Preface and acknowledgements xiv
About the companion websites xvi
1 Thinking like a population geneticist 1
1.1 Expectations 1
Parameters and parameter estimates 2
Inductive and deductive reasoning 3
1.2 Theory and assumptions 4
1.3 Simulation 5
Interact box 1.1 The textbook website 6
Chapter 1 review 7
Further reading 7
2 Genotype frequencies 8
2.1 Mendel's model of particulate genetics 8
2.2 Hardy-Weinberg expected genotype frequencies 12
Interact box 2.1 Genotype frequencies for one locus with two alleles 14
2.3 Why does Hardy-Weinberg work? 15
2.4 Applications of Hardy-Weinberg 18
Forensic DNA profiling 18
Problem box 2.1 The expected genotype frequency for a DNA profile 20
Testing Hardy-Weinberg expected genotype frequencies 20
Box 2.1 DNA profiling 21
Assuming Hardy-Weinberg to test alternative models of inheritance 24
Problem box 2.2 Proving allele frequencies are obtained from expected genotype frequencies 25
Problem box 2.3 Inheritance for corn kernel phenotypes 26
2.5 The fixation index and heterozygosity 26
Interact box 2.2 Assortative mating and genotype frequencies 27
Box 2.2 Protein locus or allozyme genotyping 30
2.6 Mating among relatives 31
Impacts of non-random mating on genotype and allele frequencies 31
Coancestry coefficient and autozygosit, 33
Box 2.3 Locating relatives using genetic genealogy methods 37
Phenotypic consequences of mating among relatives 38
The many meanings of inbreeding 41
2.7 Hardy-Weinberg for two loci 42
Gametic disequilibrium 42
Physical linkage 47
Natural selection 47
Interact box 2.3 Gametic disequilibrium under both recombination and natural selection 48
Mutation 48
Mixing of diverged populations 49
Mating system 49
Population size 50
Interact box 2.4 Estimating genotypic disequilibrium 51
Chapter 2 review 52
Further reading 52
End-of-chapter exercises 53
Problem box answers 54
3 Genetic drift and effective population size 57
3.1 The effects of sampling lead to genetic drift 57
Interact box 3.1 Genetic drift 62
3.2 Models of genetic drift 62
The binomial probability distribution 62
Problem box 3.1 Applying the binomial formula 64
Math box 3.1 Variance of a binomial variable 66
Markov chains 66
Interact box 3.2 Genetic drift simulated with a markov chain model 69
Problem box 3.2 Constructing a transition probability matrix 69
The diffusion approximation of genetic drift 70
3.3 Effective population size 76
Problem box 3.3 Estimating N e from information about N 81
3.4 Parallelism between Drift and mating among relatives 81
Interact box 3.3 Heterozygosity over time in a finite population 84
3.5 Estimating effective population size 85
Different types of effective population size 85
Interact box 3.4 Estimating N e from allele frequencies and heterozygosity over time 89
Breeding effective population size 90
Effective population sizes of different genomes 92
3.6 Gene genealogies and the coalescent model 92
Interact box 3.5 Sampling lineages in a Wright-Fisher population 94
Math box 3.2 Approximating the probability of a coalescent event with the exponential distribution 99
Interact box 3.6 Build your own coalescent genealogies 100
3.7 Effective population size in the coalescent model 103
Interact box 3.7 Simulating gene genealogies in populations with different effective sizes 103
Coalescent genealogies and population bottlenecks 105
Coalescent genealogies in growing and shrinking populations 106
Interact box 3.8 Coalescent genealogies in populations with changing size 107
3.8 Genetic drift and the coalescent with other models of life history 108
Chapter 3 review 110
Further reading 111
End of chapter exercises 111
Problem box answers 113
4 Population structure and gene flow 115
4.1 Genetic populations 115
Box 4.1 Are allele frequencies random or clumped in two dimensions? 121
4.2 Gene flow and its impact on allele frequencies in multiple subpopulations 122
Continent-island model 123
Two-island model 125
Interact box 4.1 Continent-island model of gene flow 125
Interact box 4.2 Two-island model of gene flow 126
4.3 Direct measures of gene flow 127
Problem box 4.1 Calculate the probability of a random haplotype match and the exclusion probability 133
Interact box 4.3 Average exclusion probability for a locus 134
4.4 Fixation indices to summarize the pattern of population subdivision 135
Problem box 4.2 Compute FIS, FST, and FIT 138
Estimating fixation indices 140
4.5 Population subdivision and the Wahlund effect 142
Interact box 4.4 Simulating the Wahlund effect 144
Problem box 4.3 Impact of population structure on a DNA-profile match probability 147
4.6 Evolutionary models that predict patterns of population structure 148
Infinite island model 148
Math box 4.1 The expected value of F ST in the infinite island model 150
Problem box 4.4 Expected levels of F ST for Y-chromosome and organelle loci 153
Interact box 4.5 Simulate FIS, FST, and FIT in the finite island model 154
Stepping-stone and metapopulation models 155
