Contents

Preface and acknowledgments, xi

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, 6

Interact box 1.1 The textbook website, 7 Chapter 1 review, 8 Further reading, 8

2 Genotype frequencies, 9

2.1 Mendel's model of particulate genetics, 9

2.2 Hardy-Weinberg expected genotype frequencies, 13 Interact box 2.1 Genotype frequencies, 14

2.3 Why does Hardy-Weinberg work?, 17

2.4 Applications of Hardy-Weinberg, 19 Forensic DNA profiling, 19

Problem box 2.1 The expected genotype frequency for a DNA profile, 22 Testing for Hardy-Weinberg, 22 Box 2.1 DNA profiling, 22 Interact box 2.2 %2test, 26

Assuming Hardy-Weinberg to test alternative models of inheritance, 26 Problem box 2.2 Proving allele frequencies are obtained from expected genotype frequencies, 27

Problem box 2.3 Inheritance for corn kernel phenotypes, 28

2.5 The fixation index and heterozygosity, 28 Interact box 2.3 Assortative mating and genotype frequencies, 29

Box 2.2 Protein locus or allozyme genotyping, 32

2.6 Mating among relatives, 33

Impacts of inbreeding on genotype and allele frequencies, 33 Inbreeding coefficient and autozygosity in a pedigree, 34 Phenotypic consequences of inbreeding, 37 The many meanings of inbreeding, 40

2.7 Gametic disequilibrium, 41

Interact box 2.4 Decay of gametic disequilibrium and a %2 test, 44 Physical linkage, 45 Natural selection, 46

Interact box 2.5 Gametic disequilibrium under both recombination and natural selection, 46

Mutation, 47

Mixing of diverged populations, 47 Mating system, 48 Chance, 48

Interact box 2.6 Estimating genotypic disequilibrium, 49 Chapter 2 review, 50 Further reading, 50 Problem box answers, 51

3 Genetic drift and effective population size, 53

3.1 The effects of sampling lead to genetic drift, 53 Interact box 3.1 Genetic drift, 58

3.2 Models of genetic drift, 58

The binomial probability distribution, 58 Problem box 3.1 Applying the binomial formula, 60 Math box 3.1 Variance of a binomial variable, 62 Markov chains, 62

Interact box 3.2 Genetic drift simulated with a Markov chain model, 65 Problem box 3.2 Constructing a transition probability matrix, 66 The diffusion approximation of genetic drift, 67

3.3 Effective population size, 73

Problem box 3.3 Estimating Ne from information about N, 77

3.4 Parallelism between drift and inbreeding, 78

3.5 Estimating effective population size, 80

Interact box 3.3 Heterozygosity,and inbreeding over time in finite populations, 81 Different types of effective population size, 82

Problem box 3.4 Estimating Ne from observed heterozygosity over time, 85

Breeding effective population size, 85

Effective population sizes of different genomes, 87

3.6 Gene genealogies and the coalescent model, 87

Math box 3.2 Approximating the probability of a coalescent event with the exponential distribution, 93

Interact box 3.4 Build your own coalescent genealogies, 94

3.7 Effective population size in the coalescent model, 96

Interact box 3.5 Simulating gene genealogies in populations with different effective sizes, 97 Coalescent genealogies and population bottlenecks, 98 Coalescent genealogies in growing and shrinking populations, 99 Interact box 3.6 Coalescent genealogies in populations with changing size, 101 Chapter 3 review, 101 Further reading, 102 Problem box answers, 103

4 Population structure and gene flow, 105

4.1 Genetic populations, 105

Method box 4.1 Are allele frequencies random or clumped in two dimensions?, 110

4.2 Direct measures of gene flow, 111

Problem box 4.1 Calculate the probability of a random haplotype match and the exclusion probability, 117

Interact box 4.1 Average exclusion probability for a locus, 117

4.3 Fixation indices to measure the pattern of population subdivision, 118 Problem box 4.2 Compute FIS, FST,and FIT, 122

Method box 4.2 Estimating fixation indices, 124

4.4 Population subdivision and the Wahlund effect, 124 Interact box 4.2 Simulating the Wahlund effect, 127

Problem box 4.3 Account for population structure in a DNA-profile match probability, 130

4.5 Models of population structure, 131 Continent-island model, 131

Interact box 4.3 Continent-island model of gene flow, 134 Two-island model, 134 Infinite island model, 135

