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| Preface | |
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| Introduction | |
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| Types of Genetic Data | |
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| Detecting Differences in Genotype | |
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| Allele Frequencies, Genotype Frequencies, and Hardy-Weinberg Equilibrium | |
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| Allele Frequencies | |
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| Genotype Frequencies | |
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| K-Allelic Loci | |
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| Example: The MC1R Gene | |
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| Hardy-Weinberg Equilibrium | |
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| The MC1R Gene Revisited | |
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| Probability and Independence | |
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| Derivation of HWE Genotype Frequencies | |
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| Tay-Sachs Disease | |
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| Extensions and Generalizations of HWE | |
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| Deviations from HWE 1: Assortative Mating | |
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| Deviations from HWE 2: Inbreeding | |
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| Deviations from HWE 3: Population Structure | |
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| Deviations from HWE 4: Selection | |
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| The Inbreeding Coefficient | |
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| Testing for Deviations from HWE | |
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| The Chi-Square Test | |
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| Using Allele Frequencies to Identify Individuals | |
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| Genetic Drift and Mutation | |
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| The Wright-Fisher Model | |
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| Genetic Drift and Expected Allele Frequencies | |
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| Expectation | |
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| Patterns of Genetic Drift in the Wright-Fisher Model | |
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| Effect of Population Size in the Wright-Fisher Model | |
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| Mutation | |
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| Effects of Mutation on Allele Frequency | |
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| Probability of Fixation | |
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| Species Divergence and the Rate of Substitution | |
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| The Molecular Clock | |
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| Dating the Human-Chimpanzee Divergence Time | |
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| Coalescence Theory: Relating Theory to Data | |
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| Coalescence in a Sample of Two Chromosomes (n = 2) | |
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| Coalescence in Large Populations | |
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| Mutation, Genetic Variability, and Population Size | |
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| Infinite Sites Model | |
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| The Tajima's Estimator | |
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| The Concept of Effective Population Size | |
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| Interpreting Estimates of � | |
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| The Infinite Alleles Model and Expected Heterozygosity | |
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| The Coalescence Process in a Sample of n Individuals | |
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| The Coalescence Tree and the tMRCA | |
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| Total Tree Length and the Number of Segregating Sites | |
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| The Site Frequency Spectrum (SFS) | |
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| Tree Shape as a Function of Population Size | |
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| Population Subdivision | |
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| The Wahlund Effect | |
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| F<sub>ST</sub>: Quantifying Population Subdivision | |
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| The Wright-Fisher Model with Migration | |
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| The Coalescence Process with Migration | |
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| Expected Coalescence Times for n = 2 | |
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| F<sub>ST</sub> and Migration Rates | |
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| Divergence Models | |
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| Expected Coalescence Times, Pairwise Difference and F<sub>ST</sub> in Divergence Models | |
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| Isolation by Distance | |
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| Inferring Population History and Demography | |
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| Inferring Demography Using Summary Statistics | |
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| Coalescence Simulations and Confidence Intervals | |
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| Simulating Coalescence Trees | |
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| Estimating Evolutionary Trees | |
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| The UPGMA Method for Estimating Trees | |
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| Gene Trees vs. Species Trees | |
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| Interpreting Estimated Trees from Population Genetic Data | |
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| Likelihood and the Felsenstein Equation | |
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| MCMC and Bayesian Methods | |
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| The Effect of Recombination | |
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| Population Assignment, Clustering, and Admixture | |
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| Linkage Disequilibrium and Gene Mapping | |
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| Linkage Disequilibrium | |
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| Coefficients of Linkage Disequilibrium | |
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| LD Coefficients for Two Diallelic Loci | |
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| r<sup>2</sup> as a Correlation Coefficient | |
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| Evolution of D | |
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| r<sup>2</sup> and �<sup>2</sup> | |
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| Change in D Due to Random Mating | |
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| Recurrent Mutation Reduces D′ | |
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| Two-Locus Wahlund Effect | |
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| Two-Locus Wahlund Effect | |
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| Genealogical Interpretation of LD | |
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| Recombination | |
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| Association Mapping | |
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| Example of a Case-Control Test | |
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| Selection I | |
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| Selection in Haploids | |
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| Selection in Diploids | |
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| Haploid Selection | |
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| One Generation of Viability Selection | |
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| Algebraic Calculation of Allele Frequency Changes | |
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| Special Cases of Selection | |
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| Genie Selection | |
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| Heterozygote Advantage | |
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| Estimates of Selection Coefficients for the S Allele in a West African Population | |
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| Mutation-Selection Balance | |
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| Selection in a Finite Population | |
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| Fixation Probabilities of New Mutations | |
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| Simulating Trajectories | |
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| Rates of Substitution of Selected Alleles | |
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| Accounting for Multiple Substitutions | |
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| Computing Synonymous and Nonsynonymous Rates | |
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| Genetic Hitchhiking | |
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| Selective Sweeps | |
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| Hitchhiking in a Haploid Population | |
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| Partial Sweeps | |
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| Associative Overdominance | |
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| Estimating the Age of a Mutation | |
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| The Neutral Theory and Tests of Neutrality | |
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| The HKA Test | |
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| The MacDonald-Kreitman (MK) Test | |
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| The Site Frequency Spectrum (SFS) | |
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| Tajima's D Test | |
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| Tests Based on Genetic Differentiation among Populations | |
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| Tests Using LD and Haplotype Structure | |
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| Selection II: Interactions and Conflict | |
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| Selection on Sex Ratio | |
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| Resolving Conflicts | |
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| The Prisoner's Dilemma | |
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| Kin Selection | |
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| Selfish Genes | |
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| Meiotic Drive | |
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| Transposons | |
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| Species Formation | |
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| Quantitative Genetics | |
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| Biometrical Analysis | |
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| Normal Distribution | |
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| Variance of the Mid-parental Value | |
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| Breeding Value | |
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| Quantitative Trait Loci | |
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| Multiple Quantitative Trait Loci | |
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| Genotype-Environment Interactions | |
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| Mapping Quantitative Trait Loci | |
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| Mapping Alleles When Starting with Homozygous Populations | |
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| Basic Probability Theory | |
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| The Binomial RV | |
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| PMF: Bernoulli | |
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| PMF: Binomial | |
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| Expectation | |
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| Variance | |
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| The Poisson RV | |
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| PMF: Poisson | |
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| The Geometric RV | |
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| PMF: Geometric | |
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| The Exponential Distribution and Coalescence Times | |
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| Maximum Likelihood and Bayesian Estimation | |
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| Bayesian Estimation | |
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| Critical Values of the Chi-Square Distribution with d Degrees of Freedom | |
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| Solutions to Odd-Numbered Exercises | |
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| Glossary | |
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| Credits | |
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| Index | |