Isolation by distance and by landscape connectivity 156
Math box 4.2 Analysis of a circuit to predict gene flow across a landscape 159
4.7 Population assignment and clustering 160
Maximum likelihood assignment 161
Bayesian assignment 161
Interact box 4.6 Genotype assignment and clustering 162
Math box 4.3 Bayes Theorem 166
Empirical assignment methods 167
Interact box 4.7 Visualizing principle components analysis 167
4.8 The impact of population structure on genealogical branching 169
Combining coalescent and migration events 169
Interact box 4.8 Gene genealogies with migration between two demes 171
The average length of a genealogy with migration 172
Math box 4.4 Solving two equations with two unknowns for average coalescence times 175
Chapter 4 review 176
Further reading 177
End of chapter exercises 178
Problem box answers 180
5 Mutation 183
5.1 The source of all genetic variation 183
Estimating mutation rates 187
Evolution of mutation rates 189
5.2 The fate of a new mutation 191
Chance a mutation is lost due to mendelian segregation 191
Fate of a new mutation in a finite population 193
Interact box 5.1 Frequency of neutral mutations in a finite population 194
Mutations in expanding populations 195
Geometric model of mutations fixed by natural selection 196
Muller's ratchet and the fixation of deleterious mutations 199
Interact box 5.2 Muller's Ratchet 201
5.3 Mutation models 201
Mutation models for discrete alleles 201
Interact box 5.3 Rst and Fst as examples of the consequences of different mutation models 204
Mutation models for DNA sequences 205
Box 5.1 Single nucleotide polymorphisms 206
5.4 The influence of mutation on allele frequency and autozygosity 207
Math box 5.1 Equilibrium allele frequency with two-way mutation 209
Interact box 5.4 Simulating irreversible and two-way mutation 211
Interact box 5.5 Heterozygosity and homozygosity with two-way mutation 212
5.5 The coalescent model with mutation 213
Interact box 5.6 Build your own coalescent genealogies with mutation 215
Chapter 5 review 217
Further reading 218
End-of-chapter exercises 219
6 Fundamentals of natural selection 220
6.1 Natural selection 220
Natural selection with clonal reproduction 220
Problem box 6.1 Relative fitness of HIV genotypes 224
Natural selection with sexual reproduction 225
Math box 6.1 The change in allele frequency each generation under natural selection 229
6.2 General results for natural selection on a diallelic locus 230
Selection against a recessive phenotype 231
Selection against a dominant phenotype 232
General dominance 233
Heterozygote disadvantage 234
Heterozygote advantage 235
Math box 6.2 Equilibrium allele frequency with overdominance 236
The strength of natural selection 237
6.3 How natural selection works to increase average fitness 238
Average fitness and rate of change in allele frequency 238
Problem box 6.2 Mean fitness and change in allele frequency 240
Interact box 6.1 Natural selection on one locus with two alleles 240
The fundamental theorem of natural selection 241
6.4 Ramifications of the one locus, two allele model of natural selection 243
The Classical and Balance Hypotheses 243
How to explain levels of allozyme polymorphism, 245
Chapter 6 review 246
Further reading 247
End-of-chapter exercises 247
Problem box answers 248
7 Further models of natural selection 250
7.1 Viability selection with three alleles or two loci 250
Natural selection on one locus with three alleles 250
Problem box 7.1 Marginal fitness and ¿p for the Hb C allele 253
Interact box 7.1 Natural selection on one locus with three or more alleles 254
Natural selection on two diallelic loci 254
7.2 Alternative models of natural selection 259
Natural selection via different levels of fecundity 260
Natural selection with frequency-dependent fitness 262
Math box 7.1 The change in allele frequency with frequency-dependent selection 263
Interact box 7.2 Frequency-dependent natural selection 263
Natural selection with density-dependent fitness 264
Interact box 7.3 Density-dependent natural selection 266
7.3 Combining natural selection with other processes 266
Natural selection and genetic drift acting simultaneously 266
Genetic differentiation among populations by natural selection 267
Interact box 7.4 The balance of natural selection and genetic drift at a diallelic locus 268
The balance between natural selection and mutation 271
Genetic load 272
Interact box 7.5 Natural selection and mutation 272
Math box 7.2 Mean fitness in a population at equilibrium for balancing selection 275
7.4 Natural selection in genealogical branching models 277
Directional selection and the ancestral selection graph 278
Problem box 7.2 Resolving possible selection events on an ancestral selection graph 281
Interact box 7.6 Build an ancestral selection graph 282
Genealogies and balancing selection 283
7.5 Shifting balance theory 284
Allele combinations and the fitness surface 284
Wright's view of allele frequency distribution 286
Evolutionary scenarios imagined by wright 287
