1. Genetic and Phenotypic Variation
* Relevance of Population Genetics
* Phenotypic Variation in Natural Populations
o Continuous Variation: The Normal Distribution
o Mean and Variance
o The Central Limit Theorem
o Discrete Mendelian Variation
* Multiple-Factor Inheritance
* Maintenance of Genetic Variation
* Molecular Population Genetics
o Electrophoresis
o Allele Frequencies and Genotype Frequencies
o Polymorphism and Heterozygosity
o Allozyme Polymorphisms
o Inferences from Allozyme Polymorphisms
* Polymorphisms in DNA Sequences
o Restriction Enzymes
o The Polymerase Chain Reaction
o Single Nucleotide Polymorphisms
o Synonymous and Nonsynonymous Polymorphisms
o Segregating Sites and Nucleotide Mismatches
* Utility of Genetic Polymorphisms
* Summary
2. Organization of Genetic Variation
* Random Mating
o Nonoverlapping Generations
* The Hardy-Weinberg Principle
o Random Mating of Genotypes versus Random Union of Gametes
o Implications of the Hardy-Weinberg Principle
* Testing for Hardy-Weinberg Equilibrium
o Difficulties in Testing for Hardy-Weinberg Equilibrium
o Complications of Dominance
o Frequency of Heterozygotes
* Extensions of the Hardy-Weinberg Principle
o Three or More Alleles
o X-Linked Genes
* Linkage and Linkage Disequilibrium
o Difficulties in Testing for Linkage Equilibrium
o Relative Measures of Linkage Disequilibrium: D? and r2
* Causes of Linkage Disequilibrium
o Linkage Disequilibrium Due to Population Admixture
o Linkage Disequilibrium Due to Reduced Recombination
* Summary
3. Random Genetic Drift
* Random Genetic Drift and Binomial Sampling
* The Wright-Fisher Model of Random Genetic Drift
* The Diffusion Approximation
o An Approach Looking Forward
o An Approach Looking Backward
o Absorption Time and Time to Fixation
* Random Drift in a Subdivided Population
* Effective Population Size
o Fluctuation in Population Size
o Unequal Sex Ratio, Sex Chromosomes, Organelle Genes
o Variance in Offspring Number
o Effective Size of a Subdivided Population
* Gene Trees and Coalescence
o Coalescent Effective Size
o Coalescence with Population Growth
o Coalescent Models with Mutation
o Applications of Coalescent Methods
* Theoretical Implications of Coalescence
o Coalescent Models with Recombination
o Linkage Disequilibrium Mapping
* Summary
4. Mutation and the Neutral Theory
* Mutation
o Irreversible Mutation
o Reversible Mutation
* Mutation and Random Genetic Drift
o Probability of Fixation of a New Neutral Mutation
* The Neutral Theory of Molecular Evolution
* The Infinite-Alleles Model
o The Ewens Sampling Formula
o The Ewens-Watterson Test
* Infinite-Sites Model
o Nucleotide Polymorphism and Nucleotide Diversity
o Tajimas D Statistic
o The Fu and Li Test of Fit to Neutral Coalescence
* Mutation and Recombination
o A Model for the Evolutionary Benefit of Recombination
o Mullers Ratchet
o Piecewise Recombination in Bacteria
o Animal Mitochondrial DNA
* Summary
5. Darwinian Selection
* Selection in Haploid Organisms
o Discrete Generations
o Continuous Time
o Change in Allele Frequency
o Darwinian Fitness and Malthusian Fitness
* Selection in Diploid Organisms
o Change in Allele Frequency in Diploids
o Marginal Fitness and Selection with Multiple Alleles
o Application to the Evolution of Insecticide Resistance
* Equilibria with Selection
o Overdominance
o Local Stability
o Heterozygote Inferiority
o Stable Equilibria with Multiple Alleles
o Adaptive Topography and the Role of Random Genetic Drift
* Mutation-Selection Balance
o Equilibrium Allele Frequencies
o The Haldane-Muller Principle
* More Complex Types of Selection
o Differential Selection in the Sexes
o X-linked Genes
o Frequency-Dependent Selection
o Density-Dependent Selection
o Fecundity Selection
o Age-Structured Populations
o Heterogeneous Environments and Clines
o Diversifying Selection
o Gametic Selection
o Meiotic Drive
o Multiple Loci and Gene Interaction: Epistasis
o Evolution of Recombination Rate
o Sexual Selection
o Kin Selection
* Interdeme Selection in Geographically Subdivided Populations
* Selection in a Finite Population
o Weak Selection and the Nearly Neutral Theory
o Genetic Draft
* Summary
6. Inbreeding, Population Subdivision, and Migration
* Inbreeding
o The Inbreeding Coefficient
o Genotype Frequencies with Inbreeding
o Genetic Effects of Inbreeding
o Calculation of the Inbreeding Coefficient from Pedigrees
o Regular Systems of Mating
* Population Subdivision
o Reduction in Heterozygosity Due to Population Subdivision
o Average Heterozygosity
o Wrights F Statistics
o Linanthus Revisited: Evidence for Selection Associated with Flower Color
o Inference of Population Structure from Multilocus Genotype Data
* The Wahlund Principle
o Wahlunds Principle and the Fixation Index
o Genotype Frequencies in Subdivided Populations
o Relation between the Inbreeding Coefficient and the F Statistics
* Assortative Mating
* Migration
o One-Way Migration
o The Island Model of Migration
o How Migration Limits Genetic Divergence
o Estimates of Migration Rates
o Coalescence-Based Estimates of Migration
o Migration-Selection Balance
* Summary
7. Molecular Population Genetics
* The Neutral Theory and Molecular Evolution
o Theoretical Principles of the Neutral Theory
* Estimating Rates of Molecular Sequence Divergence
o Rates of Amino Acid Replacement
o Rates of Nucleotide Substitution
