Conservation and the Genetics of Populations.

Intro -- Title page -- Copyright page -- Contents -- Guest Box authors -- Preface -- Preface to the first edition -- List of symbols -- PART I: Introduction -- CHAPTER 1: Introduction -- 1.1 Genetics and Civilization -- 1.2 What Should We Conserve? -- 1.2.1 Phylogenetic diversity -- 1.2.2 Populations, species, or ecosystems? -- 1.3 How Should We Conserve Biodiversity? -- 1.4 Applications of Genetics to Conservation -- 1.5 The Future -- Guest Box 1: L. Scott Mills and Michael E. Soulé, The role of genetics in conservation -- CHAPTER 2: Phenotypic variation in natural populations -- 2.1 Color Pattern -- 2.2 Morphology -- 2.3 Behavior -- 2.4 Phenology -- 2.5 Differences Among Populations -- 2.5.1 Countergradient variation -- 2.6 Nongenetic Inheritance -- Guest Box 2: Chris J. Foote, Looks can be deceiving: countergradient variation in secondary sexual color in sympatric morphs of sockeye salmon -- CHAPTER 3: Genetic variation in natural populations: chromosomes and proteins -- 3.1 Chromosomes -- 3.1.1 Karyotypes -- 3.1.2 Sex chromosomes -- 3.1.3 Polyploidy -- 3.1.4 Numbers of chromosomes -- 3.1.5 Supernumerary chromosomes -- 3.1.6 Chromosomal size -- 3.1.7 Inversions -- 3.1.8 Translocations -- 3.1.9 Chromosomal variation and conservation -- 3.2 Protein Electrophoresis -- 3.2.1 Strengths and limitations of protein electrophoresis -- 3.3 Genetic Variation within Natural Populations -- 3.3.1 Data from natural populations -- 3.4 Genetic Divergence Among Populations -- Guest Box 3: E. M. Tuttle, Chromosomal polymorphism in the white-throated sparrow -- CHAPTER 4: Genetic variation in natural populations: DNA -- 4.1 Mitochondrial and Chloroplast Organelle DNA -- 4.1.1 Restriction endonucleases and RFLPs -- 4.1.2 Polymerase chain reaction -- 4.2 Single-Copy Nuclear Loci -- 4.2.1 Microsatellites -- 4.2.2 PCR of protein-coding loci.

4.2.3 Single nucleotide polymorphisms -- 4.2.4 Sex-linked markers -- 4.3 Multiple Locus Techniques -- 4.3.1 Minisatellites -- 4.3.2 AFLPs and ISSRs -- 4.4 Genomic Tools and Markers -- 4.4.1 High-throughput sequencing -- 4.4.2 Inferences from sequence data -- 4.4.3 EST sequencing applications -- 4.4.4 SNP discovery and genotyping by sequencing -- 4.5 Transcriptomics -- 4.6 Other 'Omics' and The Future -- 4.6.1 Metagenomics -- Guest Box 4: Louis Bernatchez Rapid evolutionary changes of gene expression in domesticated Atlantic salmon and its consequences for the conservation of wild populations -- PART II: Mechanisms of Evolutionary Change -- CHAPTER 5: Random mating populations: Hardy-Weinberg principle -- 5.1 Hardy-Weinberg Principle -- 5.2 Hardy-Weinberg Proportions -- 5.3 Testing for Hardy-Weinberg Proportions -- 5.3.1 Small sample sizes or many alleles -- 5.3.2 Multiple simultaneous tests -- 5.4 Estimation of Allele Frequencies -- 5.4.1 Recessive alleles -- 5.4.2 Null alleles -- 5.5 Sex-Linked Loci -- 5.5.1 Pseudoautosomal inheritance -- 5.6 Estimation of Genetic Variation -- 5.6.1 Heterozygosity -- 5.6.2 Allelic richness -- 5.6.3 Proportion of polymorphic loci -- Guest Box 5: Paul Sunnucks and Birgita D. Hansen, Null alleles and Bonferroni 'abuse': treasure your exceptions (and so get it right for Leadbeater's possum) -- CHAPTER 6: Small populations and genetic drift -- 6.1 Genetic Drift -- 6.2 Changes in Allele Frequency -- 6.3 Loss of Genetic Variation: The Inbreeding Effect of Small Populations -- 6.4 Loss of Allelic Diversity -- 6.5 Founder Effect -- 6.6 Genotypic Proportions in Small Populations -- 6.7 Fitness Effects of Genetic Drift -- 6.7.1 Changes in allele frequency -- 6.7.2 Loss of allelic diversity -- 6.7.3 Inbreeding depression.

