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Contents

Guest Box authors, ix Preface to the second edition, xi Preface to the first edition, xiii List of symbols, xv PART I: INTRODUCTION, 1 1 Introduction, 3 1.1 Genetics and civilization, 4 1.2 What should we conserve?, 5 1.3 How should we conserve biodiversity?, 9 1.4 Applications of genetics to conservation, 10 1.5 The future, 12 Guest Box 1: L. Scott Mills and Michael E. Soulé, The role of genetics in conservation, 13 2 Phenotypic variation in natural populations, 14 2.1 Color pattern, 17 2.2 Morphology, 20 2.3 Behavior, 23 2.4 Phenology, 25 2.5 Differences among populations, 27 2.6 Nongenetic inheritance, 31 Guest Box 2: Chris J. Foote, Looks can be deceiving: countergradient variation in secondary sexual color in sympatric morphs of sockeye salmon, 32 3 Genetic variation in natural populations: chromosomes and proteins, 34 3.1 Chromosomes, 35 3.2 Protein electrophoresis, 45 3.3 Genetic variation within natural populations, 48 3.4 Genetic divergence among populations, 50 Guest Box 3: E. M. Tuttle, Chromosomal polymorphism in the white-throated sparrow, 52 4 Genetic variation in natural populations: DNA, 54 4.1 Mitochondrial and chloroplast organelle DNA, 56 4.2 Single-copy nuclear loci, 60 4.3 Multiple locus techniques, 68 4.4 Genomic tools and markers, 69 4.5 Transcriptomics, 72 4.6 Other 'omics' and the future, 73 Guest Box 4: Louis Bernatchez, Rapid evolutionary changes of gene expression in domesticated Atlantic salmon and its consequences for the conservation of wild populations, 74 PART II: MECHANISMS OF EVOLUTIONARY CHANGE, 77 5 Random mating populations: Hardy- Weinberg principle, 79 5.1 Hardy-Weinberg principle, 80 5.2 Hardy-Weinberg proportions, 82 5.3 Testing for Hardy-Weinberg proportions, 83 5.4 Estimation of allele frequencies, 88 5.5 Sex-linked loci, 90 5.6 Estimation of genetic variation, 92 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), 93 6 Small populations and genetic drift, 96 6.1 Genetic drift, 97 6.2 Changes in allele frequency, 100 6.3 Loss of genetic variation: the inbreeding effect of small populations, 101 6.4 Loss of allelic diversity, 102 6.5 Founder effect, 106 6.6 Genotypic proportions in small populations, 110 6.7 Fitness effects of genetic drift, 112 Guest Box 6: Menna E. Jones, Reduced genetic variation and the emergence of an extinction-threatening disease in the Tasmanian devil, 115 7 Effective population size, 117 7.1 Concept of effective population size, 118 7.2 Unequal sex ratio, 119 7.3 Nonrandom number of progeny, 121 7.4 Fluctuating population size, 125 7.5 Overlapping generations, 125 7.6 Variance effective population size, 126 7.7 Cytoplasmic genes, 126 7.8 Gene genealogies, the coalescent, and lineage sorting, 129 7.9 Limitations of effective population size, 130 7.10 Effective population size in natural populations, 132 Guest Box 7: Craig R. Miller and Lisette P. Waits, Estimation of effective population size in Yellowstone grizzly bears, 134 8 Natural selection, 136 8.1 Fitness, 138 8.2 Single locus with two alleles, 138 8.3 Multiple alleles, 144 8.4 Frequency-dependent selection, 147 8.5 Natural selection in small populations, 149 8.6 Natural selection and conservation, 151 Guest Box 8: Paul A. Hohenlohe and William A. Cresko, Natural selection across the genome of the threespine stickleback fish, 154 9 Population subdivision, 156 9.1 F-Statistics, 158 9.2 Spatial patterns of relatedness within local populations, 161 9.3 Genetic divergence among populations and gene flow, 163 9.4 Gene flow and genetic drift, 165 9.5 Continuously distributed populations, 168 9.6 Cytoplasmic genes and sex-linked markers, 169 9.7 Gene flow and natural selection, 172 9.8 Limitations of FST and other measures of subdivision, 174 9.9 Estimation of gene flow, 179 9.10 Population subdivision and conservation, 184 Guest Box 9: M.K. Schwartz and J.M. Tucker, Genetic population structure and conservation of fisher in western North America, 185 10 Multiple loci, 187 10.1 Gametic disequilibrium, 188 10.2 Small population size, 192 10.3 Natural selection, 192 10.4 Population subdivision, 196 10.5 Hybridization, 196 10.6 Estimation of gametic disequilibrium, 199 10.7 Multiple loci and conservation, 200 Guest Box 10: Robin S. Waples, Estimation of effective population size using gametic disequilibrium, 203 11 Quantitative genetics, 205 11.1 Heritability, 206 11.2 Selection on quantitative traits, 212 11.3 Finding genes underlying quantitative traits, 217 11.4 Loss of quantitative genetic variation, 220 11.5 Divergence among populations, 223 11.6 Quantitative genetics and conservation, 225 Guest Box 11: David W. Coltman, Response to trophy hunting in bighorn sheep, 229 12 Mutation, 230 12.1 Process of mutation, 231 12.2 Selectively neutral mutations, 235 12.3 Harmful mutations, 239 12.4 Advantageous mutations, 239 12.5 Recovery from a bottleneck, 241 Guest Box 12: Michael W. Nachman, Color evolution