Molecular Approaches in Natural Resource Conservation and Management

Half-title......Page 3
Title......Page 5
Copyright......Page 6
Contents......Page 7
Contributors......Page 11
Preface......Page 17
Acknowledgments......Page 18
1 Biodiversity discovery and its importance to conservation......Page 21
Why is biodiversity important?......Page 22
How is biodiversity distributed?......Page 23
Is the extinction of biodiversity a problem?......Page 24
Status of species discovery and description......Page 28
Factors limiting the rate of species discovery......Page 31
Importance of phylogenetics to the delimitation and conservation of species......Page 33
Molecular taxonomy and phylogenetics of prokaryotes......Page 37
Molecular taxonomy and phylogenetics of eukaryotes......Page 38
Molecular approaches to the discovery of cryptic species......Page 40
Box 1: Genetic Identification of Cryptic Species: an Example in Rhogeessa......Page 42
Enhancing Rate of Species Discovery......Page 44
Phylogenetic Databases......Page 47
2 Gene flow, biodiversity, and genetically modified crops: Weedy rice in Thailand......Page 55
Potential Effects of Gene Flow on Biodiversity......Page 56
Box 2: Environmental Risk Assessment of Genetically Engineered Salmon......Page 57
The Origin of Weedy Rice in Thailand......Page 61
Conclusions......Page 66
REFERENCES......Page 67
Introduction......Page 70
Conservation in a Community Context......Page 72
Heritable Community and Ecosystem Phenotypes......Page 73
Conservation Consequences of Heritable Phenotypes......Page 76
A Community Genetics Perspective on Minimum Viable Populations......Page 79
Community Phenotypes of Genetically Engineered Organisms......Page 81
Box 3: Landscape Genetics of an American Chestnut Borer......Page 83
Community Genetics and Climate Change......Page 86
Management Conclusions......Page 88
REFERENCES......Page 89
Sexing assays and conservation......Page 94
Box 4: Sex Identification and Population Size of Grizzly Bears by Using Noninvasive Genetic Sampling......Page 96
Mammals and birds......Page 97
Reptiles and amphibians......Page 99
ESD as determined by behavior......Page 101
ESD as determined by temperature......Page 102
Genetic sex determination......Page 103
Isolation of Sexing Markers for Fish Management......Page 106
Case Study: The Identification of Sex-Determining Genes in Lake Sturgeon......Page 108
Candidate genes......Page 109
Pyrosequencing of transcriptomes......Page 110
Lessons from lake sturgeon......Page 113
REFERENCES......Page 114
Introduction......Page 121
Ancient differentiation......Page 122
Erasing ancient differentiation......Page 125
Recent differentiation......Page 127
Contemporary Dynamics of Differentiation......Page 129
Components of adaptive differentiation (QST)......Page 130
Dynamics of adaptive differentiation......Page 132
Coexistence of strong adaptive differentiation and high gene flow......Page 135
Conclusion......Page 136
Box 5: Adaptive Shifts in Natural Populations of High Dispersing Species......Page 137
REFERENCES......Page 139
Introduction......Page 143
Methods for Detecting Genes for Ecologically Relevant Phenotypes......Page 145
LD or association mapping......Page 146
Quantitative trait loci (QTL)
analysis......Page 148
Hitchhiking mapping and outlier analysis......Page 149
Neutrality tests with sequence or SNP data......Page 151
Genome-wide association and QTL studies in animals......Page 152
Candidate-gene association studies in animals......Page 158
Box 6: Unraveling Counterintuitive Evolutionary Trends: Coat Color in Soay Sheep......Page 159
Genome-wide association and QTL studies in plants......Page 161
Candidate-gene association studies in plants......Page 165
Tests for signatures of natural selection in plants......Page 166
Case Study: QTL, Association Genetics, and Tests for Natural Selection in a Natural Forest-Tree Population......Page 168
The Genes of Adaptive Differentiation: Utility for Conservation and Management......Page 171
REFERENCES......Page 173
7 Hybridization in threatened and endangered animal taxa: Implications for conservation and management of biodiversity......Page 189
Box 7: Mating Opportunities in Animal Hybrid Zones......Page 191
Case Study......Page 193
Anthropogenic and natural hybridization in endangered animal taxa......Page 194
Hybrid zone dynamics in endangered taxa......Page 205
Predictors and correlates of hybridization in endangered taxa......Page 206
Hybrid zone dynamics in endangered taxa......Page 209
