Conservation and the Genomics of Populations

Name: Conservation and the Genomics of Populations
Price: 4950 ISK
Availability: InStock
Author: Fred W. Allendorf; W. Chris Funk; Sally N. Aitken; Margaret Byrne; Gordon Luikart
ISBN: 9780192598578

Höfundar: Fred W. Allendorf; W. Chris Funk; Sally N. Aitken; Margaret Byrne; Gordon Luikart (Útgáfa: 3)

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The relentless loss of biodiversity is among the greatest problems facing the world today. The third edition of this established textbook provides an updated and comprehensive overview of the essential background, concepts, and tools required to understand how genetics can be used to conserve species, reduce threat of extinction, and manage species of ecological or commercial importance. This edition is thoroughly revised to reflect the major contribution of genomics to conservation of populations and species.

It includes two new chapters: "Genetic Monitoring" and a final "Conservation Genetics in Practice" chapter that addresses the role of science and policy in conservation genetics. New genomic techniques and statistical analyses are crucial tools for the conservation geneticist. This accessible and authoritative textbook provides an essential toolkit grounded in population genetics theory, coupled with basic and applied research examples from plants, animals, and microbes.

The book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, evolutionary response to anthropogenic change, and applications in conservation and management. Conservation and the Genomics of Populations helps demystify genetics and genomics for conservation practitioners and early career scientists, so that population genetic theory and new genomic data can help raise the bar in conserving biodiversity in the most critical 20 year period in the history of life on Earth.

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Útgefandi: Oxford University Press Academic UK

ISBN: 9780192598578

Print ISBN: 9780198856566

Format: Page Fidelity (PDF)

Útgáfa: 3

Höfundar: Fred W. Allendorf; W. Chris Funk; Sally N. Aitken; Margaret Byrne; Gordon Luikart

