Population Genetics for Animal Conservation (Conservation Biology)

Cover......Page 1
Half-title......Page 3
Series-title......Page 4
Title......Page 5
Copyright......Page 6
Contents......Page 9
Contributors......Page 11
Foreword......Page 15
Acknowledgements......Page 16
The extinction crisis......Page 17
The synergy between conservation biology and genetics......Page 19
Population Genetics for Animal Conservation (PGAC) workshop......Page 25
References......Page 28
Statistical approaches, data analysis and inference......Page 39
Introduction......Page 41
Conceptual models and graphical models......Page 42
Mixture models......Page 44
A survey of methods......Page 46
The structure model with admixture......Page 47
The structure model with admixture and prior population information......Page 49
The NewHybrids model......Page 52
The BayesAss+ model......Page 53
Practical issues......Page 55
References......Page 56
3 How to use Migrate or why are Markov chain Monte Carlo programs difficult to use?......Page 58
What is 'Markov chain Monte Carlo'?......Page 59
An almost too simple example......Page 60
Migrate – a program for inferring population genetic parameters......Page 61
Coalescence theory......Page 62
Mutation models......Page 63
How are these pieces combined?......Page 64
Running in Bayes inference mode......Page 65
A short explanation of what Migrate does and does not do......Page 66
What happens when the population history violates the assumptions?......Page 67
Example data set......Page 69
Basic analysis – getting familiar with MCMC-based software and data......Page 71
Comparison of effect of gene flow using the Bayesian framework......Page 73
Comparison of Bayesian inference and maximum likelihood......Page 74
Replication and heating......Page 76
How long to wait......Page 77
Likelihood ratio tests and related test statistics......Page 79
Comparison of two different migration models......Page 80
Use of the coalescent in conservation genetics......Page 83
Summary......Page 85
References......Page 86
Appendix Data set......Page 91
Run conditions for specific examples in this chapter......Page 94
Introduction......Page 96
Network approaches require thorough sampling......Page 97
Network diagrams illustrate different types of information......Page 100
How to resolve loops and ambiguous connections......Page 102
Building the nesting design......Page 103
From haplotype network to geographical analysis using GeoDis......Page 104
Using the inference key to uncover evolutionary processes and patterns......Page 108
A special case: terrestrial versus riparian species......Page 110
Inferring biogeographic patterns......Page 111
NCPA can be used to delimit species' boundaries......Page 112
References......Page 115
5 A comparison of methods for constructing evolutionary networks from intraspecific DNA.sequences......Page 120
Reduced median network (RMN)......Page 122
Statistical parsimony network......Page 123
Union of maximum parsimonious trees (UMP)......Page 124
Comparison of methods: simulated sequence data......Page 127
Comparison of methods: Empirical data sets......Page 129
Which method(s) should be used to infer genealogical relationships among intraspecific sequences?......Page 133
Acknowledgements......Page 134
References......Page 135
Molecular approaches and applications......Page 137
Introduction......Page 139
QST-FST comparison......Page 141
Case study: the QST–FST comparison applied to two different ecotypes of the lake whitefish (Coregonus clupeaformis)......Page 143
Analysis of a candidate gene or mutation......Page 144
Case study: melanism in the rock pocket mouse......Page 145
Genome scan......Page 148
Incorporating population genomics into conservation: the Population Adaptive Index......Page 150
Transcription profiling based on a cDNA microarray......Page 151
Rapid evolutionary changes of gene expression in farmed Atlantic salmon (Salmo salar): relevance for the conservation of wild populations......Page 154
General discussion......Page 155
References......Page 158
7 Monitoring and detecting translocations using genetic data......Page 164
Genetic analyses and monitoring of well-known translocation events......Page 167
Detecting a past translocation event from genetic data......Page 176
References......Page 178
Why non-invasive genetics?......Page 183
What are the applications?......Page 184
Sample sources......Page 187
Hair samples......Page 188
Faecal samples......Page 189
Extraction kits and methods......Page 191
Recent innovations......Page 192
Molecular markers......Page 193
Technical challenges......Page 195
The need for pilot studies......Page 196
Reliability......Page 197
Demographic information......Page 198
References......Page 201
Introduction......Page 218
Laboratory......Page 219
Data analysis......Page 221
Evolutionarily significant units......Page 222
Establishing prior range......Page 223
Systematics and forensics......Page 225
Genetic diversity in historical context......Page 232
Response to long-term environmental change......Page 235
Conclusions......Page 237
References......Page 238
From genetic data to practical management: issues and case studies......Page 245
Introduction......Page 247
Current situation......Page 248
Preble's meadow jumping mouse: an example of the problem......Page 250
Getting out of ‘neutral'......Page 253
References......Page 258
Introduction......Page 261
Endangered salmonid populations......Page 264
Behaviour of juvenile salmonid fish: the importance of aggression......Page 265
Genetic diversity and competitive ability: Experiment I......Page 266
Estimating offspring genetic diversity......Page 267
Results and discussion......Page 269
Methods......Page 272
Behavioural trials......Page 273
Genetic analysis and statistics......Page 274
Results and discussion......Page 275
Experiments I and II: discussion and conclusions......Page 280
References......Page 282
Population divergence and taxonomy......Page 289
Restoration genetics......Page 290
Sample collection and genetic methods......Page 291
Genetic divergence and phylogeny of island populations......Page 292
Genetic diversity......Page 293
Phylogeny and taxon designation......Page 294
Santa Cruz......Page 296
Isabela......Page 297
The Española captive breeding system......Page 301
Genetic assignment of tortoises of unknown origin......Page 303
Conservation and management implications......Page 307
Acknowledgements......Page 309
References......Page 310
Introduction......Page 314
Kin associations......Page 315
Habitat dependence......Page 320
Migratory species and predictable habitats......Page 326
Sex-specific dispersal......Page 328
Conclusions......Page 331
References......Page 332
Future directions in conservation genetics......Page 339
Introduction......Page 341
Minisequencing......Page 344
Real-time polymerase chain reaction (RT-PCR)......Page 346
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF)......Page 348
Amplification fragment length polymorphism (AFLP) PCR......Page 349
Pyrosequencing......Page 351
Microarray technology......Page 352
Whole-genome amplification......Page 353
Metagenomics......Page 354
Conclusions and perspective......Page 355
References......Page 357
Introduction......Page 365
Genealogical modelling and demographic history......Page 366
How feasible is it to recover demographic history from genetic data?......Page 368
Recombination......Page 370
Approximations......Page 372
Improvements to current methods......Page 373
Species identification......Page 376
Multilocus genotypic methods......Page 377
Relatedness and pedigrees......Page 379
Natural selection and adaptation......Page 381
Conclusions......Page 384
References......Page 385
Software index......Page 394
Species index......Page 396
Species index......Page 399
Subject index......Page 402