The Princeton Guide to Evolution

Preface vii

Contributors ix

Section I Introduction 1

I.1 What Is Evolution? 3

I.2 The History of Evolutionary Thought 10

I.3 The Evidence for Evolution 28

I.4 From DNA to Phenotypes 40

Section II Phylogenetics and the History of Life 47

II.1 Interpretation of Phylogenetic Trees 51

II.2 Phylogenetic Inference 60

II.3 Molecular Clock Dating 67

II.4 Historical Biogeography 75

II.5 Phylogeography 82

II.6 Concepts in Character Macroevolution: Adaptation, Homology, and Evolvability 89

II.7 Using Phylogenies to Study Phenotypic Evolution: Comparative Methods and Tests of Adaptation 100

II.8 Taxonomy in a Phylogenetic Framework 106

II.9 The Fossil Record 112

II.10 The Origin of Life 120

II.11 Evolution in the Prokaryotic Grade 127

II.12 Origin and Diversification of Eukaryotes 136

II.13 Major Events in the Evolution of Land Plants 143

II.14 Major Events in the Evolution of Fungi 152

II.15 Origin and Early Evolution of Animals 159

II.16 Major Events in the Evolution ofArthropods 167

II.17 Major Features of Tetrapod Evolution 174

II.18 Human Evolution 183

Section III Natural Selection and Adaptation 189

III.1 Natural Selection, Adaptation, and Fitness: Overview 193

III.2 Units and Levels of Selection 200

III.3 Theory of Selection in Populations 206

III.4 Kin Selection and Inclusive Fitness 215

III.5 Phenotypic Selection on Quantitative Traits 221

III.6 Responses to Selection: Experimental Populations 230

III.7 Responses to Selection: Natural Populations 238

III.8 Evolutionary Limits and Constraints 247

III.9 Evolution of Modifier Genes and Biological Systems 253

III.10 Evolution of Reaction Norms 261

III.11 Evolution of Life Histories 268

III.12 Evolution of Form and Function 276

III.13 Biochemical and Physiological Adaptations 282

III.14 Evolution of the Ecological Niche 288

III.15 Adaptation to the Biotic Environment 298

Section IV Evolutionary Processes 305

IV.1 Genetic Drift 307

IV.2 Mutation 315

IV.3 Geographic Variation, Population Structure, and Migration 321

IV.4 Recombination and Sex 328

IV.5 Genetic Load 334

IV.6 Inbreeding 340

IV.7 Selfish Genetic Elements and Genetic Conflict 347

IV.8 Evolution of Mating Systems: Outcrossing versus Selfing 356

Section V Genes, Genomes, Phenotypes 363

V.1 Molecular Evolution 367

V.2 Genome Evolution 374

V.3 Comparative Genomics 380

V.4 Evolution of Sex Chromosomes 387

V.5 Gene Duplication 397

V.6 Evolution of New Genes 406

V.7 Evolution of Gene Expression 413

V.8 Epigenetics 420

V.9 Evolution of Molecular Networks 428

V.10 Evolution and Development: Organisms 436

V.11 Evolution and Development: Molecules 444

V.12 Genetics of Phenotypic Evolution 452

V.13 Dissection of Complex Trait Evolution 458

V.14 Searching for Adaptation in the Genome 466

V.15 Ancient DNA 475

Section VI Speciation and Macroevolution 483

VI.1 Species and Speciation 489

VI.2 Speciation Patterns 496

VI.3 Geography, Range Evolution, and Speciation 504

VI.4 Speciation and Natural Selection 512

VI.5 Speciation and Sexual Selection 520

VI.6 Gene Flow, Hybridization, and Speciation 529

VI.7 Coevolution and Speciation 535

VI.8 Genetics of Speciation 543

VI.9 Speciation and Genome Evolution 549

VI.10 Adaptive Radiation 559

VI.11 Macroevolutionary Rates 567

VI.12 Macroevolutionary Trends 573

VI.13 Causes and Consequences of Extinction 579

V1.14 Species Selection 586

VI.15 Key Evolutionary Innovations 592

VI.16 Evolution of Communities 599

Section VII Evolution of Behavior, Society, and Humans 605

VII.1 Genes, Brains, and Behavior 609

VII.2 Evolution of Hormones and Behavior 616

VII.3 Game Theory and Behavior 624

VII.4 Sexual Selection and Its Impact on Mating Systems 632

VII.5 Sexual Selection: Male-Male Competition 641

VII.6 Sexual Selection: Mate Choice 647

VII.7 Evolution of Communication 655

VII.8 Evolution of Parental Care 663

VII.9 Cooperation and Conflict: Microbes to Humans 671

VII.10 Cooperative Breeding 677

VII.11 Human Behavioral Ecology 683

VII.12 Evolutionary Psychology 690

VII.13 Evolution of Eusociality 697

VII.14 Cognition: Phylogeny, Adaptation, and By-Products 703

VII.15 Evolution of Apparently Nonadaptive Behavior 710

VII.16 Aging and Menopause 718

Section VIII Evolution and Modern Society 727

VIII.1 Evolutionary Medicine 733

VIII.2 Evolution of Parasite Virulence 741

VIII.3 Evolution of Antibiotic Resistance 747

VIII.4 Evolution and Microbial Forensics 754

VIII.5 Domestication and the Evolution of Agriculture 760

VIII.6 Evolution and Conservation 766

VIII.7 Directed Evolution 774

VIII.8 Evolution and Computing 780

VIII.9 Linguistics and the Evolution of Human Language 786

VIII.10 Cultural Evolution 795

VIII.11 Evolution and Notions of Human Race 801

VIII.12 The Future of Human Evolution 809

VIII.13 Evolution and Religion 817

VIII.14 Creationism and Intelligent Design 825

VIII.15 Evolution and the Media 832

Index 837