Evolution

Cover......Page 1
Title Page......Page 5
Copyright......Page 6
Brief Contents......Page 7
Contents......Page 9
About the Authors......Page 21
Preface......Page 23
Part I  Foundations of Evolutionary Biology......Page 33
1  An Overview of Evolutionary Biology......Page 35
1.1 A Brief Introduction to Evolution and Natural Selection......Page 37
1.2 Empirical and Theoretical Approaches to the Study of Evolution......Page 46
Box 1.1 A Mathematical Model of the Sex Ratio......Page 55
Key Terms......Page 57
Review Questions......Page 58
Suggested Readings......Page 59
2  Early Evolutionary Ideas and Darwin's Insight......Page 61
2.1 The Nature of Science: Natural verses Supernatural Explanations......Page 63
2.2 Time and a Changing World......Page 64
2.3 The Origins of Life and Its Diversity......Page 67
2.4 Organisms Are Well-Suited to Their Environment......Page 70
2.5 Darwin's Theory......Page 73
2.6 Darwin on Natural Selection......Page 77
2.7 Darwin on Common Ancestry......Page 82
2.8 Problems with Darwin's Theory......Page 86
2.9 The Reaction to Darwin and Early History of the Modern Synthesis......Page 87
Summary......Page 89
Review Questions......Page 90
Suggested Readings......Page 91
3  Natural Selection......Page 93
3.1 The Components of Natural Selection......Page 95
3.2 Adaptations and Fit to Environment......Page 104
3.3 Natural Selection in the Field......Page 106
3.4 Natural Selection in the Laboratory......Page 110
Box 3.1 Measuring Allele Frequencies and Fitness in E. coli......Page 113
3.5 Constraints on What Natural Selection Can Achieve......Page 115
3.6 Origin of Complex Traits......Page 121
Summary......Page 129
Review Questions......Page 130
Suggested Readings......Page 131
4  Phylogeny and Evolutionary History......Page 133
4.1 Phylogenies Reflect Evolutionary History......Page 135
Box 4.1 What Is the Difference between a Pedigree and a Phylogeny?......Page 137
4.2 Reading Phylogenetic Trees......Page 139
4.3 Traits on Trees......Page 148
4.4 Homology and Analogy......Page 150
4.5 Using Phylogenies to Generate Evolutionary Hypotheses......Page 156
Key Terms......Page 164
Review Questions......Page 165
Suggested Readings......Page 167
5  Inferring Phylogeny......Page 169
5.1 Building Trees......Page 171
5.2 Parsimony......Page 172
Box 5.1 The Fitch Algorithm......Page 176
5.3 Rooting Trees......Page 178
5.4 Distance Methods......Page 181
Box 5.2 Sequence Alignment......Page 182
5.5 How Many Different Trees Are There?......Page 185
5.6 Phylogenies and Statistical Confidence......Page 187
5.7 Evidence Used for Reconstructing Phylogenetic Trees......Page 192
5.8 Phylogeny and the Comparative Method......Page 199
Summary......Page 205
Review Questions......Page 206
Suggested Readings......Page 208
Part II Evolutionary Genetics......Page 209
6  Transmission Genetics and the Sources of Genetic Variation......Page 211
6.1 Mendel's Laws......Page 212
6.2 Transmission Genetics......Page 215
6.3 Variation and Mutation......Page 221
6.4 Effects of Mutations on Fitness......Page 226
Summary......Page 231
Key Terms......Page 232
Suggested Readings......Page 233
7  The Genetics of Populations......Page 235
7.1 Individual-Level versus Population-Level Thinking......Page 238
Box 7.1 Types of Equilibria......Page 239
7.2 The Hardy-Weinberg Model: A Null Model for Population Genetics......Page 240
Box 7.2 Basic Probability Calculations......Page 243
Box 7.3 Hardy-Weinberg Equilibrium Is a Mixed Equilibrium......Page 244
Box 7.4 Testing for Hardy-Weinberg Equilibrium......Page 247
7.3 Natural Selection......Page 248
Box 7.5 Natural Selection Favoring a Dominant Allele......Page 251
Box 7.6 Equilibrium Allele Frequencies in Overdominance and Underdominance......Page 255
Box 7.7 A Population-Genetic Model of Mutation......Page 260
Box 7.8 Mutation-Selection Balance for a Deleterious Recessive Allele......Page 262
7.5 Nonrandom Mating......Page 264
Box 7.9 Wright's F-statistic......Page 266
7.6 Migration......Page 268
7.7 Consequences on Variation within and between Populations......Page 269
Summary......Page 271
Review Questions......Page 272
Suggested Readings......Page 273
8  Evolution in Finite Populations......Page 275
8.1 Random Change and Genetic Drift......Page 277
Box 8.1 The Wright-Fisher Model......Page 278
Box 8.2 Quantifying the Effects of Genetic Drift on Variation......Page 282
Box 8.3 Effective Population Size......Page 284
8.2 Coalescent Theory and the Geneology of Genes......Page 290
Box 8.4 A Mathematical Treatment of the Coalescent Process......Page 292
8.3 Demography, Biogeography, and Drift......Page 297
Box 8.5 Wright's F-statistic at a Neutral Locus with Mutation......Page 304
8.5 The Neutral Theory of Molecular Evolution......Page 308
Summary......Page 319
Review Questions......Page 320
Suggested Readings......Page 321
9  Evolution at Multiple Loci......Page 323
9.1 Polygenic Traits and the Nature of Heredity......Page 325
Box 9.1 A Numerical Example of How Selection and Reassortment Can Generate New Phenotypes......Page 329
9.2 Population Genetics of Multiple Loci......Page 330
Box 9.2 How the Coefficient of Linkage Disequilibrium Changes over Time in the Hardy-Weinberg Model......Page 340
