Evolutionary Analysis

Cover ... 1
Title Page ... 2
Copyright Page ... 3
Contents ... 5
Preface ... 10
Acknowledgments ... 14
PART 1 INTRODUCTION ... 16
	CHAPTER 1 A Case for Evolutionary Thinking: Understanding HIV ... 16
		1.1 The Natural History of the HIV Epidemic ... 17
		1.2 Why Does HIV Therapy Using Just One Drug Ultimately Fail? ... 24
		1.3 Are Human Populations Evolving as a Result of the HIV Pandemic? ... 30
		1.4 Where Did HIV Come From? ... 33
		1.5 Why Is HIV Lethal? ... 38
		Computing Consequences 1.1 When did HIV move from chimpanzees to humans? ... 39
		Summary ... 46
		Questions ... 46
		Exploring the Literature ... 47
		Citations ... 48
	CHAPTER 2 The Pattern of Evolution ... 52
		2.1 Evidence of Microevolution: Change through Time ... 54
		2.2 Evidence of Speciation: New Lineages from Old ... 59
		2.3 Evidence of Macroevolution: New Forms from Old ... 64
		2.4 Evidence of Common Ancestry: All Life-Forms Are Related ... 70
		2.5 The Age of Earth ... 77
		Computing Consequences 2.1 A closer look at radiometric dating ... 80
		Summary ... 81
		Questions ... 82
		Exploring the Literature ... 83
		Citations ... 84
	CHAPTER 3 Evolution by Natural Selection ... 88
		3.1 Artificial Selection: Domestic Animals and Plants ... 89
		3.2 Evolution by Natural Selection ... 92
		3.3 The Evolution of Flower Color in an Experimental Snapdragon Population ... 94
		3.4 The Evolution of Beak Shape in Galápagos Finches ... 96
		Computing Consequences 3.1 Estimating heritabilities despite complications ... 99
		3.5 The Nature of Natural Selection ... 105
		3.6 The Evolution of Evolutionary Biology ... 109
		3.7 Intelligent Design Creationism ... 112
		Summary ... 119
		Questions ... 120
		Exploring the Literature ... 121
		Citations ... 121
	CHAPTER 4 Estimating Evolutionary Trees ... 124
		4.1 How to Read an Evolutionary Tree ... 125
		4.2 The Logic of Inferring Evolutionary Trees ... 129
		4.3 Molecular Phylogeny Inference and the Origin of Whales ... 138
		Computing Consequences 4.1 Calculating the likelihood of an evolutionary tree ... 144
		Computing Consequences 4.2 Neighbor joining: A distance matrix method ... 145
		4.4 Using Phylogenies to Answer Questions ... 152
		Summary ... 156
		Questions ... 156
		Exploring the Literature ... 158
		Citations ... 158
PART 2 MECHANISMS OF EVOLUTIONARY CHANGE ... 162
	CHAPTER 5 Variation Among Individuals ... 162
		5.1 Three Kinds of Variation ... 163
		Computing Consequences 5.1 Epigenetic inheritance and evolution ... 169
		5.2 Where New Alleles Come From ... 172
		5.3 Where New Genes Come From ... 176
		Computing Consequences 5.2 Measuring genetic variation in natural populations ... 177
		5.4 Chromosome Mutations ... 181
		5.5 Rates and Fitness Effects of Mutations ... 184
		Summary ... 189
		Questions ... 190
		Exploring the Literature ... 191
		Citations ... 191
	CHAPTER 6 Mendelian Genetics in Populations I: Selection and Mutation ... 194
		6.1 Mendelian Genetics in Populations: Hardy–Weinberg Equilibrium ... 195
		Computing Consequences 6.1 Combining probabilities ... 200
		Computing Consequences 6.2 The Hardy– Weinberg equilibrium principle with more than two alleles ... 204
		6.2 Selection ... 206
		Computing Consequences 6.3 A general treatment of selection ... 209
		Computing Consequences 6.4 Statistical analysis of allele and genotype frequencies using the X[sup(2)](chi-square) test ... 213
		Computing Consequences 6.5 Predicting the frequency of the CCR5-?32 allele in future generations ... 216
		6.3 Patterns of Selection: Testing Predictions of Population Genetics Theory ... 216
		Computing Consequences 6.6 An algebraic treatment of selection on recessive and dominant alleles ... 219
		Computing Consequences 6.7 Stable equilibria with heterozygote superiority and unstable equilibria with heterozygote inferiority ... 223
		6.4 Mutation ... 231
		Computing Consequences 6.8 A mathematical treatment of mutation as an evolutionary mechanism ... 233
		Computing Consequences 6.9 Allele frequencies under mutation–selection balance ... 235
		Computing Consequences 6.10 Estimating mutation rates for recessive alleles ... 237
		6.5 An Engineering Test of Population Genetics Theory ... 239
		Computing Consequences 6.11 Predicting the frequency of Medea across generations ... 241
		Summary ... 242
		Questions ... 242
