272 Gene trees and population history 272 The origin of modem Homo sapiens revisited 274
C H A P T E R 1 1
Natural Selection and Adaptation 279
Adaptations in Action: Some Examples 280
The Nature of Natural Selection 282
Design and mechanism 282
Definitions of natural selection 283
Natural selection and chance 284
Selection of and selection for 284
Examples of Natural Selection 285 Bacterial populations 285 Inversion polymorphism in Drosophila 286 Male reproductive success 287 Population size in flour beetles 288 Kin discrimination in cannibalistic salamanders 289
Selfish genetic elements 290
Levels of Selection 290 Selection of organisms and groups 291
Species selection 293
The Nature of Adaptations 294 Definitions of adaptation 294 Recognizing adaptations 294
What Not to Expect of Natural Selection and Adaptation 298
The necessity of adaptation 298 Perfection 299 Progress 299 Harmony and the balance of nature 299 Morality and ethics 300
C H A P T E R 1 2
The Genetical Theory of Natural Selection 303 Fitness 304
« Modes of selection 304 Defining fitness 305
Components of fitness 306
Models of Selection 308 Directional selection 308
Deleterious alleles in natural populations 312
Polymorphism Maintained by Balancing Selection 315 Heterozygote advantage 315 Antagonistic and varying selection 317
Frequency-dependent selection 318
Multiple Outcomes of Evolutionary Change 321 Positive frequency-dependent selection 321 Heterozygote disadvantage 321 Adaptive landscapes 322
Interaction of selection and genetic drift 322
The Strength of Natural Selection 324 Molecular Signatures of Natural Selection 325
Theoretical expectations 325
Signatures of selection 329
Adaptive evolution across the genome 332
CONTENTS
C H A P T E R 1 3 CHAPTER 1 5
Phenotypic Evolution 337 Genetic Architecture of Phenotypic Traits 338 Components of Phenotypic Variation 340
Genetic variance in natural populations 343
Genetic Drift or Natural Selection? 343 Natural Selection on Quantitative Traits 345
Response to directional selection 345 Responses to artificial selection 345 Directional selection in natural populations 347 Stabilizing and disruptive selection 348 Evolution observed 348
What Maintains Genetic Variation in Quantitative Characters? 350
Correlated Evolution of Quantitative Traits 352 Correlated selection 352 Genetic correlation 352
How genetic correlation affects evolution 354
Can Genetics Predict Long-Term Evolution? 355 Norms of Reaction 357
Canalization 357 Phenotypic plasticity 358
Evolution of variability 360
Genetic Constraints on Evolution 362
C H A P T E R 1 4
The Evolution of Life Histories 369 Individual Selection and Group Selection 371
Modeling Optimal Phenotypes 372
Life History Traits as Components of Fitness 373 Female fecundity semelparity, and iteroparity 374 Age structure and reproductive success 376
Trade-offs 377 The Evolution of Life History Traits 379
Life span and senescence 379 Age schedules of reproduction 380
Number and size of offspring 381
The Evolution of the Rate of Increase 383
Sex and Reproductive Success 387 The Evolution of Mutation Rates 388
Sexual and Asexual Reproduction 388
The Paradox of Sex 389 Parthenogenesis versus the cost of sex 389 Hypotheses for the advantage of sex and
recombination 391
Sex Ratios and Sex Allocation 393
Inbreeding and Outcrossing 395
The Concept of Sexual Selection 397
Contests between Males and between Sperm 398
Sexual Selection by Mate Choice 400 Direct benefits of mate choice 400 Indirect benefits of mate choice 402 Sensory bias 405
Antagonistic coevolution 406
Alternative Mating Strategies 408
CHAPTER 1 6
Conflict and Cooperation 413 Conflict 414
Social Interactions and Cooperation 417 Cooperation based on direct benefits 417 Reciprocity: Cooperation based On repeated
interactions 418
The evolution of altruism by shared genes 420
A Genetic Battleground: The Family 424 Mating systems and parental care 424 Infanticide, abortion, and sibhcide 426 Parent-offspring conflict 427 Cooperative breeding 427
Social insects 428
Genetic Conflict 431
Parasitism, Mutualism, and Levels of Organization 433
Human Behavior and Human Societies 435 Variation in sexual orientation 435 The question of human nature 437 Cultural evolution and gene-culture coevolution 438
CONTENTS X I
C H A P T E R 1 7
Species 445 What Are Species? 446
Phylogenetic species concepts 447 The biological species concept 447 Domain and application of the biological species
concept 448 Taxonomic versus biological species 450
When species concepts conflict 451
