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• Preface(p. xiii)
• Chapter 1. General Background and the Diversity of Genetic Variation(p. 1)
• I. Approaches to Population Genetics(p. 2)
• II. Introduction to Some Genetics Topics(p. 4)
• a. Some Genetics Terms(p. 5)
• b. The Genetic Code(p. 7)
• c. Structure of the Genome and a Typical Eukaryotic Gene(p. 8)
• III. Introduction to Some Quantitative Topics(p. 10)
• a. Models(p. 10)
• b. Means, Variances, and Confidence Intervals(p. 13)
• c. Probability(p. 17)
• d. Matrices(p. 19)
• IV. Genetic Variation(p. 21)
• a. Allozyme Variation(p. 25)
• b. Nucleotide and Amino Acid Sequence Variation(p. 29)
• c. Visible Polymorphisms(p. 34)
• d. Mutations, Lethals, and Fitness Modifiers(p. 36)
• e. Polygenic or Quantitative Traits(p. 41)
• Chapter 2. Measures of Genetic Variation(p. 47)
• I. The Hardy--Weinberg Principle(p. 48)
• II. Different Frequencies Between the Sexes(p. 56)
• a. Autosomal Genes(p. 56)
• b. X-linked Genes or Genes in Haplo-diploid Organisms(p. 59)
• III. Estimates of Allelic Frequency(p. 62)
• IV. Testing Hardy--Weinberg Proportions(p. 72)
• V. Measures of Genetic Variation(p. 75)
• a. Heterozygosity(p. 75)
• b. The Proportion of Polymorphic Loci and Other Measures(p. 79)
• VI. Measures of Nucleotide and Amino Acid Diversity(p. 80)
• VII. Measures of Genetic Distance(p. 83)
• Chapter 3. Selection: An Introduction(p. 89)
• I. Basic Selection Model(p. 93)
• a. Recessive Lethal(p. 96)
• b. Selection Against Recessives(p. 100)
• c. Intermediate Dominance (Additivity) and Gametic or Haploid Selection(p. 103)
• d. Selection Against Dominants(p. 107)
• e. General Dominance(p. 107)
• f. Heterozygote Advantage(p. 111)
• g. Heterozygote Disadvantage(p. 115)
• II. Relaxing Some Genetic Assumptions(p. 118)
• a. X-linked Genes or Genes in Haplo-diploid Organisms(p. 118)
• b. Multiple Alleles(p. 122)
• Chapter 4. Selection: Other Models and Estimation(p. 129)
• I. Fitness Components(p. 130)
• II. Viability Selection(p. 132)
• a. Viability Differences in Different Life Stages(p. 132)
• b. Viability Differences in the Sexes(p. 133)
• III. Sexual Selection(p. 135)
• a. Negative-Assortative Mating(p. 136)
• b. Rare-Male Mating Advantage(p. 139)
• IV. Gametic Selection(p. 141)
• a. Meiotic Drive(p. 141)
• b. Self-incompatibility Alleles(p. 144)
• V. Estimation of Selection(p. 147)
• a. Viability Selection(p. 148)
• b. Complete Selection(p. 152)
• c. Genotypic Frequencies(p. 153)
• VI. Ecological Genetics and Balancing Selection(p. 155)
• a. Spatial Variation(p. 161)
• b. Temporal Variation(p. 165)
• c. Frequency-dependent Selection(p. 170)
• Chapter 5. Inbreeding and Related Topics(p. 179)
• I. Inbreeding(p. 180)
• a. Self-fertilization(p. 185)
• b. Partial Self-fertilization(p. 187)
• c. Estimates of Outcrossing and Self-fertilization(p. 190)
• d. Regular Systems of Inbreeding(p. 194)
• e. Other Levels of Partial Inbreeding(p. 197)
• f. Estimation of Inbreeding from Pedigrees(p. 197)
• g. The Chain-counting Technique(p. 200)
• h. Inbreeding in Natural Animal Populations(p. 206)
• II. Inbreeding and Selection(p. 208)
• a. Inbreeding Depression(p. 208)
• b. Change in Allelic Frequency and Conditions for a Polymorphism(p. 213)
• c. Kin Selection(p. 217)
• III. Asexual or Apomictic Reproduction(p. 218)
• IV. Positive-Assortative Mating(p. 221)
• Chapter 6. Genetic Drift and Effective Population Size(p. 225)
• I. Genetic Drift(p. 229)
• a. The Probability Matrix Approach(p. 234)
• b. The Founder Effect and Bottlenecks(p. 240)
• II. Effective Population Size(p. 244)
• a. Separate Sexes(p. 246)
• b. Variation in Number of Gametes(p. 248)
• c. Inbreeding(p. 250)
• d. Variation in Time(p. 251)
• e. Age Structure(p. 254)
• f. Neighborhood Size(p. 255)
• g. Genes on the Mitochrondrion, Chloroplast, and Y Chromosome(p. 256)
• h. Genetic Techniques for Estimating Effective Population Size(p. 257)
