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Copyright, iv
Preface, xiii
Chapter 1. Evolutionary Biology, 1
What Is Evolution?, 2
Before Darwin, 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
Chapter 3. 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
Chapter 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
Chapter 5. 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
Modern human origins, 147
Geographic Range Limits: Ecology and Evolution, 150
Range limits: An evolutionary problem, 152
Evolution of Geographic Patterns of Diversity, 153
Community convergence, 153
Effects of History on Contemporary Diversity Patterns, 155
Chapter 7. 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
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
Chapter 10. 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 modern Homo sapiens revisited, 274
Chapter 11. 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
Chapter 12. 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
Chapter 13. 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
Chapter 14. 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
Chapter 15. 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 16. 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 siblicide, 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
Chapter 17. 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
Chapter 18. Speciation, 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
Chapter 19. 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
Chapter 20. 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, 538
Exon shuffling, 538
Gene chimerism, 540
Motif multiplication and exon loss, 541
The Evolution of Multigene Families, 543
Gene duplication, 543
Multigene families and the origin of key innovations, 543
Gene and Genome Duplication, 545
Duplication of whole genomes and chromosomal segments, 545
Possible fates of duplicate genes, 547
Selective fates of recently duplicated loci, 549
Rates of gene duplication, 549
Chapter 21. 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
Chapter 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, I-1
About the Book, IBC-1

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