Description
Book SynopsisThis second edition presents how genetic information can be used to conserve threatened species, as well as manage ecologically or commercially important species.
Trade Review“Summing Up: Recommended. Lower-division undergraduates and above.” (Choice, 1 October 2013)
Table of ContentsGuest 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
