Conservation and the genetics of populations

Authors of Guest Boxes. Preface. List of Symbols. PART I: INTRODUCTION. 1 Introduction. 1.1 Genetics and conservation. 1.2 What should we conserve? 1.3 How should we conserve biodiversity? 1.4 Applications of genetics to conservation. Guest Box 1 by L. S. Mills and M. E. Soule: The role of genetics in conservation. 2 Phenotypic Variation in Natural Populations. 2.1 Color pattern. 2.2 Morphology. 2.3 Behavior. 2.4 Differences among populations. Guest Box 2 by C. J. Foote: Looks can be deceiving: countergradient variation in secondary sexual color in sympatric morphs of sockeye salmon. 3 Genetic Variation in Natural Populations: Chromosomes and Proteins. 3.1 Chromosomes. 3.2 Protein electrophoresis. 3.3 Genetic variation within populations. 3.4 Genetic divergence among populations. 3.5 Strengths and limitations of protein electrophoresis. Guest Box 3 by A. Young and B. G. Murray: Management implications of polploidy in a cytologically complex self-incompatible herb. 4 Genetic Variation in Natural Populations: DNA. 4.1 Mitochondrial and chloroplast DNA. 4.2 Single copy nuclear loci. 4.3 Multilocus techniques. 4.4 Sex-linked markers. 4.5 DNA sequences. 4.6 Additional techniques and the future. 4.7 Genetic variation in natural populations. Guest Box 4 by N. N. FitzSimmons: Multiple markers uncover marine turtle behavior. PART II: MECHANISMS OF EVOLUTIONARY CHANGE. 5 Random Mating Populations: Hardy-Weinberg Principle. 5.1 The Hardy-Weinberg principle. 5.2 Hardy-Weinberg proportions. 5.3 Testing for Hardy-Weinberg proportions. 5.4 Estimation of allele frequencies. 5.5 Sex-linked loci. 5.6 Estimation of genetic variation. Guest Box 5 by V. Castric and L. Bernatchez: Testing alternative explanations for deficiencies of heterozygotes in populations of brook trout in small lakes. 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. Guest Box 6 by P. L. Leberg and D. L. Rogowski: The inbreeding effect of small population size reduces population growth rate in mosquitofish. 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 and lineage sorting. 7.9 Limitations of effective population size. 7.10 Effective population size in natural populations. Guest Box 7 by C. R. Miller and L. P. Waits: Estimation of effective population size in Yellowstone grizzly bears. 8 Natural Selection. 8.1 Fitness. 8.2 Single locus with two alleles. 8.3 Multiple alleles. 8.4 Frequency-dependent selection. 8.5 Natural selection in small populations. 8.6 Natural selection and conservation. Guest Box 8 by C. A. Stockwell and M. L. Collyer: Rapid adaptation and conservation. 9 Population Subdivision. 9.1 F-statistics. 9.2 Complete isolation. 9.3 Gene flow. 9.4 Gene flow and genetic drift. 9.5 Cytoplasmic genes and sex-linked markers. 9.6 Gene flow and natural selection. 9.7 Limitations of FST and other measures of subdivision. 9.8 Estimation of gene flow. 9.9 Population subdivision and conservation. Guest Box 9 by C. S. Baker and F. B. Pichler: Hector's dolphin population structure and conservation. 10 Multiple Loci. 10.1 Gametic disequilibrium. 10.2 Small population size. 10.3 Natural selection. 10.4 Population subdivision. 10.5 Hybridization. 10.6 Estimation of gametic disequilibrium. Guest Box 10 by S. H. Forbes: Dating hybrid populations using gametic disequilibrium. 11 Quantitative Genetics. 11.1 Heritability. 11.2 Selection on quantitative traits. 11.3 Quantitative trait loci (QTLs). 11.4 Genetic drift and bottlenecks. 11.5 Divergence among populations (QST). 11.6 Quantitative genetics and conservation. Guest Box 11 by D. W. Coltman: Response to trophy hunting in bighorn sheep. 12 Mutation. 12.1 Process of mutation. 12.2 Selectively neutral mutations. 12.3 Harmful mutations. 12.4 Advantageous mutations. 12.5. Recovery from a bottleneck. Guest Box 12 by M. W. Nachman: Color evolution via different mutations in pocket mice. PART III: GENETICS AND CONSERVATION. 13 Inbreeding Depression. 13.1 Pedigree analysis. 13.2 Gene drop analysis. 13.3 Estimation of F and relatedness with molecular markers. 13.4 Causes of inbreeding depression. 13.5 Measurement of inbreeding depression. 13.6 Genetic load and purging. Guest Box 13 by R. C. Lacy: Understanding inbreeding depression: 20 years of experiments with Peromyscus mice. 14 Demography and Extinction. 14.1 Estimation of population size. 14.2 Inbreeding depression and extinction. 14.3 Population viability analysis. 14.4 Loss of phenotypic variation. 14.5 Loss of evolutionary potential. 14.6 Mitochondrial DNA. 14.7 Mutational meltdown. 14.8 Long-term persistence. 14.9 The 50/500 rule. Guest Box 14 by A. C. Taylor: Noninvasive population size estimation in wombats. 15 Metapopulations and Fragmentation. 15.1 The metapopulation concept. 15.2 Genetic variation in metapopulations. 15.3 Effective population size. 15.4 Population divergence and fragmentation. 15.5 Genetic rescue. 15.6 Long-term population viability. Guest Box 15 by R. C. Vrijenhoek: Fitness loss and genetic rescue in stream-dwelling topminnows. 16 Units of Conservation. 16.1 What should we try to protect? 16.2 Systematics and taxonomy. 16.3 Phylogeny reconstruction. 16.4 Description of genetic relationships within species. 16.5 Units of conservation. 16.6 Integrating genetic, phenotypic, and environmental information. Guest Box 16 by R. S. Waples: Identifying conservation units in Pacific salmon. 17 Hybridization. 17.1 Natural hybridization. 17.2 Anthropogenic hybridization. 17.3 Fitness consequences of hybridization. 17.4 Detecting and describing hybridization. 17.5 Hybridization and conservation. Guest Box 17 by L. H. Rieseberg: Hybridization and the conservation of plants. 18 Conservation Breeding and Restoration. 18.1 The role of conservation breeding. 18.2 Reproductive technologies and genome banking. 18.3 Founding populations for conservation breeding programs. 18.4 Genetic drift in captive populations. 18.5 Natural selection and adaptation to captivity. 18.6 Genetic management of conservation breeding programs. 18.7 Supportive breeding. 18.8 Reintroductions and translocations. Guest Box 18 by J. V. Briskie: Effects of population bottlenecks on introduced species of birds. 19 Invasive Species. 19.1 Why are invasive species so successful? 19.2 Genetic analysis of introduced species. 19.3 Establishment and spread of invasive species. 19.4 Hybridization as a stimulus for invasiveness. 19.5 Eradication, management, and control. Guest Box 19 by J. L. Maron: Rapid adaptation of invasive populations of St John's Wort. 20 Forensic and Management Applications of Genetic Identification. 20.1 Species identification. 20.2 Individual identification and probability of identity. 20.3 Parentage testing. 20.4 Sex identification. 20.5 Population assignment. 20.6 Population composition analysis. Guest Box 20 by L. P. Waits: Microsatellite DNA genotyping identifies problem bear and cubs. Glossary. Appendix: Probability and Statistics. Guest Box A by J. F. Crow: Is mathematics necessary? References. Index