Population genetics:
"Population genetics describes the distribution of alleles in a population with regard to evolutionary processes and population structure. It is the cornerstone of modern evolutionary biology, with wide applications in fields such as conservation biology, health-oriented clinical research, bioi...
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| Format: | Book |
| Language: | English |
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Hoboken, NJ
Wiley Blackwell
2021
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| Edition: | Second edition |
| Subjects: | |
| Online Access: | Cover Inhaltsverzeichnis |
| Summary: | "Population genetics describes the distribution of alleles in a population with regard to evolutionary processes and population structure. It is the cornerstone of modern evolutionary biology, with wide applications in fields such as conservation biology, health-oriented clinical research, bioinformatics, animal and plant breeding, and molecular biology. Population genetics can also be used as a vehicle to introduce science majors to processes of abstraction and modeling common to any field of science"-- |
| Physical Description: | xv, 480 Seiten Diagramme |
| ISBN: | 9781118436943 |
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| 520 | 3 | |a "Population genetics describes the distribution of alleles in a population with regard to evolutionary processes and population structure. It is the cornerstone of modern evolutionary biology, with wide applications in fields such as conservation biology, health-oriented clinical research, bioinformatics, animal and plant breeding, and molecular biology. Population genetics can also be used as a vehicle to introduce science majors to processes of abstraction and modeling common to any field of science"-- | |
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| adam_text | Contents 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 reasoninq. 3 1.2 Theory and assumptions, 4 1.3 Simulation. 5 Interact box 1.1 The textbook website, b 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?. 13 2.4 Applications of Hardy-Weinberg. 18 Forensic USA profíluu¡. 18 Problem box 2.1 The expected genotype frequency for a DNA profile. 20 Testina Hnrd¡i֊ Ycinbcra expected qenolqpe frequencies. 20 Box 2.1 DNA profiling. 21 Assuniiiuj llardq-Weinberq to test alternative models of inheritance. 24 Problem box 2.2 Proving allele frequencies are obtained from expected genotype frequencies. Problem box 2.3 Inheritance for corn kernel phenotypes. 2Һ 2.3 The fixation index and heterozygosity. 2b Interact box 2.2 Associative mating and genotype frequencies. 27 Box 2.2 Protein locus or allozyme genotyping. 30 2.Һ Mating among relatives. 31 Impacts of non-random matina on аспоіцре ami allele frequencies. 31 Coancesirţi coefficient and autozqqositq. З 3 Box 2.3 Ixx’ating relatives using genetic genealogy methods. 3 7 Phenolļipic consequences of matina атопц relatives. 3S The manq mcaninqs of inbreedinq, 4 1 2.7 Hardy-Weinberg for two loci. 42 Gametic disequilibrium. 42 Physical linkaqc. 47 Saturai selection. 47 Interact
box 2.3 Gametic disequilibrium under both recombination and natural selection. 48 Mutation. 4$ Mixinq of divcrqcd populations. 44 Matinq system. 44
viii CONTENTS 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 rnarkov chain model. 64 Problem box 3.2 Constructing a transition probability matrix. 64 The diffusion approximation of genetic drift, 70 3.3 Effective population size, 76 Problem box 3.3 Estimating Ne from information about SI 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 λ’,, from allele frequencies and heterozygosity over tirne, 84 Breeding effective population size, 90 Effective population sizes of different genomes. 92 3.6 Gene genealogies and the coalescent model. 42 Interact box 3.5 Sampling lineages in a Wright-l- isher population. 44 Math box 3.2 Approximating the probability of a coalescent event with the exponential distribution, 44 Interact box 3.6 Build your own coalescent genealogies. 100 3.7 Effective population size in the coalescent model. 1(H Interact box 3.7 Simulating gene genealogies in populations
with different effective sizes. 10 5 Coalescent genealogies and population bottlenecks, 105 Coalescent genealogies in growing and shrinking populations. ¡06 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
