Population Genomics: Wildlife

Preface
Contents
List of Contributors
Part I: Introduction
Wildlife Population Genomics: Applications and Approaches
1 Introduction
2 Addressing Research Questions in Wildlife Biology
2.1 Population Genetics Versus Genomics in Wildlife
2.2 Populations, Demography, and Neutral Processes
2.3 Population Structure and Connectivity
2.4 Hybridization
2.5 Adaptive Variation
2.6 Deleterious Variation and Inbreeding Depression
2.7 Specific Threats and Adaptive Potential
3 Applications in Genetic Management and Conservation of Wildlife
3.1 Delineating Population Units for Management
3.2 Monitoring
3.3 Genetic Management of Wild Populations
3.4 Captive Breeding
3.5 Improving Connections Between Research and Applications
4 Approaches and Resources
4.1 Options and Challenges for Wildlife
4.2 Sampling
4.3 Library Preparation and Sequencing
4.4 Resources
4.5 Data Analysis
5 Future Prospects in Wildlife Population Genomics
5.1 Metagenomics and eDNA
5.2 Population Epigenomics
5.3 Population Transcriptomics
6 Conclusions
References
Part II: Wildlife Sampling and Genomics Technologies
Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies
1 Introduction
2 Non-invasive, Archival, and Environmental Sources of DNA for Wildlife Genetics
3 New Sequencing and SNP Genotyping Technologies
4 Amplicon Sequencing
5 SNP Genotyping Platforms
6 DNA Capture
7 Mitogenome Sequencing
8 RADseq
9 Whole-Genome Sequencing
10 Metagenome Sequencing, Metabarcoding, and Metatranscriptomics
11 Choosing a Method
References
Environmental Population Genomics: Challenges and Opportunities
1 What is eDNA?
2 Environmental Genomic Information for Insights Across Scales of Biodiversity
3 Individual Genotypes from eDNA Samples
4 Population and Community Genomics from eDNA Samples
5 Environmental RNA for Increased Insights into Population and Community Genomics
6 Conclusion
References
Surmounting the Large-Genome ``Problem´´ for Genomic Data Generation in Salamanders
1 Introduction
2 Genomic Data Generation in Salamanders
3 Restriction Site-Associated DNA Sequencing (and Related Approaches)
3.1 General Overview
3.2 Salamander Genome Limitations
3.3 Examples in Salamanders
3.4 Guidelines for RAD-Based Sequencing in Salamanders
4 Transcriptomics and RNAseq
4.1 General Overview
4.2 Salamander Genome Limitations
4.3 Examples in Salamanders
4.4 Guidelines for Applications in Salamanders
5 Sequence Capture and Enrichment
5.1 General Overview
5.2 Salamander Genome Limitations
5.3 Examples in Salamanders
5.4 Guidelines for Applications in Salamanders
6 Parallel Tagged Amplicon Sequencing
6.1 General Overview
6.2 Salamander Genome Limitations
6.3 Examples in Salamanders
6.4 Guidelines for Applications in Salamanders
7 Other Approaches
8 Conclusions and Future Perspectives
References
Part III: Wildlife Populations: Ecology, Evolution and Adaptation
Landscape Genomics for Wildlife Research
1 Adaptive Landscape Genomics and Wildlife Research
2 Data Production for Adaptive Landscape Genomics Research in Wildlife
2.1 Landscape Sampling Designs
2.2 Genomic Data Production
2.3 Environmental Data Production
2.4 Data Analysis with Genotype-Environment Associations
3 Applications and Potential of Adaptive Landscape Genomics in Wildlife Research
3.1 Current Applications of Adaptive Landscape Genomics in Wildlife Research
3.1.1 What Are the Ecological and Evolutionary Processes Underlying Spatial Patterns of Neutral and Adaptive Genetic Variation?
3.1.2 What Are the Relative Roles of Genetic Drift and Natural Selection in Structuring Genetic Variation in Small Populations?