via different mutations in pocket mice, 242 PART III: GENETICS AND CONSERVATION, 245 13 Inbreeding depression, 247 13.1 Pedigree analysis, 248 13.2 Gene drop analysis, 252 13.3 Estimation of F with molecular markers, 253 13.4 Causes of inbreeding depression, 256 13.5 Measurement of inbreeding depression, 258 13.6 Genetic load and purging, 264 13.7 Inbreeding and conservation, 267 Guest Box 13: Lukas F. Keller, Inbreeding depression in song sparrows, 268 14 Demography and extinction, 270 14.1 Estimation of census population Size, 272 14.2 Inbreeding depression and extinction, 274 14.3 Population viability analysis, 277 14.4 Loss of phenotypic variation, 286 14.5 Loss of evolutionary potential, 288 14.6 Mitochondrial DNA, 289 14.7 Mutational meltdown, 289 14.8 Long-term persistence, 291 14.9 The 50/500 rule, 292 Guest Box 14: A. G. Young, M. Pickup, and B. G. Murray, Management implications of loss of genetic diversity at the selfincompatibility locus for the button wrinklewort, 293 15 Metapopulations and fragmentation, 296 15.1 The metapopulation concept, 297 15.2 Genetic variation in metapopulations, 298 15.3 Effective population size of metapopulations, 301 15.4 Population divergence and connectivity, 303 15.5 Genetic rescue, 304 15.6 Landscape genetics, 306 15.7 Long-term population viability, 311 Guest Box 15: Robert C. Vrijenhoek, Fitness loss and genetic rescue in stream-dwelling topminnows, 313 16 Units of conservation, 316 16.1 What should we protect?, 318 16.2 Systematics and taxonomy, 320 16.3 Phylogeny reconstruction, 322 16.4 Genetic relationships within species, 327 16.5 Units of conservation, 336 16.6 Integrating genetic, phenotypic, and environmental information, 346 16.7 Communities, 348 Guest Box 16: David J. Coates, Identifying units of conservation in a rich and fragmented flora, 350 17 Hybridization, 352 17.1 Natural hybridization, 353 17.2 Anthropogenic hybridization, 358 17.3 Fitness consequences of hybridization, 360 17.4 Detecting and describing hybridization, 364 17.5 Hybridization and conservation, 370 Guest Box 17: Loren H. Rieseberg, Hybridization and the conservation of plants, 375 18 Exploited populations, 377 18.1 Loss of genetic variation, 378 18.2 Unnatural selection, 381 18.3 Spatial structure, 385 18.4 Effects of releases, 388 18.5 Management and recovery of exploited populations, 391 Guest Box 18: Guðrún Marteinsdóttir, Long-term genetic changes in the Icelandic stock of Atlantic cod in response to harvesting, 393 19 Conservation breeding and restoration, 395 19.1 The role of conservation breeding, 398 19.2 Reproductive technologies and genome banking, 400 19.3 Founding populations for conservation breeding programs, 403 19.4 Genetic drift in captive populations, 405 19.5 Natural selection and adaptation to captivity, 407 19.6 Genetic management of conservation breeding programs, 410 19.7 Supportive breeding, 412 19.8 Reintroductions and translocations, 414 Guest Box 19: Robert C. Lacy, Understanding inbreeding depression: 25 years of experiments with Peromyscus mice, 419 20 Invasive species, 421 20.1 Why are invasive species so successful?, 422 20.2 Genetic analysis of introduced species, 425 20.3 Establishment and spread of invasive species, 429 20.4 Hybridization as a stimulus for invasiveness, 430 20.5 Eradication, management, and control, 431 20.6 Emerging diseases and parasites, 433 Guest Box 20: Richard Shine, Rapid evolution of introduced cane toads and native snakes, 438 21 Climate change, 440 21.1 Predictions and uncertainty about future climates, 441 21.2 Phenotypic plasticity, 442 21.3 Maternal effects and epigenetics, 445 21.4 Adaptation, 446 21.5 Species range shifts, 448 21.6 Extirpation and extinction, 449 21.7 Management in the face of climate change, 451 Guest Box 21: S. J. Franks, Rapid evolution of flowering time by an annual plant in response to climate fluctuation, 453 22 Genetic identification and monitoring, 455 22.1 Species identification, 457 22.2 Metagenomics and species composition, 464 22.3 Individual identification, 465 22.4 Parentage and relatedness, 469 22.5 Population assignment and composition analysis, 471 22.6 Genetic monitoring, 477 Guest Box 22: C. Scott Baker, Genetic detection of illegal trade of whale meat results in closure of restaurants, 481 Appendix: Probability and statistics, 484 A1 Paradigms, 485 A2 Probability, 487 A3 Statistical measures and distributions, 489 A4 Frequentist hypothesis testing, statistical errors, and power, 496 A5 Maximum likelihood, 499 A6 Bayesian approaches and MCMC (Markov Chain Monte Carlo), 500 A7 Approximate Bayesian Computation (ABC), 504 A8 Parameter estimation, accuracy, and precision, 504 A9 Performance testing, 506 A10 The coalescent and genealogical Information, 506 Guest Box A: James F. Crow, Is mathematics necessary?, 511 Glossary, 513 References, 531 Index, 587 Color plates section between page 302 and page 303

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