Tungumál: English

Útgefið: 2022-02-10

Prent takmörkun á líftíma: 100

Prent takmörkun: 2

Afritunar takmörkun: 2

Flokkar: Náttúruvísindi

Efnisflokkar: Vísindi › Erfðafræði og erfðamengisfræði

Kaflar

titlepage
copyright
Contents
Preface to the Third Edition
Acknowledgments
Guest Box Authors
List of Symbols
List of Abbreviations
Part I Introduction
1 Introduction
1.1 Genetics and civilization
1.2 Genetics, genomics, and conservation
1.2.1 Using genetics to understand basic biology
1.2.2 Invasive species and pathogens
1.2.3 Conservation genomics
1.3 What should we conserve?
1.3.1 Phylogenetic diversity
1.3.2 Species or ecosystems
1.3.3 Populations or species
1.4 How should we conserve biodiversity?
1.5 The future
Guest Box 1: Sarah P. Otto, Extinction and evolution in a human-altered world
2 Phenotypic Variation in Natural Populations
2.1 Color pattern
2.2 Morphology
2.3 Behavior
2.4 Life history
2.5 Phenology
2.6 Disease resistance
2.7 Variation within and among populations
2.7.1 Countergradient variation
2.8 Phenotypic variation and conservation
2.8.1 Genetic basis of phenotypic variation
2.8.2 Color polymorphism and population viability
Guest Box 2: Kelly R. Zamudio, The genomic basis of variation in disease resistance
3 Genetic Variation in Natural Populations
3.1 Chromosomes
3.1.1 Karyotypes
3.1.2 Sex chromosomes
3.1.3 Polyploidy
3.1.4 Numbers of chromosomes
3.1.5 Chromosomal size
3.1.6 Inversions
3.1.7 Translocations
3.1.8 Chromosomal variation and conservation
3.2 Mitochondrial and chloroplast DNA
3.3 Single-copy nuclear loci
3.3.1 Protein electrophoresis
3.3.2 Microsatellites
3.3.3 Single nucleotide polymorphisms (SNPs)
3.3.4 Sex-linked markers
3.4 Multiple locus techniques
3.4.1 Minisatellites
3.4.2 AFLPs and ISSRs
3.5 Genetic variation within and among populations
3.5.1 Quantifying genetic variation within natural populations
3.5.2 Estimates of genetic variation within natural populations
3.5.3 Significance of the amount of variation within populations
Guest Box 3: Sally Potter and Janine E. Deakin, Widespread chromosomal diversity across rock-wallabi
4 Population Genomics
4.1 High throughput sequencing
4.1.1 History of DNA sequencing technology
4.1.2 Next-generation sequencing (NGS)
4.1.3 Single nucleotide polymorphisms (SNPs)
4.1.4 Inferences from sequence data
4.2 Linkage maps and recombination
4.3 Whole genome sequencing and reference genomes
4.4 Whole genome resequencing
4.5 Reduced representation sequencing
4.5.1 Restriction site-associated DNA sequencing (RADseq) methods
4.5.2 Targeted sequence capture
4.5.3 Sequencing of population pools (pool-seq)
4.6 Filtering sequence data
4.7 Other SNP genotyping methods
4.8 RNA sequencing and transcriptome assembly
4.9 Transcriptomics
4.10 Epigenetics
4.11 Metagenomics
4.11.1 Host-associated microbial communities
4.11.2 Environmental DNA (eDNA)
4.12 Other ``omics'' and the future
Guest Box 4: Paul A. Hohenlohe, Genomics and conservation of Tasmanian devils in the face of transmi
Part II Mechanisms of Evolutionary Change
5 Random mating populations: Hardy–Weinberg Principle
5.1 Hardy–Weinberg principle
5.2 HW proportions
5.3 Testing for HW proportions
5.3.1 Small sample sizes
5.3.2 Many alleles
5.3.3 Multiple simultaneous tests
5.3.4 Testing large-scale genomic data for HW proportions
5.4 Estimation of allele frequencies
5.4.1 Recessive alleles
5.4.2 Null alleles
5.5 Sex-linked loci
5.5.1 Pseudoautosomal inheritance
5.6 Estimation of genetic variation
5.6.1 Heterozygosity
5.6.2 Allelic richness
5.6.3 Proportion of polymorphic loci
Guest Box 5: James F. Crow, Is mathematics necessary?
6 Small Populations and Genetic Drift
6.1 Genetic drift
6.2 Changes in allele frequency
6.3 The inbreeding effect of small populations
6.4 Loss of allelic diversity
6.5 Founder effect
6.6 Genotypic proportions in small populations
6.7 Effects of genetic drift
6.7.1 Changes in allele frequency
6.7.2 Loss of allelic diversity
6.7.3 Inbreeding depression
