Conservation and the Genetics of Populations

Title page......Page 5
Copyright page......Page 6
Contents......Page 7
Guest Box authors......Page 11
Preface......Page 13
Preface to the first edition......Page 15
List of symbols......Page 17
PART I: Introduction......Page 21
CHAPTER 1: Introduction......Page 23
1.1 Genetics and Civilization......Page 24
1.2.1 Phylogenetic diversity......Page 25
1.2.2 Populations, species, or ecosystems?......Page 28
1.3 How Should We Conserve Biodiversity?......Page 29
1.4 Applications of Genetics to Conservation......Page 30
1.5 The Future......Page 32
Guest Box 1: L. Scott Mills and Michael E. Soulé, The role of genetics in conservation......Page 33
CHAPTER 2: Phenotypic variation in natural populations......Page 34
2.1 Color Pattern......Page 37
2.2 Morphology......Page 40
2.3 Behavior......Page 43
2.4 Phenology......Page 45
2.5 Differences Among Populations......Page 47
2.5.1 Countergradient variation......Page 50
2.6 Nongenetic Inheritance......Page 51
Guest Box 2: Chris J. Foote, Looks can be deceiving: countergradient variation in secondary sexual color in sympatric morphs of sockeye salmon......Page 52
CHAPTER 3: Genetic variation in natural populations: chromosomes and proteins......Page 54
3.1 Chromosomes......Page 55
3.1.1 Karyotypes......Page 56
3.1.2 Sex chromosomes......Page 57
3.1.4 Numbers of chromosomes......Page 59
3.1.7 Inversions......Page 61
3.1.8 Translocations......Page 64
3.2 Protein Electrophoresis......Page 65
3.2.1 Strengths and limitations of protein electrophoresis......Page 67
3.3.1 Data from natural populations......Page 68
3.4 Genetic Divergence Among Populations......Page 70
Guest Box 3: E. M. Tuttle, Chromosomal polymorphism in the white-throated sparrow......Page 72
CHAPTER 4: Genetic variation in natural populations: DNA......Page 74
4.1 Mitochondrial and Chloroplast Organelle DNA......Page 76
4.1.1 Restriction endonucleases and RFLPs......Page 77
4.1.2 Polymerase chain reaction......Page 78
4.2.1 Microsatellites......Page 80
4.2.3 Single nucleotide polymorphisms......Page 84
4.2.4 Sex-linked markers......Page 86
4.3.2 AFLPs and ISSRs......Page 88
4.4 Genomic Tools and Markers......Page 89
4.4.2 Inferences from sequence data......Page 90
4.4.4 SNP discovery and genotyping by sequencing......Page 91
4.5 Transcriptomics......Page 92
4.6.1 Metagenomics......Page 93
Guest Box 4: Louis Bernatchez Rapid evolutionary changes of gene expression in domesticated Atlantic salmon and its consequences for the conservation of wild populations......Page 94
PART II: Mechanisms of Evolutionary Change......Page 97
CHAPTER 5: Random mating populations: Hardy-Weinberg principle......Page 99
5.1 Hardy-Weinberg Principle......Page 100
5.2 Hardy-Weinberg Proportions......Page 102
5.3 Testing for Hardy-Weinberg Proportions......Page 103
5.3.1 Small sample sizes or many alleles......Page 104
5.3.2 Multiple simultaneous tests......Page 107
5.4.2 Null alleles......Page 108
5.5 Sex-Linked Loci......Page 110
5.5.1 Pseudoautosomal inheritance......Page 111
5.6.2 Allelic richness......Page 112
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)......Page 113
CHAPTER 6: Small populations and genetic drift......Page 116
6.1 Genetic Drift......Page 117
6.2 Changes in Allele Frequency......Page 120
6.3 Loss of Genetic Variation: The Inbreeding Effect of Small Populations......Page 121
6.4 Loss of Allelic Diversity......Page 122
6.5 Founder Effect......Page 126
6.6 Genotypic Proportions in Small Populations......Page 130
6.7.2 Loss of allelic diversity......Page 132
6.7.3 Inbreeding depression......Page 134
Guest Box 6: Menna E. Jones, Reduced genetic variation and the emergence of an extinction-threatening disease in the Tasmanian devil......Page 135
CHAPTER 7: Effective population size......Page 137
7.1 Concept of Effective Population Size......Page 138
7.2 Unequal Sex Ratio......Page 139
7.3 Nonrandom Number of Progeny......Page 141
7.5 Overlapping Generations......Page 145
7.7 Cytoplasmic Genes......Page 146
7.8 Gene Genealogies, the Coalescent, and Lineage Sorting......Page 149
7.9.1 Allelic diversity and Ne......Page 150
7.9.2 Generation interval......Page 151
7.10 Effective Population Size in Natural Populations......Page 152