		Exploring the Literature ... 244
		Citations ... 246
	CHAPTER 7 Mendelian Genetics in Populations II: Migration, Drift, and Nonrandom Mating ... 248
		7.1 Migration ... 249
		Computing Consequences 7.1 An algebraic treatment of migration as an evolutionary process ... 251
		Computing Consequences 7.2 Selection and migration in Lake Erie water snakes ... 253
		7.2 Genetic Drift ... 255
		Computing Consequences 7.3 The probability that a given allele will be the one that drifts to fixation ... 263
		Computing Consequences 7.4 Effective population size ... 266
		Computing Consequences 7.5 The rate of evolutionary substitution under genetic drift ... 271
		7.3 Genetic Drift and Molecular Evolution ... 275
		7.4 Nonrandom Mating ... 290
		Computing Consequences 7.6 Genotype frequencies in an inbred population ... 294
		7.5 Conservation Genetics of the Florida Panther ... 298
		Summary ... 300
		Questions ... 300
		Exploring the Literature ... 302
		Citations ... 303
	CHAPTER 8 Evolution at Multiple Loci: Linkage and Sex ... 306
		8.1 Evolution at Two Loci: Linkage Equilibrium and Linkage Disequilibrium ... 307
		Computing Consequences 8.1 The coefficient of linkage disequilibrium ... 310
		Computing Consequences 8.2 Hardy– Weinberg analysis for two loci ... 311
		Computing Consequences 8.3 Sexual reproduction reduces linkage disequilibrium ... 316
		8.2 Practical Reasons to Study Linkage Disequilibrium ... 322
		Computing Consequences 8.4 Estimating the age of the GBA–84GG mutation ... 324
		8.3 The Adaptive Significance of Sex ... 329
		Computing Consequences 8.5 A demographic model of the maintenance of males in the nematode Caenorhabditis elegans ... 332
		Summary ... 339
		Questions ... 340
		Exploring the Literature ... 341
		Citations ... 342
	CHAPTER 9 Evolution at Multiple Loci: Quantitative Genetics ... 344
		9.1 The Nature of Quantitative Traits ... 345
		9.2 Identifying Loci That Contribute to Quantitative Traits ... 349
		Computing Consequences 9.1 Genetic mapping and LOD scores ... 353
		9.3 Measuring Heritable Variation ... 358
		Computing Consequences 9.2 Additive genetic variation versus dominance genetic variation ... 360
		9.4 Measuring Differences in Survival and Reproductive Success ... 363
		Computing Consequences 9.3 The selection gradient and the selection differential ... 364
		9.5 Predicting the Evolutionary Response to Selection ... 365
		9.6 Modes of Selection and the Maintenance of Genetic Variation ... 371
		9.7 The Bell-Curve Fallacy and Other Misinterpretations of Heritability ... 375
		Summary ... 380
		Questions ... 380
		Exploring the Literature ... 382
		Citations ... 382
PART 3 ADAPTATION ... 384
	CHAPTER 10 Studying Adaptation: Evolutionary Analysis of Form and Function ... 384
		10.1 All Hypotheses Must Be Tested: Oxpeckers Reconsidered ... 385
		10.2 Experiments ... 388
		Computing Consequences 10.1 A primer on statistical testing ... 392
		10.3 Observational Studies ... 393
		10.4 The Comparative Method ... 397
		Computing Consequences 10.2 Calculating phylogenetically independent contrasts ... 399
		10.5 Phenotypic Plasticity ... 402
		10.6 Trade-Offs and Constraints ... 404
		10.7 Selection Operates on Different Levels ... 412
		10.8 Strategies for Asking Interesting Questions ... 416
		Summary ... 417
		Questions ... 417
		Exploring the Literature ... 419
		Citations ... 420
	CHAPTER 11 Sexual Selection ... 422
		11.1 Sexual Dimorphism and Sex ... 423
		11.2 Sexual Selection on Males: Competition ... 432
		11.3 Sexual Selection on Males: Female Choice ... 438
		Computing Consequences 11.1 Runaway sexual selection ... 445
		11.4 Sexual Selection on Females ... 453
		11.5 Sexual Selection in Plants ... 456
		11.6 Sexual Dimorphism in Humans ... 459
		Summary ... 463
		Questions ... 463
		Exploring the Literature ... 465
		Citations ... 466
	CHAPTER 12 The Evolution of Social Behavior ... 470
		12.1 Four Kinds of Social Behavior ... 471
		12.2 Kin Selection and Costly Behavior ... 474
		Computing Consequences 12.1 Calculating relatedness as the probability of identity by descent ... 476
		12.3 Multilevel Selection and Cooperation ... 486
		Computing Consequences 12.2 Different perspectives on the same evolutionary process ... 488
		12.4 Cooperation and Conflict ... 492
		12.5 The Evolution of Eusociality ... 498
		Summary ... 501