9.3 Adaptive Landscapes......Page 345
9.4 Quantitative Genetics......Page 350
Box 9.3 Additive, Dominance, and Epistatic Effects......Page 354
Box 9.4 Mapping Quantitative Trait Loci......Page 359
Key Terms......Page 363
Review Questions......Page 364
Suggested Readings......Page 365
10 Genome Evolution......Page 367
10.1 Whole-Genome Sequencing......Page 369
10.2 Resolving the Paradoxes of Genome Size......Page 370
10.3 Content and Structure of Viral Genomes......Page 373
10.4 Content and Structure of Bacterial and Archaeal Genomes......Page 376
10.5 Content and Structure of Eukaryotic Nuclear Genomes......Page 388
10.6 Tests for Selection......Page 399
Summary......Page 406
Review Questions......Page 407
Suggested Readings......Page 408
Part III The History of Life......Page 409
11 The Origin and Evolution of Early Life......Page 411
11.1 Origin and Diversification of Life on Earth......Page 412
11.2 The RNA World......Page 418
11.3 The Evolution of Single-Celled Organisms......Page 423
Box 11.1 Where did Viruses Come From?......Page 424
Box 11.2 Hypercycles in Modern Organisms......Page 426
11.4 Horizontal Gene Transfer and the Evolution of Single-Celled Life......Page 428
11.5 Metabolic Networks, Minimal Gene Sets, and Cell Evolution......Page 429
Key Terms......Page 433
Review Questions......Page 434
Suggested Readings......Page 435
12 Major Transitions......Page 437
12.1 Overview of Major Transitions......Page 440
12.2 Major Transitions: The Evolution of the Eukaryotic Cell......Page 443
12.3 Major Transitions: The Evolution of Multicellularity......Page 448
12.4 Major Transitions: The Evolution of Individuality......Page 453
12.5 Major Transitions: Solitary to Group Living......Page 455
Review Questions......Page 462
Suggested Readings......Page 463
13 Evolution and Development......Page 465
13.1 Evo-Devo: A Brief History......Page 466
13.2 Regulation, Expression, and Switches......Page 471
13.3 Evo-Devo and Gene Duplication......Page 479
13.4 Evo-Devo and the Evolution of Complex Traits......Page 481
Key Terms......Page 484
Suggested Readings......Page 485
14 Species and Speciation......Page 487
14.1 The Species Problem......Page 489
14.2 Modes of Speciation......Page 494
Box 14.1 Sympatric Speciation: A Resource Competition Model......Page 502
14.3 Reproductive Isolating Mechanisms and the Genetics of Speciation......Page 505
Box 14.2 Secondary Contract......Page 506
14.4 The Evolutionary History of Humans......Page 514
Box 14.3 Species Trees and Gene Trees......Page 516
Summary......Page 527
Review Questions......Page 528
Suggested Readings......Page 529
15 Extinction and Evolutionary Trends......Page 531
15.1 The Concepts of Extinction......Page 533
15.2 Background Extinction......Page 540
15.3 Mass Extinction......Page 547
15.4 Factors Correlated with Extinction......Page 555
15.5 Rates of Evolutionary Change and Evolutionary Trends......Page 558
Summary......Page 566
Review Questions......Page 567
Suggested Readings......Page 568
Part IV Evolutionary Interactions......Page 569
16 The Evolution of Sex......Page 571
16.1 Asexual and Sexual Reproduction......Page 574
16.2 The Costs of Sexual Reproduction......Page 577
Box 16.1 The Evolution of Different-Sized Gametes: Anisogamy......Page 579
16.3 The Benefits of Sexual Reproduction......Page 582
16.4 The Origin of Sexual Reproduction......Page 591
Key Terms......Page 592
Suggested Readings......Page 593
17 Sexual Selection......Page 595
Box 17.1 A Primer on Mating Systems......Page 597
17.2 Intersexual Selection......Page 599
17.3 Intrasexual Selection......Page 606
17.4 Postcopulatory Sexual Selection......Page 608
17.5 Conflicts of Interest between Males and Females......Page 610
Key Terms......Page 614
Suggested Readings......Page 615
18 The Evolution of Sociality......Page 617
18.1 Cooperation......Page 618
Box 18.1 Calculating Genetic Relatedness......Page 621
Box 18.2 Evolutionarily Stable Strategies (ESS)......Page 626
Box 18.3 The Tragedy of the Commons......Page 631
18.2 Conflict......Page 636
Box 18.4 The Mixed Nash Equilibria for the Hawk-Dove Game......Page 638
18.3 Information and Communication......Page 641
Key Terms......Page 650
Suggested Readings......Page 651
19 Coevolution......Page 653
19.1 Coevolution and Mutualism......Page 656
19.2 Antagonistic Coevolution......Page 664
19.3 Mosaic Coevolution......Page 669
19.4 Gene-Culture Coevolution......Page 671
Summary......Page 675
Review Questions......Page 676
Suggested Readings......Page 677
20 Evolution and Medicine......Page 679
20.1 Vulnerability to Disease......Page 682
20.2 Fever......Page 684
20.3 Coevolutionary Arms Races between Pathogens and Hosts......Page 687
20.4 Path Dependence and Vulnerability to Choking......Page 694
20.5 Senescence......Page 697
Summary......Page 707
Review Questions......Page 708
Suggested Readings......Page 709
A.1 Models of Sequence Change......Page 711
A.2 Maximum Likelihood......Page 712
A.3 Bayesian Methods......Page 715
A.4 A Conceptual Comparison of Likelihood and Bayesian Approaches......Page 716
Glossary......Page 719
References......Page 727
Credits......Page 759
Index......Page 765