CONTENTS Interact box 4.3 Average exclusion probability for a locus, 134 4.4 Fixation indices to summarize the pattern of population subdivision, 13 5 Problem box 4.2 Compute Fls, 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 FST in the infinite island model. 1 50 Problem box 4.4 Expected levels of FST for Y-chromosome and organelle loci, 1 5 3 Interact box 4.5 Simulate FIS, FSţ, and F]T in the finite island model, 1 54 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, 1 59 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 1’he 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 Eate 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 Rs, 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 ix
x CONTENTS 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, 22 5 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. 2 30 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. 2 36 The strength of natural selection, 237 6.3 How natural selection works to increase average fitness, 2 38 Average fitness and rate of change in allele frequency. 2 IS 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. 24 3 The Classical and Balance Hypotheses. 24 3 How to explain levels of allozyme polymorphism, 24 5 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 Ap for the Hb C allele. 2 5 3 Interact box 7.1 Natural selection on one locus with three or more alleles. 2 54 Natural selection on two diallelic loci, 2 54 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. 26 3 Interact box 7.2 Frequency-dependent natural selection. 26 3 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
CONTENTS xi 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. 2 75 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. 28 1 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 distributions, 286 Evolutionary scenarios imagined by wright, 287 Critique and controversy over shifting balance, 290 Chapter 7 review, 292 Further reading, 293 Knd-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 species, 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 π 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
xii CONTENTS 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, 561 Components of phenotypic variation, 362 Components of genotypic variation (Vq), 363 Inheritance of additive (VA), dominance (Vn), and epistasis (Y,) genotypic variation. 5o7 Genotype-by-environment interaction (VGxr.)· 569 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, 174 Changes in quantitative trait mean and variance due lo natural selection. 76 Math box 9.2 Selection differential with truncation selection. 576 Estimating heritability by parent-offspring regression. 579 Interact box 9.1 Estimating heritability with parent-offspring regression. 5S 1 Response to selection on correlated traits. SS 1 Interact box 9.2 Response to natural selection on two correlated traits, 5S t 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. 591 Interact box 9.4 Effective population size and genotypic variation in a neutral quantitative trait. 592 9.3 Quantitative trait loci (QTL), 393 QTL mapping with single marker loci. 594 Problem box 9.2
Compute the effect and dominance coefficient of a QTL 594 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. 40 3 Genome-wide association studies. 404 Biological significance of identifying QTL. 40 5 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 Mendeiian basis of quantitative trait variation. 413 10.1 The connection between particulate inheritance and quantitative trait variation. 41 3 Scale of genotypic values. 413 Problem box 10.1 Compute values on the genotypic scale of measurement for ftìFl in dogs. 414 10.2 Mean genotypic value in a population. 41 5 10.3 Average effect of an allele. 416 Math box 10.1 The average effect of the A։ allele. 418 Problem box 10.2 Compute average effects for IGF 1 in dogs. 420
CONTENTS 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, Va, 410 Math box 10.2 Deriving the total genotypic variance, VG, 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.l Estimating the variance, 438 Interact box A.l The central limit theorem, 439 A. 1 Covariance and Correlation, 440 Further reading, 442 Problem box answers, 442 Bibliography. 443 Index. 468 xiii