• III. Selection in Finite Populations(p. 258)
• a. Directional Selection(p. 258)
• b. Balancing Selection(p. 261)
• Chapter 7. Gene Flow and Population Structure(p. 265)
• I. Population Structure(p. 266)
• a. The Continent--Island Model(p. 267)
• b. The General Model(p. 269)
• c. Wahlund Effect(p. 272)
• d. Gametic and Zygotic Gene Flow(p. 274)
• II. Estimation of Gene Flow and Population Structure(p. 275)
• a. Hybrid Populations(p. 276)
• b. Direct Observation of Gene Flow(p. 279)
• c. F Coefficients and Other Differentiation Measures(p. 281)
• III. Population Structure and Genetic Drift(p. 287)
• a. The Continent--Island or Island Model(p. 288)
• b. The Stepping-Stone Model(p. 291)
• c. Metapopulation(p. 292)
• IV. Gene Flow and Selection(p. 295)
• a. The Continent--Island Model(p. 295)
• b. Variable Selection and Clines in a Substructured Population(p. 301)
• Chapter 8. Mutation(p. 307)
• I. Allelic Frequency Change Due to Mutation(p. 311)
• a. Forward and Backward Mutation(p. 312)
• b. The Fate of a Single Mutation(p. 314)
• II. Mutation--Selection Balance(p. 316)
• a. Recessive Mutation(p. 316)
• b. Dominant Mutation(p. 320)
• c. Intermediate Dominance and Mutation Load(p. 321)
• III. Mutation in a Finite Population(p. 324)
• a. Neutrality(p. 324)
• b. Selection(p. 328)
• IV. Estimation of Mutation Rates(p. 330)
• a. Dominant or Codominant Mutation(p. 330)
• b. Recessive Mutation(p. 332)
• c. Mutation Accumulation Estimates(p. 334)
• d. Factors Influencing the Mutation Rate(p. 335)
• Chapter 9. Molecular Population Genetics and Evolution(p. 341)
• I. Neutrality and Predictions about Molecular Variation(p. 342)
• a. Balancing Selection(p. 342)
• b. Neutrality Theory(p. 345)
• c. The Molecular Clock(p. 350)
• d. Coalescence and Gene Trees(p. 358)
• II. Evidence of Selection and Tests of Neutrality(p. 363)
• a. Codon Usage(p. 363)
• b. Synonymous and Nonsynonymous Nucleotide Substitutions(p. 365)
• c. The Ewens--Watterson Test(p. 368)
• d. The Hudson--Kreitman--Aguade and McDonald--Kreitman Tests(p. 371)
• e. The Tajima Test(p. 373)
• III. Molecular Phylogenetics(p. 374)
• a. The Unweighted-Pair-Group Method (UPGMA)(p. 376)
• b. The Neighbor-Joining Method(p. 378)
• c. Maximum Parsimony(p. 381)
• IV. Paternity Analysis and Individual Identity(p. 384)
• a. Paternity Analysis(p. 385)
• b. Individual Identity(p. 390)
• Chapter 10. Multiple-Gene Models(p. 395)
• I. An Introduction to Gametic Disequilibrium(p. 396)
• II. Gametic Disequilibrium and Inbreeding, Genetic Drift, Gene Flow, and Mutation(p. 405)
• a. Inbreeding or Reproductive System(p. 406)
• b. Genetic Drift(p. 408)
• c. Gene Flow(p. 411)
• d. Mutation(p. 412)
• III. Multilocus Selection(p. 415)
• a. Fitness Epistasis(p. 415)
• b. Directional Selection at Two Loci(p. 416)
• c. General Two-Locus Polymorphisms(p. 418)
• d. Some Implications(p. 425)
• IV. Genetic Background and Genetic Hitchhiking(p. 426)
• V. Recombination and Genetic Variation(p. 432)
• VI. Estimation of Gametic Disequilibrium(p. 437)
• a. Direct Identification of Gametes(p. 437)
• b. Two Codominant Loci(p. 441)
• c. Extension to Multiple Alleles(p. 443)
• Chapter 11. Quantitative Traits and Evolution(p. 445)
• I. The Nature of Quantitative Traits(p. 446)
• a. General Characteristics(p. 446)
• b. Genes Affecting Quantitative Traits(p. 450)
• II. Quantitative Genetics Model(p. 453)
• III. Estimation of Genetic Variance and Heritability(p. 463)
• a. Reduction or Elimination of One Component of Variance(p. 463)
• b. Resemblance Between Relatives(p. 465)
• c. Realized Heritability(p. 472)
• d. Factors Affecting Genetic Variance(p. 475)
• IV. Selection of Quantitative Traits(p. 480)
• a. Selection in Natural Populations(p. 480)
• b. Response to Selection(p. 484)
• c. Estimation of Selection in Natural Populations(p. 490)
• V. Identifying QTLS(p. 493)
• Bibliography(p. 501)
• Answers to Numerical Problems(p. 541)
• Index(p. 545)