Guest Box 6: Yasmin Foster, Nicolas Dussex, and Bruce C. Robertson, Detecting bottlenecks in the cri
7 Effective Population Size
7.1 Concept of effective population size
7.2 Unequal sex ratio
7.3 Nonrandom number of progeny
7.4 Fluctuating population size
7.5 Overlapping generations
7.6 Variance versus inbreeding effective population size
7.7 Cytoplasmic genes
7.8 The coalescent
7.9 Limitations of effective population size
7.9.1 Allelic diversity and Ne
7.9.2 Generation interval
7.9.3 Gene flow
7.10 Effective population size in natural populations
7.11 How can genomics advance understanding of Ne?
Guest Box 7: Linda Laikre and Nils Ryman, Effective population size in brown trout: Lessons for cons
8 Natural Selection
8.1 Fitness
8.2 Single locus with two alleles
8.2.1 Directional selection
8.2.2 Heterozygous advantage (overdominance)
8.2.3 Heterozygous disadvantage (underdominance)
8.2.4 Selection and HW proportions
8.3 Multiple alleles
8.3.1 Heterozygous advantage and multiple alleles
8.4 Frequency-dependent selection
8.4.1 Two alleles
8.4.2 Frequency-dependent selection in nature
8.4.3 Self-incompatibility locus in plants
8.4.4 Complementary sex determination locus in invertebrates
8.5 Adaptive significance of cytoplasmic genomes
8.5.1 Plants
8.5.2 Animals
8.6 Natural selection in small populations
8.6.1 Directional selection
8.6.2 Underdominance and drift
8.6.3 Heterozygous advantage and drift
8.7 Detection of natural selection
8.8 Natural selection and conservation
Guest Box 8: Shane C. Campbell-Staton, Winter storms drive rapid phenotypic, regulatory, and genomic
9 Population Subdivision
9.1 F-statistics
9.1.1 The Wahlund effect
9.1.2 When is FIS not zero?
9.2 Spatial patterns of relatedness within local populations
9.2.1 Effects of dispersal distance and population density
9.2.2 Effects of spatial distribution of relatives on inbreeding probability
9.3 Genetic divergence among populations and gene flow
9.3.1 Complete isolation
9.3.2 Gene flow
9.4 Gene flow and genetic drift
9.4.1 Island model
9.4.2 Stepping-stone model
9.5 Continuously distributed populations
9.6 Cytoplasmic genes and sex-linked markers
9.6.1 Cytoplasmic genes
9.6.2 Sex-linked loci
9.7 Gene flow, genetic drift, and natural selection
9.7.1 Heterozygous advantage
9.7.2 Divergent directional selection
9.7.3 Comparisons among loci
9.8 Limitations of FST and other measures of subdivision
9.8.1 Genealogical information
9.8.2 High heterozygosity within subpopulations
9.8.3 Other measures of divergence
9.8.4 Hierarchical structure
9.9 Estimation of gene flow
9.9.1 FST and indirect estimates of mN
9.9.2 Private alleles
9.9.3 Maximum likelihood and the coalescent
9.9.4 Assignment tests and direct estimates
9.9.5 Current versus historical gene flow
9.10 Population subdivision and conservation
Guest Box 9: Uma Ramakrishnan, A decade of tiger conservation genetics in the Indian subcontinent
10 Beyond Individual Loci
10.1 Gametic disequilibrium
10.1.1 Other measures of gametic disequilibrium
10.1.2 Associations between cytoplasmic and nuclear genes
10.2 Small population size
10.3 Natural selection
10.3.1 Genetic hitchhiking
10.3.2 Associative overdominance
10.3.3 Genetic draft
10.4 Population subdivision
10.5 Hybridization
10.6 Estimation of gametic disequilibrium
10.6.1 Two loci with two alleles each
10.6.2 More than two alleles per locus
10.7 Strand theory: Junctions and chromosome segments
10.7.1 Microhaplotypes
10.8 Multiple loci and conservation
Guest Box 10: Robin S. Waples, Estimation of effective population size using gametic disequilibrium
11 Quantitative Genetics
11.1 Heritability
11.1.1 Broad-sense heritability
11.1.2 Narrow-sense heritability
11.1.3 Estimating heritability
11.1.4 Genotype-by-environment interactions
11.2 Selection on quantitative traits
11.2.1 Heritabilities and allele frequencies
11.2.2 Genetic correlations
11.3 Finding genes underlying quantitative traits
11.3.1 QTL mapping
11.3.2 Candidate gene approaches
11.3.3 Genome-wide association mapping
