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Preface | |
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Acronyms and Abbreviations | |
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Genetic Variation | |
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Genetic and Molecular Essentials | |
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Genotype and Phenotype | |
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Gene Expression | |
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DNA Cleavage, Manipulation, and Amplification | |
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Types of Polymorphisms | |
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DNA Polymorphisms | |
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Uses of DNA Polymorphisms | |
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Protein Polymorphisms | |
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Gene and Genotype Frequencies | |
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Organization of Genetic Variation | |
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Populations | |
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Models | |
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Random Mating | |
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The Hardy-Weinberg Principle | |
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Implications of Random Mating | |
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Chi-square Test for HWE | |
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Recessive Alleles Hidden in Heterozygotes | |
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Multiple Alleles and X-Linked Genes | |
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Multiple Loci: Linkage and Linkage Disequilibrium | |
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Inbreeding | |
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Genotype Frequencies with Inbreeding | |
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The Inbreeding Coefficient | |
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Inbeeding Depression | |
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Calculation of the Inbreeding Coefficient from Pedigrees | |
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Regular Systems of Mating | |
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Further Readings | |
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Problems | |
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The Causes of Evolution | |
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Mutation | |
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Forward Mutation | |
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Reversible Mutation | |
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Remote Inbreeding in a Finite Population | |
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Equilibrium Heterozygosity with Mutation | |
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Migration | |
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The Island Model of Migration | |
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How Migration Limits Genetic Divergence | |
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Wahlund's Principle | |
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Hierarchical Population Structure | |
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Natural Selection | |
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Haploid Selection | |
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Diploid Selection | |
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Time Required for Changes in Gene Frequency | |
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Overdominance and Underdominance | |
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Mutation-Selection Balance | |
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More Complex Modes of Selection | |
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Random Genetic Drift | |
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Diffusion Approximations | |
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Probability of Fixation and Time to Fixation | |
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Effective Population Number | |
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Further Readings | |
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Problems | |
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Molecular Population Genetics | |
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Molecular Polymorphisms | |
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The Information Content of Molecular Sequences | |
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The Coalescent | |
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Nucleotide Polymorphism | |
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Nucleotide Diversity | |
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Tajima's D Statistic | |
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Patterns of Change in Nucleotide and Amino Acid Sequences | |
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Synonymous and Nonsynonymous Substitutions | |
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Codon Usage Bias | |
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Selection for Optimal Codons and Amino Acids | |
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Selective Sweeps versus Background Selection | |
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Polymorphism and Divergence | |
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The Hudson-Kreitman-Aguade (HKA) Test | |
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The McDonald-Kreitman Test | |
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Polymorphism and Divergence in a Poisson Random Field | |
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Convergence to Adaptation | |
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Molecular Phylogenetics | |
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The Multiple-Hit Problem | |
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Phylogenetic Inference | |
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Molecular Clocks | |
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Transposable Elements | |
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Insertion Sequences and Transposons in Bacteria | |
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Transposable Elements in Eukaryotes | |
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Further Readings | |
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Problems | |
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The Genetic Architecture of Complex Traits | |
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Types of Complex Traits | |
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Phenotypic Variation | |
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Genetics and Environment | |
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Genotypic Variance and Environmental Variance | |
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Broad-Sense Heritability | |
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Genotype-Environment and Other Interactions | |
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Genetic Effects on Complex Traits | |
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Components of Genotypic Variation | |
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Artificial Selection | |
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Prediction Equation for Individual Selection | |
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Genetic Basis of Complex Traits | |
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Change in Allele Frequency | |
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Change in Mean Phenotype | |
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Correlation between Relatives | |
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Parent-Offspring Correlation | |
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Heritability Estimates from Resemblance between Relatives | |
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Offspring-on-Parent Regression | |
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Quantitative Genetics of Natural Populations | |
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Directional Selection with Mutation-Selection-Drift | |
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Stabilizing Selection with Mutation-Selection-Drift | |
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Antagonistic Pleiotropy | |
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Complex Traits with Discrete Expression | |
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Threshold Traits: Genes as Risk Factors | |
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Heritability of Liability | |
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Applications to Human Disease | |
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Linkage Analysis and Lod Scores | |
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Quantitative Trait Loci (QTLs) | |
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Number of Genes | |
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QTL Mapping | |
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Candidate Genes | |
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Further Readings | |
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Problems | |
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Literature Cited | |
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Index | |