Conservation and the Genetics of Populations

Contents
......Page 6
Authors of Guest Boxes......Page 12
Preface......Page 14
List of Symbols......Page 17
Part I Introduction......Page 22
1 Introduction......Page 24
1.1 Genetics and conservation......Page 25
1.2 What should we conserve?......Page 26
1.3 How should we conserve biodiversity?......Page 31
1.4 Applications of genetics to conservation......Page 32
Guest Box 1 The role of genetics in conservation......Page 34
2 Phenotypic Variation in Natural Populations......Page 36
2.1 Color pattern......Page 39
2.2 Morphology......Page 41
2.3 Behavior......Page 44
2.4 Differences among populations......Page 47
Guest Box 2 Looks can be deceiving: countergradient variation in secondary sexual color in sympatric morphs of sockeye salmon......Page 50
3 Genetic Variation in Natural Populations: Chromosomes and Proteins......Page 54
3.1 Chromosomes......Page 56
3.2 Protein electrophoresis......Page 68
3.3 Genetic variation within natural populations......Page 72
3.4 Genetic divergence among populations......Page 73
3.5 Strengths and limitations of protein electrophoresis......Page 75
Guest Box 3 Management implications of polyploidy in a cytologically complex self-incompatible herb......Page 76
4 Genetic Variation in Natural Populations: DNA......Page 84
4.1 Mitochondrial and chloroplast DNA......Page 85
4.2 Single copy nuclear loci......Page 90
4.3 Multilocus techniques......Page 95
4.4 Sex-linked markers......Page 98
4.6 Additional techniques and the future......Page 99
4.7 Genetic variation in natural populations......Page 102
Guest Box 4 Multiple markers uncover marine turtle behavior......Page 103
Part II Mechanisms of Evolutionary Change......Page 112
5 Random Mating Populations: Hardy–Weinberg Principle......Page 114
5.1 The Hardy–Weinberg principle......Page 115
5.2 Hardy–Weinberg proportions......Page 118
5.3 Testing for Hardy–Weinberg proportions......Page 120
5.4 Estimation of allele frequencies......Page 126
5.5 Sex-linked loci......Page 129
5.6 Estimation of genetic variation......Page 131
Guest Box 5 Testing alternative explanations for deficiencies of heterozygotes in populations of brook trout in small lakes......Page 133
6 Small Populations and Genetic Drift......Page 138
6.1 Genetic drift......Page 139
6.2 Changes in allele frequency......Page 143
6.3 Loss of genetic variation: the inbreeding effect of small populations......Page 144
6.4 Loss of allelic diversity......Page 147
6.5 Founder effect......Page 150
6.6 Genotypic proportions in small populations......Page 157
6.7 Fitness effects of genetic drift......Page 159
Guest Box 6 The inbreeding effect of small population size reduces population growth rate in mosquitofish......Page 162
7 Effective Population Size......Page 168
7.1 Concept of effective population size......Page 169
7.2 Unequal sex ratio......Page 172
7.3 Nonrandom number of progeny......Page 174
7.4 Fluctuating population size......Page 178
7.5 Overlapping generations......Page 179
7.7 Cytoplasmic genes......Page 180
7.8 Gene genealogies and lineage sorting......Page 183
7.9 Limitations of effective population size......Page 184
7.10 Effective population size in natural populations......Page 187
Guest Box 7 Estimation of effective population size in Yellowstone grizzly bears......Page 188
8 Natural Selection......Page 192
8.1 Fitness......Page 194
8.2 Single locus with two alleles......Page 195
8.3 Multiple alleles......Page 200
8.4 Frequency-dependent selection......Page 205
8.5 Natural selection in small populations......Page 207
8.6 Natural selection and conservation......Page 209
Guest Box 8 Rapid adaptation and conservation......Page 213
9 Population Subdivision......Page 218
9.1 F-statistics......Page 220
9.2 Complete isolation......Page 225
9.3 Gene flow......Page 226
9.4 Gene flow and genetic drift......Page 227
9.5 Cytoplasmic genes and sex-linked markers......Page 231
9.6 Gene flow and natural selection......Page 235
9.7 Limitations of F(ST) and other measures of subdivision......Page 239
9.8 Estimation of gene flow......Page 241
9.9 Population subdivision and conservation......Page 247
Guest Box 9 Hector’s dolphin population structure and conservation......Page 248
10 Multiple Loci......Page 254
10.1 Gametic disequilibrium......Page 255
10.2 Small population size......Page 260
10.3 Natural selection......Page 261
10.4 Population subdivision......Page 266
10.5 Hybridization......Page 267
10.6 Estimation of gametic disequilibrium......Page 271
Guest Box 10 Dating hybrid populations using gametic disequilibrium......Page 273
11 Quantitative Genetics......Page 278
11.1 Heritability......Page 279
11.2 Selection on quantitative traits......Page 285
11.3 Quantitative trait loci (QTLs)......Page 290