11.4 Loss of quantitative genetic variation
11.4.1 Effects of genetic drift and bottlenecks
11.4.2 Effects of selection
11.5 Divergence among populations
11.6 Quantitative genetics and conservation
11.6.1 Response to selection in the wild
11.6.2 Can molecular genetic variation within populations estimate quantitative variation?
11.6.3 Does population divergence for molecular markers estimate divergence for quantitative traits?
Guest Box 11: Victoria L. Sork, How genome-enhanced breeding values can assist conservation of tree
12 Mutation
12.1 Process of mutation
12.1.1 Chromosomal mutations
12.1.2 Molecular mutations
12.1.3 Quantitative characters
12.1.4 Transposable elements, stress, and mutation rates
12.2 Selectively neutral mutations
12.2.1 Genetic variation within populations
12.2.2 Population subdivision
12.3 Harmful mutations
12.4 Advantageous mutations
12.5 Recovery from a bottleneck
Guest Box 12: Philip W. Hedrick, Mutation, inbreeding depression, and adaptation
Part III Evolutionary Response to Anthropogenic Changes
13 Hybridization
13.1 Detecting and describing hybridization
13.1.1 Diagnostic loci
13.1.2 Using many single nucleotide polymorphism loci to detect hybridization
13.1.3 Gametic disequilibrium
13.2 Natural hybridization
13.2.1 Intraspecific hybridization
13.2.2 Interspecific hybridization
13.2.3 Hybrid zones
13.2.4 Hybrid taxa
13.3 Anthropogenic hybridization
13.3.1 Hybridization without introgression
13.3.2 Hybridization with introgression
13.3.3 Hybridization between wild species and their domesticated relatives
13.3.4 Hybridization and climate change
13.4 Fitness consequences of hybridization
13.4.1 Hybrid superiority
13.4.2 Intrinsic outbreeding depression
13.4.3 Extrinsic outbreeding depression
13.4.4 Long-term fitness effects of hybridization
13.5 Hybridization and conservation
13.5.1 Protection of hybrids
13.5.2 Ancient hybrids versus recent hybridization
13.5.3 How much admixture is acceptable?
13.5.4 Predicting outbreeding depression
Guest Box 13: Danielle Stephens, Peter J.S. Fleming, and Oliver F. Berry, Hybridization in Australia
14 Invasive Species
14.1 Why are invasive species so successful?
14.1.1 Why are invasive species that have gone through a founding bottleneck so successful?
14.1.2 Why are introduced species that are not locally adapted so successful at replacing native spe
14.2 Genetic analysis of introduced species
14.2.1 Molecular identification of invasive species
14.2.2 Molecular identification of origins of invasive species
14.2.3 Distribution of genetic variation in invasive species
14.2.4 Mechanisms of reproduction
14.2.5 Quantitative genetic variation
14.3 Establishment and spread of invasive species
14.3.1 Propagule pressure
14.3.2 Spread
14.4 Hybridization as a stimulus for invasiveness
14.5 Eradication, management, and control
14.5.1 Units of eradication
14.5.2 Genetics and biological control
14.5.3 Pesticides and herbicides
14.5.4 Gene editing and gene drive
14.6 Emerging diseases and parasites
14.6.1 Detection and quantification of disease vectors
14.6.2 Tracking origins of infectious disease outbreaks
14.6.3 Assessing transmission routes
Guest Box 14: Richard Shine and Lee Ann Rollins, Rapid evolution of introduced cane toads
15 Exploited Populations
15.1 Loss of genetic variation
15.2 Unnatural selection
15.3 Spatial structure
15.4 Effects of releases
15.4.1 Genetic effects of releases
15.4.2 Effects on species and ecosystem diversity
15.4.3 Monitoring large-scale releases
15.5 Management and recovery of exploited populations
15.5.1 Loss of genetic variation
15.5.2 Unnatural selection
15.5.3 Subdivision
15.5.4 Protected areas
Guest Box 15: Paolo Momigliano and Juha Merilä, Baltic Sea flounder: Cryptic species, undetected st
16 Climate Change
16.1 Predictions and uncertainties of future climates
16.2 Phenotypic plasticity
16.3 Epigenetic effects
16.4 Adaptation to climate change
16.4.1 Theoretical predictions of capacity for adaptation
