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Table of Contents 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 the Coalescent 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 Tajima?s 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 Muller?s 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 o Application to the Evolution of Insecticide Resistance o Estimation of Selection Coefficients * Equilibria with Selection o Overdominance o Local Stability o Heterozygote Inferiority o Multiple Alleles o The 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 X-linked Genes o Frequency-Dependent Selection o Density-Dependent Selection o Fecundity Selection o Age-Structured Populations and Evolution of Senescence o Heterogeneous Environments and Clines o Diversifying Selection o Differential Selection in the Sexes o Gametic Selection o Meiotic Drive o Multiple Loci and Gene Interaction: Epistasis o Sexual Selection and Sex Ratio o Kin Selection * Weak selection o Balance of random drift and selection * 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 Wright?s 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 Wahlund?s 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 Behavior * Summary 7. Molecular Population Genetics * The Neutral Theory and Molecular Evolution o Theoretical Principles * Estimating Rates of Molecular Sequence Divergence o Rates of Amino Acid Replacement?AA o Rates of Nucleotide Substitution?Jukes?Cantor Model o Other Measures of Molecular Divergence VNTR, Microsats, RNA Editing, Imprinting * 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 Does the Constancy of Substitution Prove the Neutral Theory? * Patterns of Nucleotide and Amino Acid Substitution o Calculating Synonymous and Nonsynonymous Substitution Rates o Within-species Polymorphism o Implications of Codon Bias * Polymorphism and Divergence in Nucleotide Sequence Data o McDonald?Kreitman and Sawyer?Hartl; HKA o Impact of Local Recombination Rates o X?Y-autosomes?Miyata, Li o Secondary Structure and Intron Evolution (Leicht et al.) o Regulatory Variation?Crawford; Ludwig and stripe-2 of eve. * Gene Genealogies o Hypothesis Testing using Trees o Inferences about Migration Based on Gene 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 * Transposable Elements o Factors Controlling the Population Dynamics o Insertion Sequences and Composite Transposons in Bacteria o Transposable Elements in Eukaryotes o Horizontal Transmission of Transposable Elements * Molecular Phylogenetics o Algorithms for Phylogenetic Tree Reconstruction o Distance Methods versus Parsimony o Bayesian Methods o Trans-species Polymorphism?MHC; Simulans Clade; S-alleles * Multigene Families o Concerted Evolution?Gene Identity and Copy Number Evolution o Multigene Family Evolution through a Birth and Death Process o Ribosomal RNA Gene Family and Compensatory Substitutions o Multigene Superfamilies o Dispersed Repetitive DNA o Cryptic Genes * 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 * 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 Mutation?Accumulation 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 Structure?Function Analysis * Sexual Selection and the Sex Chromosomes o Faster-Male Molecular Evolution o Molecular Evolution of Genes in the X Chromosome o Haldane?s 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 * Levels of Polymorphism * Genome-wide Search for SNPs o dbSNP and How SNPs are Found o Hardy-Weinberg o Site Frequency Spectrum and Human Population Growth * Linkage Disequilibrium across the Human Genome o Why It Matters o What It Says about Past Human Demographic History * Population Structure o Departure from Panmixia o The Meaning of Race o Admixture and Admixture Mapping o Estimating the Time of Splitting of Populations o Inbred Populations and Homozygosity Mapping * Mendelian Disease and Population Genetics o Sickle Cell, Thalassemia, G6PD Deficiency o Dating the Origin of Mutant Alleles * Genetic Basis for Variation in Risk of Complex Disease o The Challenge o Case-control and Cohort Designs o Methods for Testing Association o The International HapMap Project * Human Origins o The Fossil Record o Coalescence Times and Human Origins o Mitochondrial Eve o Out of Africa versus Multiregional Hypothesis o Population Genetics and the Individual o Properties of the Group and the Absolute Uniqueness of Every Individual (Even Clones) * Summary
Library of Congress Subject Headings for this publication:
Population genetics -- Problems, exercises, etc.