11.4 Genetic drift and bottlenecks......Page 295
11.5 Divergence among populations (Q(ST))......Page 297
11.6 Quantitative genetics and conservation......Page 299
Guest Box 11 Response to trophy hunting in bighorn sheep......Page 303
12 Mutation......Page 306
12.1 Process of mutation......Page 307
12.2 Selectively neutral mutations......Page 312
12.3 Harmful mutations......Page 317
12.5 Recovery from a bottleneck......Page 318
Guest Box 12 Color evolution via different mutations in pocket mice......Page 320
Part III Genetics and Conservation......Page 324
13 Inbreeding Depression......Page 326
13.1 Pedigree analysis......Page 328
13.2 Gene drop analysis......Page 331
13.3 Estimation of F and relatedness with molecular markers......Page 334
13.4 Causes of inbreeding depression......Page 336
13.5 Measurement of inbreeding depression......Page 338
13.6 Genetic load and purging......Page 344
Guest Box 13 Understanding inbreeding depression: 20 years of experiments with Peromyscus mice......Page 348
14 Demography and Extinction......Page 355
14.1 Estimation of census population size......Page 357
14.2 Inbreeding depression and extinction......Page 359
14.3 Population viability analysis......Page 363
14.4 Loss of phenotypic variation......Page 371
14.6 Mitochondrial DNA......Page 376
14.8 Long-term persistence......Page 378
14.9 The 50/500 rule......Page 380
Guest Box 14 Noninvasive population size estimation in wombats......Page 381
15 Metapopulations and Fragmentation......Page 384
15.1 The metapopulation concept......Page 385
15.2 Genetic variation in metapopulations......Page 386
15.3 Effective population size......Page 390
15.4 Population divergence and fragmentation......Page 392
15.5 Genetic rescue......Page 393
15.6 Long-term population viability......Page 395
Guest Box 15 Fitness loss and genetic rescue in stream-dwelling topminnows......Page 398
16 Units of Conservation......Page 401
16.1 What should we try to protect?......Page 403
16.2 Systematics and taxonomy......Page 406
16.3 Phylogeny reconstruction......Page 408
16.4 Description of genetic relationships within species......Page 413
16.5 Units of conservation......Page 425
16.6 Integrating genetic, phenotypic, and environmental information......Page 436
Guest Box 16 Identifying conservation units in Pacific salmon......Page 438
17 Hybridization......Page 442
17.1 Natural hybridization......Page 444
17.2 Anthropogenic hybridization......Page 449
17.3 Fitness consequences of hybridization......Page 450
17.4 Detecting and describing hybridization......Page 455
17.5 Hybridization and conservation......Page 464
Guest Box 17 Hybridization and the conservation of plants......Page 467
18 Conservation Breeding and Restoration......Page 470
18.1 The role of conservation breeding......Page 473
18.2 Reproductive technologies and genome banking......Page 478
18.3 Founding populations for conservation breeding programs......Page 480
18.4 Genetic drift in captive populations......Page 482
18.5 Natural selection and adaptation to captivity......Page 485
18.6 Genetic management of conservation breeding programs......Page 487
18.7 Supportive breeding......Page 491
18.8 Reintroductions and translocations......Page 493
Guest Box 18 Effects of population bottlenecks on introduced species of birds......Page 500
19 Invasive Species......Page 503
19.1 Why are invasive species so successful?......Page 505
19.2 Genetic analysis of introduced species......Page 508
19.3 Establishment and spread of invasive species......Page 512
19.4 Hybridization as a stimulus for invasiveness......Page 513
19.5 Eradication, management, and control......Page 515
Guest Box 19 Rapid adaptation of invasive populations of St John’s Wort......Page 520
20 Forensic and Management Applications of Genetic Identification......Page 523
20.1 Species identification......Page 525
20.2 Individual identification and probability of identity......Page 530
20.3 Parentage testing......Page 534
20.5 Population assignment......Page 536
20.6 Population composition analysis......Page 539
Guest Box 20 Microsatellite DNA genotyping identifies problem bear and cubs......Page 542
Glossary......Page 547
Appendix Probability and Statistics......Page 564
A1 Probability......Page 567
A2 Statistical measures and distributions......Page 569
A3 Frequentist hypothesis testing, statistical errors, and power......Page 578
A4 Maximum likelihood......Page 582
A5 Bayesian approaches and MCMC (Markov chain Monte Carlo)......Page 583
A7 Parameter estimation, accuracy, and precision......Page 588
A8 Performance testing......Page 590
A9 The coalescent and genealogical information......Page 591
Guest Box A Is mathematics necessary?......Page 596
References......Page 598
Index......Page 647