Interact box 4.4 Two-island model of gene flow, 136

Math box 4.1 The expected value of FST in the infinite island model, 138

Problem box 4.4 Expected levels of FST for Y-chromosome and organelle loci, 139

Interact box 4.5 Finite island model of gene flow, 139

Stepping-stone and metapopulation models, 141

4.6 The impact of population structure on genealogical branching, 142 Combining coalescent and migration events, 143

The average length of a genealogy with migration, 144 Interact box 4.6 Coalescent events in two demes, 145

Math box 4.2 Solving two equations with two unknowns for average coalescence times, 148 Chapter 4 review, 149 Further reading, 150 Problem box answers, 151

5 Mutation, 154

5.1 The source of all genetic variation, 154

5.2 The fate of a new mutation, 160

Chance a mutation is lost due to Mendelian segregation, 160 Fate of a new mutation in a finite population, 162

Interact box 5.1 Frequency of neutral mutations in a finite population, 163 Geometric model of mutations fixed by natural selection, 164 Muller's Ratchet and the fixation of deleterious mutations, 166 Interact box 5.2 Muller's Ratchet, 168

5.3 Mutation models, 168

Mutation models for discrete alleles, 169

Interact box 5.3 RST and FSTas examples of the consequences of different mutation models, 172 Mutation models for DNA sequences, 172

5.4 The influence of mutation on allele frequency and autozygosity, 173 Math box 5.1 Equilibrium allele frequency with two-way mutation, 176 Interact box 5.4 Simulating irreversible and bi-directional mutation, 177

5.5 The coalescent model with mutation, 178

Interact box 5.5 Build your own coalescent genealogies with mutation, 181 Chapter 5 review, 183 Further reading, 183

6 Fundamentals of natural selection, 185

6.1 Natural selection, 185

Natural selection with clonal reproduction, 185 Problem box 6.1 Relative fitness of HIV genotypes, 189 Natural selection with sexual reproduction, 189

6.2 General results for natural selection on a diallelic locus, 193

Math box 6.1 The change in allele frequency each generation under natural selection, 194 Selection against a recessive phenotype, 195 Selection against a dominant phenotype, 196

General dominance, 197 Heterozygote disadvantage, 198 Heterozygote advantage, 198 The strength of natural selection, 199

Math box 6.2 Equilibrium allele frequency with overdominance, 200 6.3 How natural selection works to increase average fitness, 200 Average fitness and rate of change in allele frequency, 201 Problem box 6.2 Mean fitness and change in allele frequency, 203 The fundamental theorem of natural selection, 203 Interact box 6.1 Natural selection on one locus with two alleles, 203 Chapter 6 review, 206 Further reading, 206 Problem box answers, 206

7 Further models of natural selection, 208

7.1 Viability selection with three alleles or two loci, 208 Natural selection on one locus with three alleles, 209

Problem box 7.1 Marginal fitness and Ap for the Hb C allele, 211

Interact box 7.1 Natural selection on one locus with three or more alleles, 211

Natural selection on two diallelic loci, 212

7.2 Alternative models of natural selection, 216 Natural selection via different levels of fecundity, 216 Natural selection with frequency-dependent fitness, 218 Natural selection with density-dependent fitness, 219

Math box 7.1 The change in allele frequency with frequency-dependent selection, 219 Interact box 7.2 Frequency-dependent natural selection, 220 Interact box 7.3 Density-dependent natural selection, 222

7.3 Combining natural selection with other processes, 222 Natural selection and genetic drift acting simultaneously, 222

Interact box 7.4 The balance of natural selection and genetic drift at a diallelic locus, 224 The balance between natural selection and mutation, 225 Interact box 7.5 Natural selection and mutation, 226

7.4 Natural selection in genealogical branching models, 226 Directional selection and the ancestral selection graph, 227

Problem box 7.2 Resolving possible selection events on an ancestral selection graph, 230 Genealogies and balancing selection, 230

Interact box 7.6 Coalescent genealogies with directional selection, 231 Chapter 7 review, 232 Further reading, 233 Problem box answers, 234

8 Molecular evolution, 235

8.1 The neutral theory, 235 Polymorphism, 236 Divergence, 237

Nearly neutral theory, 240

Interact box 8.1 The relative strengths of genetic drift and natural selection, 241

8.2 Measures of divergence and polymorphism, 241 Box 8.1 DNA sequencing, 242

DNA divergence between species, 242 DNA sequence divergence and saturation, 243 DNA polymorphism, 248

8.3 DNA sequence divergence and the molecular clock, 250 Interact box 8.2 Estimating n and Sfrom DNA sequence data, 251 Dating events with the molecular clock, 252