Critique and controversy over shifting balance 290
Chapter 7 review 292
Further reading 293
End-of-chapter exercises 293
Problem box answers 294
8 Molecular evolution 296
8.1 Neutral theory 296
Polymorphism 297
Divergence 299
Nearly neutral theory 301
Interact box 8.1 Compare the neutral theory and nearly neutral theory 302
The selectionist-neutralist debates 302
8.2 Natural selection 305
Hitch-hiking and rates of divergence 310
Empirical studies 310
8.3 Measures of divergence and polymorphism 313
Box 8.1 DNA sequencing 313
DNA divergence between specie, 314
DNA sequence divergence and saturation 315
Interact box 8.2 Compare nucleotide substitution models 316
DNA polymorphism measured by segregating sites and nucleotide diversity 319
Interact box 8.3 Estimating ¿ and S from DNA sequence data 323
8.4 DNA sequence divergence and the molecular clock 324
Dating events with the molecular clock 325
Problem box 8.1 Estimating divergence times with the molecular clock 327
Interact box 8.4 Molecular clock estimates of evolutionary events 328
8.5 Testing the molecular clock hypothesis and explanations for rate variation in molecular evolution 329
The molecular clock and rate variation 329
Ancestral polymorphism and poisson process molecular clock 331
Math box 8.1 The dispersion index with ancestral polymorphism and divergence 333
Relative rate tests of the molecular clock 334
Patterns and causes of rate heterogeneity 336
8.6 Testing the neutral theory null model of DNA sequence polymorphism 339
HKA test of neutral theory expectations for DNA sequence evolution 340
The McDonald-Kreitman (MK) test 342
Mismatch distributions 343
Tajima's D 346
Problem box 8.2 Computing Tajima's D from DNA sequence data 348
8.7 Recombination in the genealogical branching model 350
Interact box 8.5 Build an ancestral recombination graph 353
Consequences of recombination 353
Chapter 8 review 354
Further reading 355
End-of-chapter exercises 356
Problem box answers 357
9 Quantitative trait variation and evolution 359
9.1 Quantitative traits 359
Problem box 9.1 Phenotypic distribution produced by Mendelian inheritance of three diallelic loci 361
Components of phenotypic variation 362
Components of genotypic variation (VG) 363
Inheritance of additive (VA), dominance (VD), and epistasis (VI) genotypic variation 367
Genotype-by-environment interaction (VG×E) 369
Additional sources of phenotypic variance 372
Math box 9.1 Summing two variances 372
9.2 Evolutionary change in quantitative traits 374
Heritability and the Breeder's equation 374
Changes in quantitative trait mean and variance due to natural selection 376
Math box 9.2 Selection differential with truncation selection 376
Estimating heritability by parent-offspring regression 379
Interact box 9.1 Estimating heritability with parent-offspring regression 381
Response to selection on correlated traits 381
Interact box 9.2 Response to natural selection on two correlated traits 384
Long-term response to selection 384
Interact box 9.3 Response to selection and the number of loci that cause quantitative trait variation 387
Neutral evolution of quantitative traits 391
Interact box 9.4 Effective population size and genotypic variation in a neutral quantitative trait 392
9.3 Quantitative trait loci (QTL) 393
QTL mapping with single marker loci,394
Problem box 9.2 Compute the effect and dominance coefficient of a QTL 399
QTL mapping with multiple marker loci 400
Problem box 9.3 Derive the expected marker-class means for a backcross mating design 402
Limitations of QTL mapping studies 403
Genome-wide association studies 404
Biological significance of identifying QTL 405
Interact box 9.5 Effect sizes and response to selection at QTLs 407
Chapter 9 review 408
Further reading 409
End-of-chapter exercises 409
Problem box answers 410
10 The Mendelian basis of quantitative trait variation 413
10.1 The connection between particulate inheritance and quantitative trait variation 413
Scale of genotypic values 413
Problem box 10.1 Compute values on the genotypic scale of measurement for IGF1 in dogs 414
10.2 Mean genotypic value in a population 415
10.3 Average effect of an allele 416
Math box 10.1 The average effect of the A 1 allele 418
Problem box 10.2 Compute average effects for IGF1 in dogs 420
10.4 Breeding value and dominance deviation 420
Interact box 10.1 Average effects, breeding values, and dominance deviations 424
Dominance deviation 425
10.5 Components of total genotypic variance 428
Interact box 10.2 Components of total genotypic variance, V G 430
Math box 10.2 Deriving the total genotypic variance, V G 430
10.6 Genotypic resemblance between relatives 431
Chapter 10 review 433
Further reading 434
End-of-chapter exercises 434
Problem box answers 434
Appendix 436
Problem A.1 Estimating the variance 438
Interact box A.1 The central limit theorem 439
A.1 Covariance and Correlation 440
Further reading 442
Problem box answers 442
Bibliography 443
Index 468