Guest Box 7: Craig R. Miller and Lisette P. Waits, Estimation of effective population size in Yellowstone grizzly bears......Page 154
CHAPTER 8: Natural selection......Page 156
8.2 Single Locus with Two Alleles......Page 158
8.2.2 Heterozygous advantage (overdominance)......Page 159
8.2.3 Heterozygous disadvantage (underdominance)......Page 161
8.3 Multiple Alleles......Page 164
8.3.1 Heterozygous advantage and multiple alleles......Page 166
8.4.3 Self-incompatibility locus in plants......Page 167
8.5 Natural Selection in Small Populations......Page 169
8.5.3 Heterozygous advantage and drift......Page 170
8.6 Natural Selection and Conservation......Page 171
Guest Box 8: Paul A. Hohenlohe and William A. Cresko, Natural selection across the genome of the threespine stickleback fish......Page 174
CHAPTER 9: Population subdivision......Page 176
9.1 F-Statistics......Page 178
9.1.1 The Wahlund effect......Page 179
9.1.2 When is FIS not zero?......Page 180
9.2.1 Effects of dispersal distance and population density on patterns of relatedness......Page 181
9.3.1 Complete isolation......Page 183
9.3.2 Gene flow......Page 184
9.4.1 Island model......Page 185
9.4.2 Stepping-stone model......Page 186
9.5 Continuously Distributed Populations......Page 188
9.6.1 Cytoplasmic genes......Page 189
9.6.2 Sex-linked loci......Page 190
9.7.1 Heterozygous advantage......Page 192
9.7.3 Comparisons among loci......Page 193
9.8 Limitations of FST and Other Measures of Subdivision......Page 194
9.8.1 Genealogical information......Page 195
9.8.3 Other measures of divergence......Page 197
9.8.4 Hierarchical structure......Page 198
9.9.1 FST and indirect estimates of mN......Page 199
9.9.3 Maximum likelihood and the coalescent......Page 200
9.9.4 Assignment tests and direct estimates of mN......Page 201
9.10 Population Subdivision and Conservation......Page 204
Guest Box 9: M.K. Schwartz and J.M. Tucker, Genetic population structure and conservation of fisher in Western North America......Page 205
CHAPTER 10: Multiple loci......Page 207
10.1 Gametic Disequilibrium......Page 208
10.1.2 Associations between cytoplasmic and nuclear genes......Page 211
10.3 Natural Selection......Page 212
10.3.2 Associative overdominance......Page 213
10.3.3 Genetic draft......Page 215
10.5 Hybridization......Page 216
10.6.1 Two loci with two alleles each......Page 219
10.7 Multiple Loci and Conservation......Page 220
Guest Box 10: Robin S. Waples, Estimation of effective population size using gametic disequilibrium......Page 223
CHAPTER 11: Quantitative genetics......Page 225
11.1 Heritability......Page 226
11.1.2 Narrow-sense heritability......Page 228
11.1.3 Estimation of heritability......Page 229
11.2 Selection on Quantitative Traits......Page 232
11.2.1 Heritabilities and allele frequencies......Page 234
11.2.2 Genetic correlations......Page 235
11.3 Finding Genes Underlying Quantitative Traits......Page 237
11.3.1 QTL mapping......Page 238
11.4 Loss of Quantitative Genetic Variation......Page 240
11.4.1 Effects of genetic drift and bottlenecks......Page 241
11.4.2 Effects of selection......Page 242
11.5 Divergence Among Populations......Page 243
11.6 Quantitative Genetics and Conservation......Page 245
11.6.1 Response to selection in the wild......Page 246
11.6.2 Can molecular genetic variation within populations estimate quantitative variation?......Page 247
11.6.3 Does population divergence for molecular markers estimate divergence for quantitative traits?......Page 248
Guest Box 11: David W. Coltman, Response to trophy hunting in bighorn sheep......Page 249
CHAPTER 12: Mutation......Page 250
12.1 Process of Mutation......Page 251
12.1.1 Chromosomal mutations......Page 252
12.1.2 Molecular mutations......Page 253
12.1.4 Transposable elements, mutation rates, and stress......Page 254
12.2 Selectively Neutral Mutations......Page 255
12.2.1 Genetic variation within populations......Page 256
12.2.2 Population subdivision......Page 257
12.4 Advantageous Mutations......Page 259
12.5 Recovery from a Bottleneck......Page 261
Guest Box 12: Michael W. Nachman, Color evolution via different mutations in pocket mice......Page 262
PART III: Genetics and Conservation......Page 265
CHAPTER 13: Inbreeding depression......Page 267
13.1 Pedigree Analysis......Page 268
13.1.1 Estimation of the pedigree inbreeding coefficient......Page 270
