Gene genealogies, variation and evolution : a primer in coalescent theory / Jotun Hein, Mikkel H. Schierup, and Carsten Wiuf.

Includes bibliographical references (pages 259-271) and index.

Print version record.

The basic coalescent -- A Y-chromosome data set -- Data and theory -- The Wright-Fisher model -- Assumptions of the Wright-Fisher model -- The number of descendants of a gene in one generation -- The geometric distribution -- The exponential distribution -- The discrete-time coalescent -- Coalescence of a sample of two genes -- Coalescence of a sample of n genes -- Example: Effect of approximations -- The continuous time coalescent -- Calculating simple quantities on a coalescent tree -- The height of a tree -- The total branch length of a tree -- The effect of sampling more sequences -- The effective population size -- The Moran model -- Robustness of the coalescent -- From genealogies to sequences -- Mathematical models of alleles -- The infinite alleles model -- The infinite sites model -- Finite sites model -- The Wright-Fisher model with mutation -- Algorithms for simulating sequence evolution -- The probability of a sample configuration -- Infinite alleles model -- Infinite sites model -- Impossible ancestral states -- Quantities related to the infinite sites model -- The number of segregating sites -- Haplotypes -- Pairwise mismatch distribution -- Estimators of [theta] and Tajima's D -- Evolutionary versus sampling variance -- Example 1: The variable S[subscript n] -- Example 2: Tajima's estimator [pi] -- Trees and topologies -- Some terminology -- The jump process and the waiting time process -- The coalescent and phylogenetic trees -- Counting trees and topologies -- Gene trees -- How to build a gene tree.

"This text presents a straightforward and elementary account of coalescent theory, which is a central concept in the study of genetic sequence variation observed in a population. Authored by leading experts, and rich in examples and illustrations, Gene Genealogies, Variation and Evolution is highly suitable for a graduate course in statistics; population, molecular and medical genetics; and for bioscience and medicine and students studying the evolution of human population and disease. It is also a reference for bioscientists and statisticians in the pharmaceutical industry and academia."--Jacket.

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