Cover -- Title -- Copyright -- Contents -- Preface and Acknowledgments -- Introduction -- I Genetic Variation -- 1 Genetics -- 1.1 Genetic Variation -- 1.1.1 Gene structure and function -- 1.1.2 Molecular genetic variation -- 2 Conservation of Variation -- 2.1 Stochastic Fluctuations -- 2.2 Wright-Fisher Process -- 2.2.1 Multiple alleles -- 2.3 Gene Identity in a Finite Population -- 2.4 Coalescence of Genes -- 2.5 Characteristic Time Unit -- 2.6 Diffusion Approximation -- 2.6.1 The Wright-Fisher model -- 2.6.2 The coalescent -- 2.6.3 The ∞-coalescent -- 2.7 Moran's Model -- 3 Diploid Populations -- 3.1 Random Mating -- 3.1.1 Mating of individuals -- 3.1.2 Random mating and selfing -- 3.2 Effective Population Size -- 3.2.1 Lose variation or gain identity -- 3.2.2 An exponentially growing population -- 3.2.3 Overlapping generations -- 3.3 Genotypic Frequencies -- 4 Mutation and Variation -- 4.1 Mutation -- 4.1.1 Induced mutation -- 4.1.2 Somatic mutation -- 4.1.3 Effects of mutations -- 4.2 The Two-Allele Model -- 4.2.1 Distribution of the gene frequency -- 4.3 Genealogy and Variation -- 4.3.1 Alcohol dehydrogenase in Drosophila -- 4.4 Mutation and Coalescence -- 4.4.1 The appearance of a sample -- 4.4.2 Gene identity and mutation -- 4.5 The Infinite Alleles Model -- 4.5.1 Heterozygosity in the infinite alleles model -- 4.6 The Infinite Sites Model -- 4.7 Age of an Allele -- 4.8 Numerical Simulations -- 5 Migration -- 5.1 Population Genetics of Migration -- 5.1.1 Genealogy in a structured population -- 5.1.2 The final waiting time -- 5.2 Population Structure -- 5.2.1 The simple two-island model -- 5.2.2 Coalescence in a widespread population -- 5.2.3 Strong migration -- 5.2.4 The stepping-stone model -- 5.3 Genotypic Proportions -- 5.3.1 Description of population structure -- 6 Linkage -- 6.1 The Karyotype -- 6.1.1 Sex linkage -- 6.1.2 Linkage map.

6.2 Population Genetics of Linkage -- 6.3 Linkage Equilibrium -- 6.3.1 The forward equations -- 6.3.2 Population mixing -- 6.3.3 Recurrent mixing and migration -- 6.3.4 Stochastic effects -- 6.3.5 Backcrosses -- 6.4 The Ancestral Recombination Graph -- 6.4.1 Genealogy and recombination -- 6.4.2 The mechanism of recombination -- 6.4.3 Gene conversion -- 6.4.4 The APOE risk factor in Alzheimer's disease -- 6.5 Recombination and Physical Distance -- 7 Phenotypic Variation -- 7.1 Quantitative Inheritance -- 7.1.1 Conservation of variation -- 7.1.2 Random genetic drift -- 7.2 Kin Resemblance -- 7.2.1 The additive model -- 7.2.2 Parent-offspring covariance -- 7.2.3 Covariance between sibs -- 7.3 Inference on the Genotypic Variance -- 7.3.1 Comparison of populations -- 7.3.2 Random genetic drift -- 7.3.3 Applications of quantitative genetics -- 7.4 Mapping of Quantitative Trait Loci -- 7.4.1 Diallel crosses -- 7.4.2 Inference -- II Variation and Selection -- 8 Effects of Selection -- 8.1 Selection Components -- 8.2 Viability Selection -- 8.2.1 Viability selection in Zoarces -- 8.3 Selection on a Quantitative Character -- 8.3.1 Genetic effects of selection -- 8.3.2 Fitness maximization -- 8.3.3 An experiment on growth rate in Mus -- 8.4 Mutation and Selection -- 8.4.1 Mutation, selection, and variation -- 8.5 Stability of an Equilibrium -- 8.6 The Coalescent and Selection -- 8.6.1 Microcephalin alleles in humans -- 8.6.2 Adh alleles in Drosophila -- 9 Genomic Effects of Selection -- 9.1 Multilocus Selection -- 9.1.1 Selection on one of the loci -- 9.1.2 Tight linkage -- 9.1.3 Loose linkage and weak selection -- 9.1.4 Intermediate linkage -- 9.2 Selection Experiments in Drosophila -- 9.2.1 An experiment using the ebony allele -- 9.2.2 An experiment using white alleles -- 9.3 Hitchhiking -- 9.3.1 An experiment on a bristle character in Drosophila.

9.4 Inbreeding Depression -- 9.4.1 Inbreeding in inbred populations -- 9.4.2 Hitchhiking and inbreeding depression -- 9.4.3 Inbreeding effects on a bristle character -- 9.5 Sweeps by Selection -- 9.5.1 Selection on a bristle character -- 10 Population Structure -- 10.1 Polymorphism -- 10.1.1 Local and global effects of selection -- 10.1.2 Transient polymorphism -- 10.1.3 Migration-selection balance -- 10.1.4 Environmental homogeneity -- 10.1.5 A butterfly metapopulation -- 10.1.6 Geographical variation in another butterfly -- 10.2 Introgression -- 10.2.1 Karyotypic variation -- 10.2.2 Genetic barrier -- 10.2.3 Introgression of a microcephalin allele -- 10.2.4 Vertical transmission of infection -- 10.2.5 Emerging barrier -- 10.3 Divergence of Populations -- A Probability Theory and Statistics -- A.1 Discrete Stochastic Variables -- A.1.1 Moments -- A.1.2 Conditional probabilities -- A.1.3 The binomial distribution -- A.1.4 The geometric distribution -- A.1.5 The Poisson distribution -- A.2 Markov Chains -- A.3 Continuous Random Variables -- A.3.1 The exponential distribution -- A.3.2 The Gaussian distribution -- B Solutions to Exercises -- Bibliography -- Index.