Barriers to Gene Flow 451 Premating barriers 451 Postmating, prezygotic barriers 453
Postzygotic barriers 455
How Species Are Diagnosed 456 Differences among Species 456 The Genetic Basis of Reproductive Barriers 458
Genes affecting reproductive isolation 458 Functions of genes that cause reproductive isolation 461 Chromosome differences and postzygotic isolation 461
The significance of genetic studies of reproductive isolation 462
Molecular Divergence among Species 463
Hybridization 464 Primary and secondary hybrid zones 464 Genetic dynamics in a hybrid zone 465 The fate of hybrid zones 467
C H A P T E R 1 8
Speaation 471 Modes of Speciation 472
Allopatric Speciation 473 Evidence for allopatric speciation 473
Mechanisms of vicariant allopatric speciation 476 Ecological selection and speciation 477 Sexual selection and speciation 480
Reinforcement of reproductive isolation 481
Peripatric speciation 484
Alternatives to Allopatric Speciation 486 Parapatric speciation 486
Sympatric speciation 487
Polyploidy and Recombinational Speciation 490 Polyploidy 490 Recombinational speciation 492
How Fast Is Speciation? 493
Consequences of Speciation 495
C H A P T E R 1 9
Coevolution: Evolving Interactions among Species 499 The Nature of Coevolution 500
Phylogenetic Aspects of Species Associations 501
Coevolution of Enemies and Victims 503 Models of enemy-victim coevolution 504 Examples of predator-prey coevolution 506 Plants and herbivores 507 Infectious disease and the evolution of parasite
virulence 510
Mutualisms 513
The Evolution of Competitive Interactions 516 Multispecies interactions and community structure 518
C H A P T E R 2 0
Evolution of Genes and Genomes 523 , New Molecules and Processes in Genomes 525
Genome Diversity and Evolution 525 Diversity of genome structure 525
Viral and microbial genomes—the smallest genomes 527
Repetitive sequences and transposable elements 529
New genomes reveal major events in the history of life 531
Protein Evolution and Translational Robustness 532 Codon bias 532
Gene expression and selection on translation errors 533
Natural Selection across the Genome 534 Adaptive molecular evolution in primates 535
Molecular evolution in the human lineage 536
Scaling up: From gene to genome 536
Origin of New Genes 537 Lateral gene transfer 537
Origin of new genes from noncoding regions 537
Exon shuffling 538
Gene chimerism 540
Motif multiplication and exon loss 541
X l i CONTENTS
The Evolution of Multigene Families 542 Gene dupHcation 542
Multigene famiUes and the origin of key innovations 543
Gene and Genome Duplication 545 Duplication of whole genomes and chromosomal
segments 545 Possible fates of dupHcate genes 546 Selective fates of recently dupHcated loci 548 Rates of gene duplication 549
CHAPTER 2 1
Evolution and Development 553 Hox Genes and the Dawn of Modern EDB 554
Types of Evidence in Contemporary EDB 559
The Evolving Concept of Homology 560
Evolutionarily Conserved Developmental Pathways 563
Gene Regulation: A Keystone of Developmental Evolution 565
Evolution of protein-coding sequences is also an important contributor to phenotypic evolution 569
Modularity in morphological evolution 569 Co-option and the evolution of novel characters 570 The developmental genetics of heterochrony 571 The evolution of allometry 573
Developmental Constraints and Morphological Evolution 574
The Molecular Genetic Basis of Gene Regulatory Evolution 578
Toward the EDB of Homo sapiens 581
C H A P T E R 22
Macroevolution: Evolution above the Species Level 585 Rates of Evolution 586
Punctuated equilibrium and stasis 587
Gradualism and Saltation 590 Phylogenetic Conservatism and Change 592
The Evolution of Novelty 595 Accounting for incipient and novel features 595
Complex characteristics 597
Trends and Progress 600 Trends: Kinds and causes 600 Examples of trends 601 Are there major trends in the history of life? 602 The question of progress 605
CHAPTER 23
Evolutionary Science, Creationism, and Society 609 Creationists and Other Skeptics 610 Science, Belief, and Education 611 The Evidence for Evolution 614
The fossil record 614
Phylogenetic and comparative studies 615 Genes and genomes 615 Biogeography 616 Failures of the argument from design 616 Evolution and its mechanisms, observed 618
Refuting Creationist Arguments 619 On arguing for evolution 623
Why Should We Teach Evolution? 623 Health and medicine 624 Agriculture and natural resources 627 Environment and conservation 628 Human behavior 629 Understanding nature and humanity 631
Glossary G-1
Literature Cited LC-1
Index 1-1