16.4.2 Phenotypic approaches for detecting adaptation to climate change
16.4.3 Genomic approaches for predicting adaptation to climate change
16.5 Species range shifts
16.5.1 Modeling species distribution
16.5.2 Observed species range shifts
16.6 Extirpation and extinction
16.7 Management in the face of climate change
16.7.1 Assisted migration
16.7.2 Ex situ conservation
Guest Box 16: Rachael A. Bay, Genomic prediction of coral adaptation to warming
Part IV Conservation and Management
17 Inbreeding Depression
17.1 Inbreeding
17.1.1 The pedigree inbreeding coefficient
17.1.2 Expected versus realized proportion of the genome IBD
17.2 Estimation of F with molecular markers
17.2.1 Using unmapped loci to estimate F
17.2.2 Using mapped loci to estimate F
17.3 Causes of inbreeding depression
17.4 Detection and measurement of inbreeding depression
17.4.1 Lethal equivalents
17.4.2 Estimates of inbreeding depression
17.4.3 Estimates of inbreeding depression with marker-based estimates of F
17.4.4 Founder-specific inbreeding effects
17.4.5 Are there species without inbreeding depression?
17.5 Genetic load and purging
17.5.1 Effectiveness of purging
17.5.2 Why is purging not more effective?
17.5.3 Evidence for selection against homozygosity in inbred individuals
17.6 Inbreeding depression and conservation
Guest Box 17: Marty Kardos, The genomics of inbreeding depression in Scandinavian wolves
18 Demography and Extinction
18.1 Estimation of population size
18.1.1 One-sample
18.1.2 Two–sample: Capture–mark–recapture
18.1.3 Other methods for estimating census population size
18.2 Inbreeding depression and extinction
18.2.1 Evidence that inbreeding depression affects population dynamics
18.2.2 Are small populations doomed?
18.3 Loss of phenotypic variation
18.3.1 Life history variation
18.3.2 Mating types and sex determination
18.3.3 Phenotypic plasticity
18.4 Loss of evolutionary potential
18.5 Mitochondrial DNA
18.6 Mutational meltdown
18.7 Long-term persistence
18.8 The 50/500 rule
18.9 Population viability analysis
18.9.1 Incorporation of inbreeding depression into PVA
18.9.2 Incorporation of evolutionary potential into PVA
18.9.3 What is a viable population?
18.9.4 Are plants different?
18.9.5 Beyond viability
18.9.6 Complex models: Multiple species and environmental interactions
Guest Box 18: Lukas F. Keller and Iris Biebach, Inbreeding depression reduces population growth rate
19 Population Connectivity
19.1 Metapopulations
19.1.1 Genetic variation in metapopulations
19.1.2 Effective size of a metapopulation
19.2 Landscape genetics
19.2.1 Landscape connectivity and complex models
19.2.2 Corridor mapping
19.2.3 Neutral landscape genomics
19.2.4 Adaptive landscape genomics
19.3 Genetic effects of habitat fragmentation
19.4 Genetic versus demographic connectivity
19.5 Genetic rescue
19.5.1 Evidence for genetic rescue
19.5.2 Call for paradigm shift in use of genetic rescue
19.5.3 Genomics and genetic rescue
19.6 Long-term viability of metapopulations
Guest Box 19: Kyle D. Gustafson and Holly B. Ernest, The eroding genomes of fragmented urban puma p
20 Conservation Units
20.1 What are we trying to protect?
20.2 Systematics and taxonomy
20.3 Phylogeny reconstruction
20.3.1 Methods
20.3.2 Gene trees and species trees
20.4 Genetic relationships within species
20.4.1 Population-based approaches
20.4.2 Individual-based approaches
20.4.3 Phylogeography
20.5 Units of conservation
20.5.1 Species
20.5.2 Evolutionarily significant units
20.5.3 Management units
20.6 Integrating genetic, phenotypic, and environmental information
20.6.1 Adaptive genetic variation
20.7 Communities
Guest Box 20: Kenneth K. Askelson, Armando Geraldes, and Darren Irwin, Using genomics to reveal cons
21 Conservation Breeding and Restoration
21.1 The role of conservation breeding
21.1.1 When is conservation breeding an appropriate tool for conservation?
21.1.2 Priorities for conservation breeding
21.1.3 Potential dangers of captive propagation
