Conservation and the genomics of populations

cover
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-wallabies and implications for conservation
	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 transmissible cancer
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 critically endangered kākāpō
	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 conservation
	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 shifts in the green anole lizard
	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 with genomic data
	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 populations facing climate warming
	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 Australian dingoes
	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 species?
		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 stock structure, and the decline of a local fishery
	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 rates in reintroduced alpine ibex
	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 populations in California
	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 conservation units: The case of Haida Gwaii goshawks
	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 genetic monitoring: The Cape mountain zebra in South Africa
	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 conservation genetics
References
Index