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Contents 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 reasoninq. 3 1.2 Theory and assumptions, 4 1.3 Simulation. 5 Interact box 1.1 The textbook website, b 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?. 13 2.4 Applications of Hardy-Weinberg. 18 Forensic USA profíluu¡. 18 Problem box 2.1 The expected genotype frequency for a DNA profile. 20 Testina Hnrd¡i֊\Ycinbcra expected qenolqpe frequencies. 20 Box 2.1 DNA profiling. 21 Assuniiiuj llardq-Weinberq to test alternative models of inheritance. 24 Problem box 2.2 Proving allele frequencies are obtained from expected genotype frequencies. Problem box 2.3 Inheritance for corn kernel phenotypes. 2Һ 2.3 The fixation index and heterozygosity. 2b Interact box 2.2 Associative mating and genotype frequencies. 27 Box 2.2 Protein locus or allozyme genotyping. 30 2.Һ Mating among relatives. 31 Impacts of non-random matina on аспоіцре ami allele frequencies. 31 Coancesirţi coefficient and autozqqositq. З 3 Box 2.3 Ixx’ating relatives using genetic genealogy methods. 3 7 Phenolļipic consequences of matina атопц relatives. 3S The manq mcaninqs of inbreedinq, 4 1 2.7 Hardy-Weinberg for two loci. 42 Gametic disequilibrium. 42 Physical linkaqc. 47 Saturai selection. 47 Interact
box 2.3 Gametic disequilibrium under both recombination and natural selection. 48 Mutation. 4$ Mixinq of divcrqcd populations. 44 Matinq system. 44
viii CONTENTS 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 rnarkov chain model. 64 Problem box 3.2 Constructing a transition probability matrix. 64 The diffusion approximation of genetic drift, 70 3.3 Effective population size, 76 Problem box 3.3 Estimating Ne from information about SI 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 λ’,, from allele frequencies and heterozygosity over tirne, 84 Breeding effective population size, 90 Effective population sizes of different genomes. 92 3.6 Gene genealogies and the coalescent model. 42 Interact box 3.5 Sampling lineages in a Wright-l-'isher population. 44 Math box 3.2 Approximating the probability of a coalescent event with the exponential distribution, 44 Interact box 3.6 Build your own coalescent genealogies. 100 3.7 Effective population size in the coalescent model. 1(H Interact box 3.7 Simulating gene genealogies in populations
with different effective sizes. 10 5 Coalescent genealogies and population bottlenecks, 105 Coalescent genealogies in growing and shrinking populations. ¡06 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
CONTENTS Interact box 4.3 Average exclusion probability for a locus, 134 4.4 Fixation indices to summarize the pattern of population subdivision, 13 5 Problem box 4.2 Compute Fls, 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 FST in the infinite island model. 1 50 Problem box 4.4 Expected levels of FST for Y-chromosome and organelle loci, 1 5 3 Interact box 4.5 Simulate FIS, FSţ, and F]T in the finite island model, 1 54 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, 1 59 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 1’he 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 Eate 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 Rs, 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 ix
x CONTENTS 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, 22 5 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. 2 30 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. 2 36 The strength of natural selection, 237 6.3 How natural selection works to increase average fitness, 2 38 Average fitness and rate of change in allele frequency. 2 IS 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. 24 3 The Classical and Balance Hypotheses. 24 3 How to explain levels of allozyme polymorphism, 24 5 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 Ap for the Hb C allele. 2 5 3 Interact box 7.1 Natural selection on one locus with three or more alleles. 2 54 Natural selection on two diallelic loci, 2 54 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. 26 3 Interact box 7.2 Frequency-dependent natural selection. 26 3 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
CONTENTS xi 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. 2 75 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. 28 1 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 distributions, 286 Evolutionary scenarios imagined by wright, 287 Critique and controversy over shifting balance, 290 Chapter 7 review, 292 Further reading, 293 Knd-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 species, 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 π 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