Can hybridization in threatened or endangered species promote conservation?......Page 210
Bridging basic and applied studies of hybridization for conservation of endangered taxa......Page 212
REFERENCES......Page 213
Immediate consequences......Page 218
Short-term effects......Page 219
Long-term effects of fragmentation......Page 220
Estimates of Pollen Flow......Page 221
Box 8–2: Allelic Recharge in Populations Recovering from Bottleneck Events......Page 222
Seed Dispersal in Disturbed Landscapes......Page 228
Case Studies......Page 229
Dinizia excelsa (Fabaceae)......Page 230
S. globulifera (Clusiaceae)......Page 231
E. cyclocarpum (Fabaceae)......Page 232
Conservation Implications......Page 234
Conclusions......Page 235
REFERENCES......Page 236
9 Implications of landscape alteration for the conservation of genetic diversity of endangered species......Page 240
Box 9: Dune Restoration Introduces Genetically Distinct American Beachgrass, Ammophila breviligulata, into a Threatened Local Population......Page 242
Fragmentation Effects in Two Endangered Passerines......Page 245
The golden-cheeked warbler......Page 246
The black-capped vireo......Page 250
Literature Survey of Fragmentation Effects on Genetic Variation......Page 254
Genetic responses to fragmentation......Page 256
Conservation status......Page 257
Vagility......Page 258
Habitat structure......Page 260
Conclusions......Page 261
REFERENCES......Page 262
10 Integrating evolutionary considerations into recovery planning for Pacific salmon......Page 267
A Short Primer on Pacific Salmon Evolution......Page 269
Federal Protection......Page 271
Recovery Planning......Page 272
Population identification......Page 274
Abundance and productivity......Page 276
Spatial structure and diversity......Page 279
Integrating across risk factors......Page 280
ESU viability......Page 282
Future Prospects......Page 285
Case Study......Page 287
REFERENCES......Page 289
11 Using molecular methods to improve the genetic management of captive breeding programs for threatened species......Page 295
Inbreeding coefficient......Page 297
Gene diversity......Page 298
Applying concepts to incomplete pedigrees......Page 299
An Introduction to Captive Breeding Programs......Page 300
Sources of pedigree errors and types of pedigree gaps......Page 304
Using molecular data to identify errors and resolve gaps......Page 306
Estimating relatedness between individuals with unknown ancestry......Page 307
Directly replacing f with an estimate of r derived from molecular data......Page 308
Using molecular estimates of r to identify relationship categories......Page 310
Using molecular data to manage breeding programs for organisms living in groups......Page 312
Box 11:  Pedigree Reconstruction: An Alternative to Systematic Breeding......Page 313
Identifying individuals with rare or important alleles......Page 316
Incorporating molecular estimates of r into genetic management......Page 317
Resources for quantitative genetic analysis......Page 318
Summary......Page 319
REFERENCES......Page 320
12 Wildlife reintroductions: The conceptual development and application of theory......Page 324
Genetic Consequences of Reintroductions......Page 327
Founding event phase......Page 331
Population establishment phase......Page 333
Box 12: Genetic Ramifications of Restoration of Blight-Resistant American Chestnut......Page 335
Population growth phase......Page 338
Conclusion and Recommendations......Page 341
REFERENCES......Page 342
13 Evolutionary toxicology......Page 348
Disruption of Gene Structure by Environmental Pollutants......Page 349
Background......Page 350
Significance of early studies with DNA adducts......Page 352
Population-level consequences......Page 353
Overview......Page 357
Microsatellites......Page 358
Dominant anonymous DNA markers......Page 359
Organellar DNA......Page 360
DNA sequencing and single nucleotide polymorphisms......Page 361
DNA microarrays......Page 362
Box 13: Microarrays and Molecular Phenotypes......Page 363
Which marker to use......Page 364
Assessing causality......Page 365
Strength of association......Page 366
Consistency of association......Page 367
Specificity of association......Page 368
Time order or temporality......Page 370
Experimental evidence......Page 372
Plausibility......Page 374
Azerbaijan......Page 375
Pigeon River......Page 379
Statistical Methods for Evaluating Population Genetic Structure......Page 380
REFERENCES......Page 383
Index......Page 391