Problem box 8.1 Estimating divergence times with the molecular clock, 254

8.4 Testing the molecular clock hypothesis and explanations for rate variation in molecular evolution, 255

The molecular clock and rate variation, 255

Ancestral polymorphism and Poisson process molecular clock, 257

Math box 8.1 The dispersion index with ancestral polymorphism and divergence, 259 Relative rate tests of the molecular clock, 260 Patterns and causes of rate heterogeneity, 261

8.5 Testing the neutral theory null model of DNA sequence evolution, 265 HKA test of neutral theory expectations for DNA sequence evolution, 265 MKtest, 267

Tajima's D, 269

Problem box 8.2 Computing Tajima's D from DNA sequence data, 271 Mismatch distributions, 272

Interact box 8.3 Mismatch distributions for neutral genealogies in stable, growing, or shrinking populations, 274

8.6 Molecular evolution of loci that are not independent, 274 Genetic hitch-hiking due to background or balancing selection, 278 Gametic disequilibrium and rates of divergence, 278

Chapter 8 review, 2 79 Further reading, 280 Problem box answers, 281

9 Quantitative trait variation and evolution, 283

9.1 Quantitative traits, 283

Problem box 9.1 Phenotypic distribution produced by Mendelian inheritance of three diallelic loci, 285

Components of phenotypic variation, 286

Components of genotypic variation (VG), 288

Inheritance of additive (VA), dominance (VD), and epistasis (VI) genotypic variation, 291 Genotype-by-environment interaction (VGxE), 292 Additional sources ofphenotypic variance, 295 Math box 9.1 Summing two variances, 296

9.2 Evolutionary change in quantitative traits, 29 7 Heritability, 297

Changes in quantitative trait mean and variance due to natural selection, 299 Estimating heritability by parent-offspring regression, 302 Interact box 9.1 Estimating heritability with parent-offspring regression, 303 Response to selection on correlated traits, 304

Interact box 9.2 Response to natural selection on two correlated traits, 306 Long-term response to selection, 307

Interact box 9.3 Response to selection and the number of loci that cause quantitative trait variation, 309

Neutral evolution of quantitative traits, 313

Interact box 9.4 Effective population size and genotypic variation in a neutral quantitative trait, 314

9.3 Quantitative trait loci (QTL), 315

QTL mapping with single marker loci, 316

Problem box 9.2 Compute the effect and dominance coefficient of a QTL, 321 QTL mapping with multiple marker loci, 322

Problem box 9.3 Derive the expected marker-class means for a backcross mating design, 324 Limitations of QTL mapping studies, 325 Biological significance of QTL mapping, 326

Interact box 9.5 Effect sizes and response to selection at QTLs, 328 Chapter 9 review, 330 Further reading, 330 Problem box answers, 331

10 The Mendelian basis of quantitative trait variation, 334

10.1 The connection between particulate inheritance and quantitative trait variation, 334 Scale of genotypic values, 334

Problem box 10.1 Compute values on the genotypic scale of measurement for IGF1 in dogs, 335

10.2 Mean genotypic value in a population, 336

10.3 Average effect of an allele, 337

Math box 10.1 The average effect of the A1 allele, 339

Problem box 10.2 Compute the allele average effect of the IGF1 A2 allele in dogs, 341

10.4 Breeding value and dominance deviation, 341

Interact box 10.1 Average effects, breeding values, and dominance deviations, 345 Dominance deviation, 345

10.5 Components of total genotypic variance, 348

Interact box 10.2 Components of total genotypic variance, VG, 350 Math box 10.2 Deriving the total genotypic variance, VG, 350

10.6 Genotypic resemblance between relatives, 351 Chapter 10 review, 354

Further reading, 354 Problem box answers, 355

11 Historical and synthetic topics, 356

11.1 Historical controversies in population genetics, 356 The classical and balance hypotheses, 356

How to explain levels of allozyme polymorphism, 358 Genetic load, 359

Math box 11.1 Mean fitness in a population at equilibrium for balancing selection, 362 The selectionist/neutralist debates, 363

11.2 Shifting balance theory, 366

Allele combinations and the fitness surface, 366 Wright's view of allele-frequency distributions, 368 Evolutionary scenarios imagined by Wright, 369 Critique and controversy over shifting balance, 372 Chapter 11 review, 374 Further reading, 374

Appendix, 376

Statistical uncertainty, 376

Problem box A.1 Estimating the variance, 3 78

Interact box A.1 The central limit theorem, 379

Covariance and correlation, 380

Further reading, 382

Problem box answers, 382

References, 383 Index, 396

Color plates appear in between pages 114-115

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