13.2 Gene Drop Analysis......Page 272
13.3 Estimation of F with Molecular Markers......Page 273
13.4 Causes of Inbreeding Depression......Page 276
13.5 Measurement of Inbreeding Depression......Page 278
13.5.1 Lethal equivalents......Page 279
13.5.2 Estimates of inbreeding depression......Page 280
13.5.3 Founder-specific inbreeding effects......Page 281
13.6 Genetic Load and Purging......Page 284
13.7 Inbreeding and Conservation......Page 287
Guest Box 13: Guest Box 13, Inbreeding depression in song sparrows......Page 288
CHAPTER 14: Demography and extinction......Page 290
14.1.1 One sample......Page 292
14.1.2 Two sample: capture–mark–recapture......Page 293
14.2 Inbreeding Depression and Extinction......Page 294
14.2.1 Evidence that inbreeding depression affects population dynamics......Page 295
14.2.2 Are small populations doomed?......Page 296
14.3.1 The vortex simulation model......Page 297
14.3.2 What is a viable population?......Page 302
14.3.4 Beyond viability......Page 304
14.4.1 Life history variation......Page 306
14.4.2 Mating types and sex determination......Page 307
14.5 Loss of Evolutionary Potential......Page 308
14.7 Mutational Meltdown......Page 309
14.8.1 How large do populations need to be to maintain sufficient genetic variation?......Page 311
14.9 The 50/500 Rule......Page 312
Guest Box 14: A. G. Young, M. Pickup, and B. G. Murray, Management implications of loss of genetic diversity at the self-incompatibility locus for the button wrinklewort......Page 313
CHAPTER 15: Metapopulations and fragmentation......Page 316
15.1 The Metapopulation Concept......Page 317
15.2 Genetic Variation in Metapopulations......Page 318
15.3 Effective Population Size of Metapopulations......Page 321
15.4 Population Divergence and Connectivity......Page 323
15.5 Genetic Rescue......Page 324
15.6.1 Landscape connectivity and complex models......Page 326
15.6.2 Corridor mapping......Page 328
15.6.3 Landscape genomics......Page 329
15.7 Long-Term Population Viability......Page 331
Guest Box 15: Robert C. Vrijenhoek, Fitness loss and genetic rescue in stream-dwelling topminnows......Page 333
CHAPTER 16: Units of conservation......Page 336
16.1 What Should We Protect?......Page 338
16.2 Systematics and Taxonomy......Page 340
16.3 Phylogeny Reconstruction......Page 342
16.3.2 Gene trees and species trees......Page 343
16.4 Genetic Relationships within Species......Page 347
16.4.1 Population-based approaches......Page 348
16.4.2 Individual-based methods......Page 352
16.4.3 Phylogeography......Page 355
16.5.1 Species......Page 356
16.5.2 Evolutionarily significant units......Page 359
16.5.3 Management units......Page 365
16.6 Integrating Genetic, Phenotypic, and Environmental Information......Page 366
16.6.1 Adaptive genetic variation......Page 367
16.7 Communities......Page 368
Guest Box 16: David J. Coates, Identifying units of conservation in a rich and fragmented flora......Page 370
CHAPTER 17: Hybridization......Page 372
17.1 Natural Hybridization......Page 373
17.1.1 Intraspecific hybridization......Page 374
17.1.2 Interspecific hybridization......Page 375
17.1.3 Hybrid taxa......Page 377
17.2 Anthropogenic Hybridization......Page 378
17.2.2 Hybridization with introgression......Page 379
17.3 Fitness consequences of Hybridization......Page 380
17.3.1 Hybrid superiority......Page 381
17.3.2 Intrinsic outbreeding depression......Page 382
17.3.3 Extrinsic outbreeding depression......Page 383
17.4 Detecting and Describing Hybridization......Page 384
17.4.1 Multiple loci and gametic disequilibrium......Page 386
17.5.1 Intentional hybridization......Page 390
17.5.2 Protection of hybrids......Page 393
17.5.3 Prediction of outbreeding depression......Page 394
Guest Box 17: Loren H. Rieseberg, Hybridization and the conservation of plants......Page 395
CHAPTER 18: Exploited populations......Page 397
18.1 Loss of Genetic Variation......Page 398
18.2 Unnatural Selection......Page 401
18.3 Spatial Structure......Page 405
18.4.1 Genetic effects of releases......Page 408
18.4.3 Monitoring of large-scale releases......Page 410
18.5.1 Loss of genetic variation......Page 411
18.5.3 Subdivision......Page 412
Guest Box 18: Guðrún Marteinsdóttir, Long-term genetic changes in the Icelandic stock of Atlantic cod in response to harvesting......Page 413
