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Introduction to Population Genetics Theory and Applications

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ISBN-10: 1605351539

ISBN-13: 9781605351537

Edition: 2013

Authors: Rasmus Nielsen, Montgomery Slatkin

List price: $102.95
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"A text for a one-semester course in population genetics. It introduces students to classical population genetics (in terms of allele and haplotype frequencies) and modern population genetics (in terms of coalescent theory). It presents numerous applications of population genetic methods to practical problems, including testing for natural selection, detecting genetic hitchhiking and inferring the history of populations"--Provided by publisher.
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Book details

List price: $102.95
Copyright year: 2013
Publisher: Oxford University Press, Incorporated
Publication date: 3/1/2013
Binding: Hardcover
Pages: 298
Size: 7.20" wide x 9.49" long x 0.71" tall
Weight: 1.760
Language: English

Types of Genetic Data
Detecting Differences in Genotype
Allele Frequencies, Genotype Frequencies, and Hardy-Weinberg Equilibrium
Allele Frequencies
Genotype Frequencies
K-Allelic Loci
Example: The MC1R Gene
Hardy-Weinberg Equilibrium
The MC1R Gene Revisited
Probability and Independence
Derivation of HWE Genotype Frequencies
Tay-Sachs Disease
Extensions and Generalizations of HWE
Deviations from HWE 1: Assortative Mating
Deviations from HWE 2: Inbreeding
Deviations from HWE 3: Population Structure
Deviations from HWE 4: Selection
The Inbreeding Coefficient
Testing for Deviations from HWE
The Chi-Square Test
Using Allele Frequencies to Identify Individuals
Genetic Drift and Mutation
The Wright-Fisher Model
Genetic Drift and Expected Allele Frequencies
Patterns of Genetic Drift in the Wright-Fisher Model
Effect of Population Size in the Wright-Fisher Model
Effects of Mutation on Allele Frequency
Probability of Fixation
Species Divergence and the Rate of Substitution
The Molecular Clock
Dating the Human-Chimpanzee Divergence Time
Coalescence Theory: Relating Theory to Data
Coalescence in a Sample of Two Chromosomes (n = 2)
Coalescence in Large Populations
Mutation, Genetic Variability, and Population Size
Infinite Sites Model
The Tajima's Estimator
The Concept of Effective Population Size
Interpreting Estimates of �
The Infinite Alleles Model and Expected Heterozygosity
The Coalescence Process in a Sample of n Individuals
The Coalescence Tree and the tMRCA
Total Tree Length and the Number of Segregating Sites
The Site Frequency Spectrum (SFS)
Tree Shape as a Function of Population Size
Population Subdivision
The Wahlund Effect
F<sub>ST</sub>: Quantifying Population Subdivision
The Wright-Fisher Model with Migration
The Coalescence Process with Migration
Expected Coalescence Times for n = 2
F<sub>ST</sub> and Migration Rates
Divergence Models
Expected Coalescence Times, Pairwise Difference and F<sub>ST</sub> in Divergence Models
Isolation by Distance
Inferring Population History and Demography
Inferring Demography Using Summary Statistics
Coalescence Simulations and Confidence Intervals
Simulating Coalescence Trees
Estimating Evolutionary Trees
The UPGMA Method for Estimating Trees
Gene Trees vs. Species Trees
Interpreting Estimated Trees from Population Genetic Data
Likelihood and the Felsenstein Equation
MCMC and Bayesian Methods
The Effect of Recombination
Population Assignment, Clustering, and Admixture
Linkage Disequilibrium and Gene Mapping
Linkage Disequilibrium
Coefficients of Linkage Disequilibrium
LD Coefficients for Two Diallelic Loci
r<sup>2</sup> as a Correlation Coefficient
Evolution of D
r<sup>2</sup> and �<sup>2</sup>
Change in D Due to Random Mating
Recurrent Mutation Reduces D&#8242;
Two-Locus Wahlund Effect
Two-Locus Wahlund Effect
Genealogical Interpretation of LD
Association Mapping
Example of a Case-Control Test
Selection I
Selection in Haploids
Selection in Diploids
Haploid Selection
One Generation of Viability Selection
Algebraic Calculation of Allele Frequency Changes
Special Cases of Selection
Genie Selection
Heterozygote Advantage
Estimates of Selection Coefficients for the S Allele in a West African Population
Mutation-Selection Balance
Selection in a Finite Population
Fixation Probabilities of New Mutations
Simulating Trajectories
Rates of Substitution of Selected Alleles
Accounting for Multiple Substitutions
Computing Synonymous and Nonsynonymous Rates
Genetic Hitchhiking
Selective Sweeps
Hitchhiking in a Haploid Population
Partial Sweeps
Associative Overdominance
Estimating the Age of a Mutation
The Neutral Theory and Tests of Neutrality
The HKA Test
The MacDonald-Kreitman (MK) Test
The Site Frequency Spectrum (SFS)
Tajima's D Test
Tests Based on Genetic Differentiation among Populations
Tests Using LD and Haplotype Structure
Selection II: Interactions and Conflict
Selection on Sex Ratio
Resolving Conflicts
The Prisoner's Dilemma
Kin Selection
Selfish Genes
Meiotic Drive
Species Formation
Quantitative Genetics
Biometrical Analysis
Normal Distribution
Variance of the Mid-parental Value
Breeding Value
Quantitative Trait Loci
Multiple Quantitative Trait Loci
Genotype-Environment Interactions
Mapping Quantitative Trait Loci
Mapping Alleles When Starting with Homozygous Populations
Basic Probability Theory
The Binomial RV
PMF: Bernoulli
PMF: Binomial
The Poisson RV
PMF: Poisson
The Geometric RV
PMF: Geometric
The Exponential Distribution and Coalescence Times
Maximum Likelihood and Bayesian Estimation
Bayesian Estimation
Critical Values of the Chi-Square Distribution with d Degrees of Freedom
Solutions to Odd-Numbered Exercises