21.2 Reproductive technologies and genome banking
21.3 Founding populations for conservation breeding programs
21.3.1 Source populations
21.3.2 Admixed founding populations
21.3.3 Number of founder individuals
21.4 Genetic drift in captive populations
21.4.1 Minimizing genetic drift
21.4.2 Accumulation of deleterious alleles
21.4.3 Inbreeding or genetic drift?
21.5 Natural selection and adaptation to captivity
21.5.1 Adaptation to captivity
21.5.2 Minimizing adaptation to captivity
21.5.3 Interaction of genetic drift and natural selection
21.6 Genetic management of conservation breeding programs
21.6.1 Pedigreed populations
21.6.2 Nonpedigreed populations
21.7 Supportive breeding
21.7.1 Genetic drift and supportive breeding
21.7.2 Natural selection and supportive breeding
21.8 Reintroductions and translocations
21.8.1 Reintroduction of animals
21.8.2 Restoration of plant communities
Guest Box 21: Robert H. Robichaux, Genetic management and reintroduction of Hawaiian silverswords
22 Genetic Identification
22.1 Species identification
22.1.1 DNA barcoding
22.1.2 DNA metabarcoding and metagenomics
22.1.3 Diet analysis
22.1.4 Environmental DNA
22.1.5 Forensic genetics
22.2 Individual identification
22.2.1 Probability of identity
22.2.2 Match probability
22.3 Parentage and relatedness
22.3.1 Parentage
22.3.2 Mating systems and dispersal
22.3.3 Relatedness
22.4 Population assignment and composition analysis
22.4.1 Assignment of individuals
22.4.2 Assignment of groups
22.4.3 Population composition analysis
Guest Box 22: Eleanor E. Dormontt and Andrew J. Lowe, Tracking illegal logging using genomics
23 Genetic Monitoring
23.1 Species presence
23.2 Population abundance
23.3 Genetic variation
23.3.1 Changes in genetic variation in declining populations
23.3.2 Changes in genetic variation in response to environmental perturbations
23.3.3 Changes in genetic variation in response to management actions
23.3.4 Meta-analyses of changes in genetic variation
23.4 Effective population size
23.4.1 Estimating effective population size at multiple time points
23.4.2 Inferring changes in effective population size from contemporary samples
23.5 Population subdivision and gene flow
23.6 Adaptive variation
23.7 Integrative genetic monitoring and the future
Guest Box 23: Antoinette Kotzé and J. Paul Grobler, African mammal conservation benefiting from gen
24 Conservation Genetics in Practice
24.1 Basic and applied science
24.2 The role of science in the development of policy
24.2.1 The best available science
24.2.2 Advice versus advocacy
24.3 Integrating genetic data into conservation strategy
24.3.1 The conservation genetics gap
24.3.2 What drives the gap and helps it persist?
24.3.3 Bridging the gap
24.3.4 Could genomics widen the gap?
24.3.5 The genetics gap within conservation science
24.4 How do I become a conservation geneticist?
24.4.1 What is a conservation geneticist?
24.4.2 Diverse skill sets
24.4.3 Communication and collaboration
24.5 The future
Guest Box 24: Michael K. Schwartz, Making genetics applicable to managers
Glossary
Appendix Probability, Statistics, and Coding
A1 Paradigms
A2 Probability
A2.1 Joint and conditional probabilities
A2.2 Odds ratios and LOD scores
A3 Statistical measures and distributions
A3.1 Types of statistical descriptors or tests
A3.2 Measures of location and dispersion
A3.3 Probability distributions
A4 Frequentist hypothesis testing, statistical errors, and power
A4.1 One- versus two-tailed tests
A4.2 Statistical power
A4.3 Problems with P-values
A5 Maximum likelihood
A6 Bayesian approaches and Markov chain Monte Carlo
A6.1 Markov chain Monte Carlo (MCMC)
A7 Approximate Bayesian Computation (ABC)
A8 Parameter estimation, accuracy, and precision
A9 Performance evaluation
A10 The coalescent and genealogical information
A11 Bioinformatics, Linux, and coding
A12 Filtering and data quality
A13 Why simulations?
Guest Box A: Mark A. Beaumont and Jo Howard-McCombe, A testable model-based perspective for conserva
References
Index