CHAPTER 19: Conservation breeding and restoration......Page 415
19.1.1 When is conservation breeding an appropriate tool for conservation?......Page 418
19.1.2 Priorities for conservation breeding......Page 419
19.2 Reproductive Technologies and Genome Banking......Page 420
19.3 Founding Populations for Conservation Breeding Programs......Page 423
19.3.2 Admixed founding populations......Page 424
19.4.2 Deleterious alleles and mutational meltdown......Page 425
19.4.3 Inbreeding or genetic drift?......Page 426
19.5 Natural Selection and Adaptation to Captivity......Page 427
19.5.2 Minimizing adaptation to captivity......Page 428
19.5.3 Interaction of genetic drift and natural selection......Page 429
19.6.1 Pedigreed populations......Page 430
19.6.2 Nonpedigreed populations......Page 431
19.7.1 Genetic drift and supportive breeding......Page 432
19.8 Reintroductions and Translocations......Page 434
19.8.1 Reintroductions......Page 435
19.8.2 Restoration of plant communities......Page 437
Guest Box 19: Robert C. Lacy, Understanding inbreeding depression: 25 years of experiments with Peromyscus mice......Page 439
CHAPTER 20: Invasive species......Page 441
20.1 Why are Invasive Species So Successful?......Page 442
20.1.1 If population bottlenecks are harmful, then why are invasive species that have gone through a founding bottleneck so successful?......Page 443
20.1.2 If local adaptation is important, then why are introduced species so successful at replacing native species?......Page 444
20.2.1 Molecular identification of invasive species......Page 445
20.2.2 Distribution of genetic variation in invasive species......Page 446
20.2.4 Quantitative genetic variation......Page 448
20.3.2 Spread......Page 449
20.4.3 Fixed heterosis......Page 450
20.5 Eradication, Management, and Control......Page 451
20.5.1 Units of eradication......Page 452
20.6 Emerging Diseases and Parasites......Page 453
20.6.1 Detection of parasites......Page 455
20.6.3 Tracking origins of infectious disease outbreaks......Page 457
Guest Box 20: Richard Shine, Rapid evolution of introduced cane toads and native snakes......Page 458
CHAPTER 21: Climate change......Page 460
21.1 Predictions and Uncertainty about Future Climates......Page 461
21.2 Phenotypic Plasticity......Page 462
21.3 Maternal Effects and Epigenetics......Page 465
21.4.1 Theoretical predictions......Page 466
21.4.2 Empirical studies......Page 467
21.5 Species Range Shifts......Page 468
21.6 Extirpation and Extinction......Page 469
21.7 Management in the Face of Climate Change......Page 471
21.7.2 Assisted colonization......Page 472
Guest Box 21: S. J. Franks, Rapid evolution of flowering time by an annual plant in response to climate fluctuation......Page 473
CHAPTER 22: Genetic identification and monitoring......Page 475
22.1.1 DNA barcoding......Page 477
22.1.2 Diet analysis......Page 479
22.1.4 Forensic genetics......Page 480
22.2 Metagenomics and Species Composition......Page 484
22.3 Individual Identification......Page 485
22.3.1 Probability of identity......Page 486
22.4.1 Parentage......Page 489
22.5.1 Assignment of individuals......Page 491
22.5.3 Population composition analysis......Page 494
22.6 Genetic Monitoring......Page 497
22.6.1 Traditional ecological monitoring......Page 498
22.6.3 Adaptive change......Page 500
Guest Box 22: C. Scott Baker, Genetic detection of illegal trade of whale meat results in closure of restaurants......Page 501
Appendix: Probability and statistics......Page 504
A1 Paradigms......Page 505
A2 Probability......Page 507
A2.2 Odds ratios and LOD scores......Page 508
A3.1 Types of statistical descriptors or tests......Page 509
A3.2 Measures of location and dispersion......Page 510
A3.3 Probability distributions......Page 511
A4 Frequentist Hypothesis Testing, Statistical Errors, and Power......Page 516
A4.2 Statistical power......Page 517
A5 Maximum Likelihood......Page 519
A6 Bayesian Approaches and MCMC (Markov Chain Monte Carlo)......Page 520
A6.1 Markov chain Monte Carlo (MCMC)......Page 522
A8 Parameter Estimation, Accuracy, and Precision......Page 524
A10 The Coalescent and Genealogical Information......Page 526
Guest Box A: James F. Crow, Is mathematics necessary?......Page 531
Glossary......Page 533
References......Page 551
Index......Page 607
Supplemental Images......Page 623