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Coalescent Theory An Introduction

ISBN-10: 0974707759
ISBN-13: 9780974707754
Edition: 2009
Authors: John Wakeley
List price: $65.99
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Book details

List price: $65.99
Copyright year: 2009
Publisher: W. H. Freeman & Company
Publication date: 6/1/2008
Binding: Paperback
Pages: 352
Size: 7.00" wide x 8.75" long x 0.75" tall
Weight: 1.716
Language: English

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

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