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
A ... 830
B ... 830
C ... 830
D ... 831
E ... 831
F ... 832
G ... 832
H ... 832
I ... 833
K ... 833
L ... 833
M ... 833
N ... 834
O ... 834
P ... 834
Q ... 835
R ... 835
S ... 835
T ... 836
U ... 836
V ... 836
W ... 836
Credits ... 837
Index ... 845
A ... 845
B ... 846
C ... 847
D ... 849
E ... 850
F ... 851
G ... 852
H ... 853
I ... 855
J ... 855
K ... 855
L ... 856
M ... 856
N ... 858
O ... 859
P ... 859
Q ... 861
R ... 861
S ... 862
T ... 864
U ... 865
V ... 865
W ... 865
X ... 865
Y ... 865
Z ... 865