o Statistical Fitting of Nucleotide Substitution Models
* The Molecular Clock
o Variation across Genes in the Rate of the Molecular Clock
o Variation across Lineages in Clock Rate
o The Generation-Time Effect
o The Overdispersed Molecular Clock and the Neutral Theory
o The Nearly Neutral Theory
* Patterns of Nucleotide and Amino Acid Substitution
o Calculating Synonymous and Nonsynonymous Substitution Rates
o Codon Substitution Models
o Observations of Synonymous and Nonsynonymous Substitution Rates
o Polymorphism within Species
o Implications of Codon Usage Bias
* Polymorphism and Divergence in Nucleotide SequenceThe McDonald-Kreitman and HKA Tests
o Polymorphism and Divergence in Noncoding Sequences
o Impact of Local Recombination Rates
o Substitution Models for Structural RNA Genes
* Gene Genealogies
o Hypothesis Testing Using Trees
* Mitochondrial and Chloroplast DNA Evolution
o Chloroplast DNA and Organelle Transmission in Plants
o Maintenance of Variation in Organelle Genomes
o Evidence for Selection in mtDNA
* Molecular Phylogenetics
o Algorithms for Phylogenetic Tree Reconstruction
o Distance Methods versus Parsimony
o Bootstrapping and Statistical Confidence in a Tree
o Bayesian Methods
o Trans-Species Polymorphism
* Multigene Families
o Concerted Evolution
o Subfunctionalization
o Birth-and-Death Process
* Summary
8. Evolutionary Quantitative Genetics
* Types of Quantitative Traits
* Resemblance between Relatives and the Concept of Heritability
* Artificial Selection and Realized Heritability
o Contribution of New Mutations to the Response to Selection
o Prediction Equation for Individual Selection
o Limits to Selection
* Genetic Models for Quantitative Traits
o Change in Allele Frequency
o Change in Mean Phenotype
o Linearity of Response
* Components of Phenotypic Variance
o Genetic and Environmental Sources of Variation
o Components of Genotypic Variation
* Covariance among Relatives
o Twin Studies and Inferences of Heritability in Humans
o Estimation of Genetic Variance Components in Natural Populations
* Norm of Reaction, Threshold Traits, and Genetic Correlation
o Norm of Reaction and Phenotypic Plasticity
o Threshold Traits: Genes as Risk Factors in Disease
o Genetic Correlation and Correlated Response
* Evolutionary Quantitative Genetics
o Inference of Selection from Phenotypic Data
o Evolution of Multiple Intercorrelated Traits
o Random Genetic Drift and Phenotypic Evolution
o Mutational Variance and MutationAccumulation Experiments
o Mutation-Selection Balance for Quantitative Traits
* Genes That Affect Quantitative Traits
o The Number of Genes Affecting Quantitative Traits
o Methods for Mapping QTLs
* Summary
9. Population Genomics
* Evolution of Genome Size and Composition
o Organismic Complexity and the C-Value Paradox
o Base Composition of Genomic DNA
* Genome-Wide Patterns of Polymorphism
o Excess Polymorphism in Subtelomeric Regions
o Polymorphism and Rates of Recombination
o Hitchhiking versus Background Selection
o Linkage Disequilibrium and Haplotype Structures
o Decline of Linkage Disequilibrium with Genetic Distance
* Differences between Species
o Comparison of Nonsynonymous and Synonymous Divergence
o Positive Selection
o Exploiting a Phylogenetic Signal
o Polymorphism and Divergence
o Compensated Pathogenic Deviations
o StructureFunction Analysis
* Sexual Selection and the Sex Chromosomes
o Faster-Male Molecular Evolution
o Molecular Evolution of Genes in the X Chromosome
o Haldanes Rule
o Demasculinization of the X Chomosome
* Transposable Elements
o Diverse Types of Transposable Elements
o Factors Controlling the Population Dynamics of Transposable Elements
o Insertion Sequences and Composite Transposons in Bacteria
o Transposable Elements in Eukaryotes
o Population Dynamics of Transposable Elements
o Nonuniformity of Transposition Rates
o Horizontal Transmission of Transposable Elements
* Summary
10. Human Population Genetics
* Human Polymorphism
o Public SNP Resources and the HapMap Project
* Population Genetic Inferences from Human SNPs
o Ascertainment Bias of SNP Genotypes
o Departures from Hardy-Weingerg Frequencies
o Site Frequency Spectrum and Human Population Growth
o Rooting Human Polymorphism
o Inference of Inhomogeneities in the Mutation Process
o Inferences about Male and Female Mutation Rates
* Linkage Disequilibrium across the Human Genome
o The Landscape of Human Linkage Disequilibrium
o Inferences about Local Rates of Recombination
* Population Structure Inferred from Human Polymorphism
o Multilocus Methods of Inference of Stratification
o Heterogeneity in Linkage Disequilibrium across Human Populations
o Linkage Disequilibrium in Admixed Populations: Admixture Mapping
o Inbred Populations and Homozygosity Mapping
* Mendelian Disease and Population Genetics
o Mutation-Selection Balance
o Dating the Origin of Mutant Alleles
* Genetic Basis for Variation in Risk of Complex Disease
o Mapping Methods Based on Linkage
o Linkage Disequilibrium Mapping
o Genome-Wide Association Studies
* Seeking Signatures of Human-Specific Genetic Adaptations
o Interspecific Divergence
o McDonald-Kreitman and Poisson Random Field Tests
o Local Distortions in Linkage Disequilibrium
o FST Tests
o Genome Scans for Selection-Skewed Site Frequency Spectrum
* Human Origins
o Neanderthal Genome Sequence
* Summary