Coalescent theory : an introduction / John Wakeley.

Includes bibliographical references (pages 293-316) and indexes.

"An introduction to coalescent theory, which provides the foundation for molecular population genetics and genomics. Coalescent theory is the conceptual framework for studies of DNA sequence variation within species, and is the source of essential tools for making inferences about mutation, recombination, population structure and natural selection from DNA sequence data"--Provided by publisher.

1. Gene genealogies. 1.1. Genealogies and genealogical thinking ; 1.2. Mutation and mutation models ; 1.3. Measures of DNA sequence polymorphism ; 1.4. Variation at the PDHA1 locus in humans -- 2. Probability theory. 2.1. Fundamentals of probability theory. 2.1.1. Events, probabilities, and random variables. 2.1.2. Four famous probability distributions ; 2.2. Poisson processes. 2.2.1. Poisson process results for the coalescent. 2.2.2. Convolutions of exponential distributions -- 3. The coalescent. 3.1. Population genetic models. 3.1.1. The Wright-Fisher model. 3.1.2. The Moran model ; 3.2. The standard coalescent model. 3.2.1. Wright-Fisher model derivation. 3.2.2. Moran model derivation. 3.2.3. Breeding structure and exchangability ; 3.3. Some properties of coalescent genealogies. 3.3.1. Two measures of the size of genealogy. 3.3.2. The branching structure of genealogies ; 3.4. Human-Neanderthal couples? -- 4. Neutral genetic variation. 4.1. The infinite-sites model and measures of DNA sequence polymorphism. 4.1.1. The number segregating sites. 4.1.2. Pairwise differences. 4.1.3. Site frequencies ; 4.2. The infinite-alleles model and the Ewens sampling formula ; 4.3. Deviations from the coalescent : testing "neutrality". 4.3.1. Test statistics based on site frequencies. 4.3.2. Demographic history and patterns of polymorphism ; 4.4. Footprints of positive selection in Drosophila simulans -- 5. The structured coalescent. 5.1. Markov processes. 5.1.1. Classification of states and limiting behavior. 5.1.2. Continuous-time approximations and jump chains. 5.1.3. First-step analysis ; 5.2. The structured coalescent. 5.2.1. Predictions for samples of size 2 ; 5.3. Geographic structure. 5.3.1. Subdivision with migration. 5.3.2. Gene trees versus species trees in Australian grass finches ; 5.4. Strong natural selection. 5.4.1. Selective sweeps. 5.4.2. Balancing selection at the Adh Locus in Drosophila melanogaster -- 6. Separation of time scales. 6.1. Diploidy and two sexes ; 6.2. Markov processes with two time scales ; 6.3. Strong migration ; 6.4. Partial selfing ; 6.5. Many demes ; 6.6. Samples larger than two and other extensions -- 7. Ancestral graphs. 7.1. The ancestral selection graph. 7.1.1. The ancestry of a highly deleterious allele ; 7.2. The ancestral recombination events. 7.2.1. The two-locus model : covariance in ancestry. 7.2.2. The number of segregating sites. 7.2.3. The number of recombination events. 7.2.4. Linkage disequilibrium and coalescence times ; 7.3. Linkage disequilibrium in the human genome -- 8. Simulation and inference. 8.1. The age of the ZFY intron in humans ; 8.2. Monte Carlo integration and the coalescent. 8.2.1. Mutation models ; 8.3. Concepts of statistical inference and the coalescent. 8.3.1. Frequentist versus Bayesian approaches ; 8.4. Computing likelihoods of full data patterns. 8.4.1. Importance sampling methods. 8.4.2. Markov chain Monte Carlo methods ; 8.5. Future directions.