xii CONTENTS 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, 561 Components of phenotypic variation, 362 Components of genotypic variation (Vq), 363 Inheritance of additive (VA), dominance (Vn), and epistasis (Y,) genotypic variation. 5o7 Genotype-by-environment interaction (VGxr.)· 569 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, 174 Changes in quantitative trait mean and variance due lo natural selection. 76 Math box 9.2 Selection differential with truncation selection. 576 Estimating heritability by parent-offspring regression. 579 Interact box 9.1 Estimating heritability with parent-offspring regression. 5S 1 Response to selection on correlated traits. SS 1 Interact box 9.2 Response to natural selection on two correlated traits, 5S t 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. 591 Interact box 9.4 Effective population size and genotypic variation in a neutral quantitative trait. 592 9.3 Quantitative trait loci (QTL), 393 QTL mapping with single marker loci. 594 Problem box 9.2
Compute the effect and dominance coefficient of a QTL 594 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. 40 3 Genome-wide association studies. 404 Biological significance of identifying QTL. 40 5 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 Mendeiian basis of quantitative trait variation. 413 10.1 The connection between particulate inheritance and quantitative trait variation. 41 3 Scale of genotypic values. 413 Problem box 10.1 Compute values on the genotypic scale of measurement for ftìFl in dogs. 414 10.2 Mean genotypic value in a population. 41 5 10.3 Average effect of an allele. 416 Math box 10.1 The average effect of the A։ allele. 418 Problem box 10.2 Compute average effects for IGF 1 in dogs. 420
CONTENTS 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, Va, 410 Math box 10.2 Deriving the total genotypic variance, VG, 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.l Estimating the variance, 438 Interact box A.l The central limit theorem, 439 A. 1 Covariance and Correlation, 440 Further reading, 442 Problem box answers, 442 Bibliography. 443 Index. 468 xiii |
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| author | Hamilton, Matthew B. |
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| id | DE-604.BV047211901 |
| illustrated | Not Illustrated |
| index_date | 2024-07-03T16:54:35Z |
| indexdate | 2024-07-10T09:05:47Z |
| institution | BVB |
| isbn | 9781118436943 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-032616687 |
| oclc_num | 1249658990 |
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| owner_facet | DE-355 DE-BY-UBR DE-703 DE-11 |
| physical | xv, 480 Seiten Diagramme |
| publishDate | 2021 |
| publishDateSearch | 2021 |
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| publisher | Wiley Blackwell |
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| spelling | Hamilton, Matthew B. Verfasser (DE-588)1227761457 aut Population genetics Matthew B. Hamilton Second edition Hoboken, NJ Wiley Blackwell 2021 xv, 480 Seiten Diagramme txt rdacontent n rdamedia nc rdacarrier "Population genetics describes the distribution of alleles in a population with regard to evolutionary processes and population structure. It is the cornerstone of modern evolutionary biology, with wide applications in fields such as conservation biology, health-oriented clinical research, bioinformatics, animal and plant breeding, and molecular biology. Population genetics can also be used as a vehicle to introduce science majors to processes of abstraction and modeling common to any field of science"-- Populationsgenetik (DE-588)4046804-5 gnd rswk-swf Molekulare Evolution (DE-588)4812902-1 gnd rswk-swf Population genetics Populationsgenetik (DE-588)4046804-5 s Molekulare Evolution (DE-588)4812902-1 s DE-604 Erscheint auch als Online-Ausgabe, PDF 978-1-118-43692-9 Erscheint auch als Online-Ausgabe, EPUB 978-1-118-43689-9 V:DE-576;X:WILEY image/jpeg http://swbplus.bsz-bw.de/bsz1700283332cov.htm 20201217150207 Cover Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032616687&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Hamilton, Matthew B. Population genetics Populationsgenetik (DE-588)4046804-5 gnd Molekulare Evolution (DE-588)4812902-1 gnd |
| subject_GND | (DE-588)4046804-5 (DE-588)4812902-1 |
| title | Population genetics |
| title_auth | Population genetics |
| title_exact_search | Population genetics |
| title_exact_search_txtP | Population genetics |
| title_full | Population genetics Matthew B. Hamilton |
| title_fullStr | Population genetics Matthew B. Hamilton |
| title_full_unstemmed | Population genetics Matthew B. Hamilton |
| title_short | Population genetics |
| title_sort | population genetics |
| topic | Populationsgenetik (DE-588)4046804-5 gnd Molekulare Evolution (DE-588)4812902-1 gnd |
| topic_facet | Populationsgenetik Molekulare Evolution |
| url | http://swbplus.bsz-bw.de/bsz1700283332cov.htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032616687&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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