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| Preface | |
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| Gene Genealogies | |
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| Genealogies and Genealogical Thinking | |
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| Mutation and Mutation Models | |
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| Measures of DNA Sequence Polymorphism | |
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| Variation at the PDHA1 Locus in Humans | |
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| Probability Theory | |
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| Fundamentals of Probability Theory | |
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| Events, Probabilities, and Random Variables | |
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| Four Famous Probability Distributions | |
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| Poisson Processes | |
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| Poisson Process Results for the Coalescent | |
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| Convolutions of Exponential Distributions | |
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| The Coalescent | |
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| Population Genetic Models | |
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| The Wright-Fisher Model | |
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| The Moran Model | |
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| The Standard Coalescent Model | |
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| Wright-Fisher Model Derivation | |
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| Moran Model Derivation | |
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| Breeding Structure and Exchangeability | |
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| Some Properties of Coalescent Genealogies | |
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| Two Measures of the Size of a Genealogy | |
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| The Branching Structure of Genealogies | |
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| Human-Neanderthal Couples? | |
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| Neutral Genetic Variation | |
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| The Infinite-Sites Model and Measures of DNA Sequence Polymorphism | |
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| The Number Segregating Sites | |
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| Pairwise Differences | |
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| Site Frequencies | |
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| The Infinite-Alleles Model and the Ewens Sampling Formula | |
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| Deviations from the Coalescent: Testing "Neutrality" | |
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| Test Statistics Based on Site Frequencies | |
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| Demographic History and Patterns of Polymorphism | |
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| Footprints of Positive Selection in Drosophila simulans | |
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| The Structured Coalescent | |
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| Markov Processes | |
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| Classification of States and Limiting Behavior | |
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| Continuous-Time Approximations and Jump Chains | |
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| First-Step Analysis | |
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| The Structured Coalescent | |
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| Predictions for Samples of Size 2 | |
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| Geographic Structure | |
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| Subdivision with Migration | |
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| Gene Trees versus Species Trees in Australian Grass Finches | |
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| Strong Natural Selection | |
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| Selective Sweeps | |
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| Balancing Selection at the Adh Locus in Drosophila melanogaster | |
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| Separation of Time Scales | |
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| Diploidy and Two Sexes | |
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| Markov Processes with Two Time Scales | |
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| Strong Migration | |
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| Partial Selfing | |
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| Many Demes | |
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| Samples Larger than Two and Other Extensions | |
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| Ancestral Graphs | |
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| The Ancestral Selection Graph | |
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| The Ancestry of a Highly Deleterious Allele | |
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| The Ancestral Recombination Graph | |
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| The Two-Locus Model: Covariance in Ancestry | |
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| The Number of Segregating Sites | |
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| The Number of Recombination Events | |
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| Linkage Disequilibrium and Coalescence Times | |
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| Linkage Disequilibrium in the Human Genome | |
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| Simulations and Inference | |
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| The Age of the ZFY Intron in Humans | |
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| Monte Carlo Integration and the Coalescent | |
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| Mutation Models | |
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| Concepts of Statistical Inference and the Coalescent | |
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| Frequentist versus Bayesian Approaches | |
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| Computing Likelihoods of Full Data Patterns | |
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| Importance Sampling Methods | |
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| Markov Chain Monte Carlo Methods | |
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| Future Directions | |
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| References | |
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| Author Index | |
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| Subject Index | |