		Questions ... 502
		Exploring the Literature ... 503
		Citations ... 504
	CHAPTER 13 Aging and Other Life-History Characters ... 506
		13.1 Basic Issues in Life-History Analysis ... 508
		13.2 Why Do Organisms Age and Die? ... 510
		Computing Consequences 13.1 Late-acting deleterious mutations are weakly selected ... 516
		Computing Consequences 13.2 Alleles conferring early benefits and late costs can be adaptive ... 519
		13.3 How Many Offspring Should an Individual Produce in a Given Year? ... 528
		13.4 How Big Should Each Offspring Be? ... 532
		13.5 Conflicts of Interest between Life Histories ... 537
		13.6 Life Histories in a Broader Evolutionary Context ... 540
		Summary ... 545
		Questions ... 545
		Exploring the Literature ... 547
		Citations ... 547
	CHAPTER 14 Evolution and Human Health ... 550
		14.1 Evolving Pathogens: Evasion of the Host’s Immune Response ... 552
		14.2 Evolving Pathogens: Antibiotic Resistance ... 560
		14.3 Evolving Pathogens: Virulence ... 563
		14.4 Tissues as Evolving Populations of Cells ... 568
		14.5 Selection Thinking Applied to Humans ... 571
		14.6 Adaptation and Medical Physiology: Fever ... 579
		14.7 Adaptation and Human Behavior: Parenting ... 582
		Computing Consequences 14.1 Is cultural evolution Darwinian? ... 584
		Summary ... 590
		Questions ... 590
		Exploring the Literature ... 592
		Citations ... 592
	CHAPTER 15 Genome Evolution and the Molecular Basis of Adaptation ... 596
		15.1 Diversity among Genomes ... 597
		15.2 Mobile Genetic Elements ... 601
		15.3 The Evolution of Mutation Rates ... 606
		15.4 Gene Duplication and Gene Families ... 609
		15.5 The Locus of Adaptation in Natural Populations ... 616
		Summary ... 621
		Questions ... 621
		Exploring the Literature ... 622
		Citations ... 623
PART 4 THE HISTORY OF LIFE ... 624
	CHAPTER 16 Mechanisms of Speciation ... 624
		16.1 Species Concepts ... 625
		16.2 Mechanisms of Isolation ... 631
		16.3 Mechanisms of Divergence ... 638
		16.4 Hybridization and Gene Flow between Species ... 644
		16.5 What Drives Diversification? ... 652
		Summary ... 655
		Questions ... 656
		Exploring the Literature ... 657
		Citations ... 658
	CHAPTER 17 The Origins of Life and Precambrian Evolution ... 660
		17.1 What Was the First Living Thing? ... 662
		17.2 Where Did the First Living Thing Come From? ... 670
		17.3 What Was the Last Common Ancestor of All Extant Organisms and What Is the Shape of the Tree of Life? ... 678
		17.4 How Did LUCA’s Descendants Evolve into Today’s Organisms? ... 693
		Summary ... 698
		Questions ... 699
		Exploring the Literature ... 701
		Citations ... 701
	CHAPTER 18 Evolution and the Fossil Record ... 706
		18.1 The Nature of the Fossil Record ... 707
		18.2 Evolution in the Fossil Record ... 711
		Computing Consequences 18.1 Evolutionary trends ... 721
		18.3 Taxonomic and Morphological Diversity over Time ... 722
		18.4 Mass and Background Extinctions ... 724
		18.5 Macroevolution ... 734
		18.6 Fossil and Molecular Divergence Timing ... 742
		Summary ... 745
		Questions ... 746
		Exploring the Literature ... 747
		Citations ... 747
	CHAPTER 19 Development and Evolution ... 750
		19.1 The Divorce and Reconciliation of Development and Evolution ... 751
		19.2 Hox Genes and the Birth of Evo-Devo ... 753
		19.3 Post Hox: Evo-Devo 2.0 ... 759
		19.4 Hox Redux: Homology or Homoplasy? ... 778
		19.5 The Future of Evo-Devo ... 779
		Summary ... 780
		Questions ... 781
		Exploring the Literature ... 781
		Citations ... 782
	CHAPTER 20 Human Evolution ... 784
		20.1 Relationships among Humans and Extant Apes ... 785
		20.2 The Recent Ancestry of Humans ... 795
		20.3 Origin of the Species Homo sapiens ... 805
		Computing Consequences 20.1 Using allele frequencies and linkage disequilibrium to date the modern human expansion from Africa ... 812
		20.4 The Evolution of Distinctive Human Traits ... 817
		Summary ... 822
		Questions ... 822
		Exploring the Literature ... 824
		Citations ... 825
Glossary ... 830
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Credits ... 837
Index ... 845
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	E ... 850
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	M ... 856
	N ... 858
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	Q ... 861
	R ... 861
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