Guest Box 6: Menna E. Jones, Reduced genetic variation and the emergence of an extinction-threatening disease in the Tasmanian devil -- CHAPTER 7: Effective population size -- 7.1 Concept of Effective Population Size -- 7.2 Unequal Sex Ratio -- 7.3 Nonrandom Number of Progeny -- 7.4 Fluctuating Population Size -- 7.5 Overlapping Generations -- 7.6 Variance Effective Population Size -- 7.7 Cytoplasmic Genes -- 7.8 Gene Genealogies, the Coalescent, and Lineage Sorting -- 7.9 Limitations of Effective Population Size -- 7.9.1 Allelic diversity and Ne -- 7.9.2 Generation interval -- 7.10 Effective Population Size in Natural Populations -- Guest Box 7: Craig R. Miller and Lisette P. Waits, Estimation of effective population size in Yellowstone grizzly bears -- CHAPTER 8: Natural selection -- 8.1 Fitness -- 8.2 Single Locus with Two Alleles -- 8.2.1 Directional selection -- 8.2.2 Heterozygous advantage (overdominance) -- 8.2.3 Heterozygous disadvantage (underdominance) -- 8.2.4 Selection and Hardy-Weinberg proportions -- 8.3 Multiple Alleles -- 8.3.1 Heterozygous advantage and multiple alleles -- 8.4 Frequency-Dependent Selection -- 8.4.1 Two alleles -- 8.4.2 Frequency-dependent selection in nature -- 8.4.3 Self-incompatibility locus in plants -- 8.4.4 Complementary sex determination (csd) locus in invertebrates -- 8.5 Natural Selection in Small Populations -- 8.5.1 Directional selection -- 8.5.2 Underdominance and drift -- 8.5.3 Heterozygous advantage and drift -- 8.6 Natural Selection and Conservation -- Guest Box 8: Paul A. Hohenlohe and William A. Cresko, Natural selection across the genome of the threespine stickleback fish -- CHAPTER 9: Population subdivision -- 9.1 F-Statistics -- 9.1.1 The Wahlund effect -- 9.1.2 When is FIS not zero? -- 9.2 Spatial Patterns of Relatedness Within Local Populations.

9.2.1 Effects of dispersal distance and population density on patterns of relatedness -- 9.2.2 Effects of spatial distribution of relatives on inbreeding probability -- 9.3 Genetic Divergence Among Populations and Gene Flow -- 9.3.1 Complete isolation -- 9.3.2 Gene flow -- 9.4 Gene Flow and Genetic Drift -- 9.4.1 Island model -- 9.4.2 Stepping-stone model -- 9.5 Continuously Distributed Populations -- 9.6 Cytoplasmic Genes and Sex-Linked Markers -- 9.6.1 Cytoplasmic genes -- 9.6.2 Sex-linked loci -- 9.7 Gene Flow and Natural Selection -- 9.7.1 Heterozygous advantage -- 9.7.2 Divergent directional selection -- 9.7.3 Comparisons among loci -- 9.8 Limitations of FST and Other Measures of Subdivision -- 9.8.1 Genealogical information -- 9.8.2 High heterozygosity within subpopulations -- 9.8.3 Other measures of divergence -- 9.8.4 Hierarchical structure -- 9.9 Estimation of Gene Flow -- 9.9.1 FST and indirect estimates of mN -- 9.9.2 Private alleles and mN -- 9.9.3 Maximum likelihood and the coalescent -- 9.9.4 Assignment tests and direct estimates of mN -- 9.10 Population Subdivision and Conservation -- Guest Box 9: M.K. Schwartz and J.M. Tucker, Genetic population structure and conservation of f isher in Western North America -- CHAPTER 10: Multiple loci -- 10.1 Gametic Disequilibrium -- 10.1.1 Other measures of gametic disequilibrium -- 10.1.2 Associations between cytoplasmic and nuclear genes -- 10.2 Small Population Size -- 10.3 Natural Selection -- 10.3.1 Genetic hitchhiking -- 10.3.2 Associative overdominance -- 10.3.3 Genetic draft -- 10.4 Population Subdivision -- 10.5 Hybridization -- 10.6 Estimation of Gametic Disequilibrium -- 10.6.1 Two loci with two alleles each -- 10.6.2 More than two alleles per locus -- 10.7 Multiple Loci and Conservation.

Guest Box 10: Robin S. Waples, Estimation of effective population size using gametic disequilibrium -- CHAPTER 11: Quantitative genetics -- 11.1 Heritability -- 11.1.1 Broad-sense heritability -- 11.1.2 Narrow-sense heritability -- 11.1.3 Estimation of heritability -- 11.1.4 Genotype-by-environment interactions -- 11.2 Selection on Quantitative Traits -- 11.2.1 Heritabilities and allele frequencies -- 11.2.2 Genetic correlations -- 11.3 Finding Genes Underlying Quantitative Traits -- 11.3.1 QTL mapping -- 11.3.2 Candidate gene approaches -- 11.3.3 Genome-wide association mapping -- 11.4 Loss of Quantitative Genetic Variation -- 11.4.1 Effects of genetic drift and bottlenecks -- 11.4.2 Effects of selection -- 11.5 Divergence Among Populations -- 11.6 Quantitative Genetics and Conservation -- 11.6.1 Response to selection in the wild -- 11.6.2 Can molecular genetic variation within populations estimate quantitative variation? -- 11.6.3 Does population divergence for molecular markers estimate divergence for quantitative traits? -- Guest Box 11: David W. Coltman, Response to trophy hunting in bighorn sheep -- CHAPTER 12: Mutation -- 12.1 Process of Mutation -- 12.1.1 Chromosomal mutations -- 12.1.2 Molecular mutations -- 12.1.3 Quantitative characters -- 12.1.4 Transposable elements, mutation rates, and stress -- 12.2 Selectively Neutral Mutations -- 12.2.1 Genetic variation within populations -- 12.2.2 Population subdivision -- 12.3 Harmful Mutations -- 12.4 Advantageous Mutations -- 12.5 Recovery from a Bottleneck -- Guest Box 12: Michael W. Nachman, Color evolution via different mutations in pocket mice -- PART III: Genetics and Conservation -- CHAPTER 13: Inbreeding depression -- 13.1 Pedigree Analysis -- 13.1.1 Estimation of the pedigree inbreeding coefficient -- 13.2 Gene Drop Analysis -- 13.3 Estimation of F with Molecular Markers.

13.4 Causes of Inbreeding Depression.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.