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Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genetics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or commercial importance. New molecular techniques, statistical methods, and computer programs, genetic principles, and methods are becoming increasingly useful in the conservation of biological diversity. Using a balance of data and theory, coupled with…mehr
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Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genetics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or commercial importance. New molecular techniques, statistical methods, and computer programs, genetic principles, and methods are becoming increasingly useful in the conservation of biological diversity. Using a balance of data and theory, coupled with basic and applied research examples, this book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, the interpretation of genetic data from natural populations, and how these can be applied to conservation. The book includes examples from plants, animals, and microbes in wild and captive populations.
This second edition contains new chapters on Climate Change and Exploited Populations as well as new sections on genomics, genetic monitoring, emerging diseases, metagenomics, and more. One-third of the references in this edition were published after the first edition.
Each of the 22 chapters and the statistical appendix have a Guest Box written by an expert in that particular topic (including James Crow, Louis Bernatchez, Loren Rieseberg, Rick Shine, and Lisette Waits).
This book is essential for advanced undergraduate and graduate students of conservation genetics, natural resource management, and conservation biology, as well as professional conservation biologists working for wildlife and habitat management agencies.
Additional resources for this book can be found at: www.wiley.com/go/allendorf/populations.
Hinweis: Dieser Artikel kann nur an eine deutsche Lieferadresse ausgeliefert werden.
This second edition contains new chapters on Climate Change and Exploited Populations as well as new sections on genomics, genetic monitoring, emerging diseases, metagenomics, and more. One-third of the references in this edition were published after the first edition.
Each of the 22 chapters and the statistical appendix have a Guest Box written by an expert in that particular topic (including James Crow, Louis Bernatchez, Loren Rieseberg, Rick Shine, and Lisette Waits).
This book is essential for advanced undergraduate and graduate students of conservation genetics, natural resource management, and conservation biology, as well as professional conservation biologists working for wildlife and habitat management agencies.
Additional resources for this book can be found at: www.wiley.com/go/allendorf/populations.
Hinweis: Dieser Artikel kann nur an eine deutsche Lieferadresse ausgeliefert werden.
Produktdetails
- Produktdetails
- Verlag: Wiley & Sons / Wiley-Blackwell
- Artikelnr. des Verlages: 14567145000
- 2. Aufl.
- Seitenzahl: 624
- Erscheinungstermin: 17. Dezember 2012
- Englisch
- Abmessung: 246mm x 189mm x 30mm
- Gewicht: 1205g
- ISBN-13: 9780470671450
- ISBN-10: 0470671459
- Artikelnr.: 35676404
- Verlag: Wiley & Sons / Wiley-Blackwell
- Artikelnr. des Verlages: 14567145000
- 2. Aufl.
- Seitenzahl: 624
- Erscheinungstermin: 17. Dezember 2012
- Englisch
- Abmessung: 246mm x 189mm x 30mm
- Gewicht: 1205g
- ISBN-13: 9780470671450
- ISBN-10: 0470671459
- Artikelnr.: 35676404
Fred W. Allendorf is a Regents Professor at the University of Montana and a Professorial Research Fellow at Victoria University of Wellington in New Zealand. He has published over 200 articles on the population genetics and conservation of fish, amphibians, mammals, invertebrates, and plants. He is a past President of the American Genetic Association, and has served as Director of the Population Biology Program of the National Science Foundation. He has taught conservation genetics at the University of Montana, University of Oregon, University of Minnesota, University of Western Australia, Victoria University of Wellington, and the US National Conservation Training Center. Gordon Luikart is an Associate Professor at the Flathead Lake Biological Station of the University of Montana and a Visiting Scientist in the Center for Investigation of Biodiversity and Genetic Resources at the University of Porto, Portugal. He is also an award winning (Bronze Medal) Research Scientist with the Centre National de la Recherche Scientifique at the University Joseph Fourier in Grenoble, France. His research focuses on the conservation and genetics of wild and domestic animals, and includes over 100 publications. He was a Fulbright Scholar at La Trobe University, Melbourne, and he is a member of the IUCN Specialist Group for Caprinae (mountain ungulates) conservation. Sally N. Aitken is a Professor in the Department of Forest Sciences and Director of the Centre for Forest Conservation Genetics at the University of British Columbia. She studies the population, conservation, ecological genetics, and genomics of forest trees. She received her PhD from the University of California, Berkeley, and she was a faculty member at Oregon State University. She has received the Canadian Forestry Scientific Achievement Award, a Killam Faculty Research Fellowship, and a Killam Teaching Prize. She teaches forest biology, alpine ecology, and conservation genetics, and she is involved in forest genetic conservation initiatives in North America and Europe.
Guest 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
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
Guest 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
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