3.1.3 How Can Knowledge of Adaptive Differentiation Inform the Delineation of Conservation Units?
3.1.4 How Can Adaptive Landscape Genomics Inform the Design of Conservation Monitoring Programs?
3.1.5 What Are the Genomic Implications of Range Expansion Under Climate Change?
3.1.6 Can We Predict the Spatial Distribution of Adaptive Genetic Variation Under Changing Climates?
3.2 Underutilized Applications of Adaptive Landscape Genomics in Wildlife Research
3.2.1 Using Adaptive Landscape Genomics to Inform Genetic Rescue
3.2.2 Using Adaptive Landscape Genomics to Inform Assisted Gene Flow
3.2.3 Using Adaptive Landscape Genomics to Inform Site Prioritization to Maximize Evolutionary Potential
3.2.4 Using Museum Collections to Better Understand Changes in Adaptive Variation over Time
3.2.5 Using Adaptive Landscape Genomics to Inform the Management of Hybridization
4 Future Research Avenues in Wildlife Landscape Genomics: Improving and Moving Beyond Genotype-Environment Associations
4.1 Integrating Phenotypic Data Through Environmentally Stratified GWAS and GEA
4.2 The Value of Experimental Manipulations in Informing Assessments of Adaptation
4.3 Epigenetics as a Mechanism for Rapid Adaptive Responses
4.4 The Importance of Differential Gene Expression Across Landscapes
5 Conclusions
References
Population Genomics of Ungulates
1 Introduction to Ungulates
2 A Brief History of Whole-Genome Assemblies in Ungulates
3 The Importance of Domestic Genomes
4 Alternatives to Whole-Genome Sequencing
5 From Phylogenomics to Population Demography
6 Adaptive Divergence in Ungulates
7 Future Perspectives
8 Summary
References
Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing
1 Introduction
2 Opportunities for Advancing Understanding of Amphibian Evolution, Ecology, and Behavior with Genomics
2.1 Phylogenomics
2.2 Genomic Data for Phylogeographic Inference
2.3 Sex Chromosome Evolution
2.4 Population Structure and Demography
2.5 Local Adaptation
2.6 Mating Systems and Sexual Selection
3 Opportunities for Improving Amphibian Conservation with Genomics
3.1 Hybridization
3.2 Disease Evolution and Ecology: Lessons from Chytridiomycosis
3.3 Captive Breeding
4 Challenges and Solutions for Genomic Studies of Amphibians
4.1 Few Reference Genomes
4.2 The Genome Size Problem
4.3 High Population Structure
5 Recommendations
5.1 Maximizing the Potential of Genomics to Transform Amphibian Research
5.2 Getting Started
References
Population Genomics of Birds: Evolutionary History and Conservation
1 Introduction
2 The Architecture of Avian Genomes
2.1 Avian Genome Size and Arrangement
2.2 Avian Chromosomes
2.3 The Recombination Landscape
2.4 Structural Rearrangements Associated with Complex Traits
3 Linking Genotype to Phenotype in Avian Genomes
3.1 Candidate Genes Versus Genome-Wide Associations
3.2 Genomics of Feather Coloration
3.3 Genes Underlying Morphometric Differences
3.4 Genes for Avian Migration
4 Phylogenomics and Demographic Histories of Birds
4.1 Biogeographic Inferences in the Era of Phylogenomics
4.2 Inferring Population Demographic Histories from Genomic Data
4.3 Timing of Divergence and Gene Flow Using Genomic Data
4.4 Understanding Deep Patterns of Divergence in the Avian Tree
5 Detecting Signals of Divergence and Hybridization
5.1 Hybridization in Recently Diverged Taxa
5.2 Hybrid Speciation
6 Informing Conservation Using Genomic Data
6.1 Population Structure and Delineation
6.2 Genomic Insights into Inbreeding and Population Decline
6.3 Assessing Population Response to Climate Change
7 Concluding Remarks
References
Population Genomics Provides Key Insights into Admixture, Speciation, and Evolution of Closely Related Ducks of the Mallard Co...
1 Introduction
1.1 Background
1.2 History of the Mallard Complex
1.3 Mitochondrial DNA and the Onset of Fear of Hybrid Swarms
1.4 Hybridization Versus Gene Flow
2 How Population Genomics Has Increased Our Understanding of the Mallard Complex and Its Implications for Conservation
2.1 The History of the New World Mallard Complex: How the Phenotype Lies and What Genetics Has Revealed
2.2 The Curious Case of the Hawaiian Duck: Conservation Implications When a Hybrid Species Meets Its Feral Parent
2.3 The Genetic and Conservation Consequences of Feral Mallards
2.4 Attaining a Historical Perspective to Reconstruct Evolutionary Histories
3 Integrating Population Genomics Results into Wildlife Management
4 Future Perspectives
5 Conclusions
References
Part IV: Challenges Facing Wildlife Populations
Population Genomics and Wildlife Adaptation in the Face of Climate Change
1 Introduction
2 Genomics
3 How to Study Adaptations to Climate Change?
3.1 Phenotypes
3.2 Environmental Association Studies
3.3 Phenology and Range Shifts
3.4 Cline Studies
3.5 Natural and Anthropogenic Induced ``Experiments´´
3.6 Common Garden Experiments
3.7 Candidate Genes
3.8 Expression Studies
3.9 Historical Reconstructions
4 Relevant Case Studies
4.1 Reviews
4.2 Fruit Flies
4.3 Fish
4.4 Amphibians
4.5 Li zards
4.6 Birds
4.7 Mammals
5 Concluding Remarks
References
Applications of Population Genomics for Understanding and Mitigating Wildlife Disease
1 Introduction
2 Case Studies
2.1 Colony Collapse Disorder
2.2 Chytridiomycosis
2.3 White-Nose Syndrome
2.4 Feline Immunodeficiency Virus
2.5 Tasmanian Devil Facial Tumor Disease
3 Future Directions
References
Population Genomics of Wildlife Cancer
1 Introduction: Cancer in Wildlife
2 Causes of Cancer
2.1 Environmental Conditions
2.2 Viruses and Other Pathogens
2.3 Transmissible Cancers
2.4 Hereditary Factors
3 Genomics and Evolution of Cancer in Wildlife
3.1 Evolution of Cancer Resistance
3.2 Genetics of Population Susceptibility
3.3 Population Genomics Studies of Wildlife Cancer
4 Tasmanian Devils and DFTD
4.1 An Epidemic Transmissible Cancer
4.2 Devil Genomics
4.3 Tumor Genomics
4.4 Conservation of Tasmanian Devils
5 Future Directions in Population Genomics of Wildlife Cancer
5.1 Monitoring and Population Management
5.2 Captive Breeding Programs
5.3 Interventions in Wildlife Cancer
5.4 Advances in Wildlife Cancer Genomics Research
6 Conclusions
References
Part V: Wildlife Conservation and Management
Population Genomics for the Management of Wild Vertebrate Populations
1 Introduction and General Overview
2 Applications of Population Genomics in Fish and Wildlife Management
2.1 Increased Resolution
2.1.1 Introgression/Hybridization
2.1.2 Genetic Rescue
2.1.3 Neutral Population Substructure: Population/Stock Genetic Differentiation and Conservation Units
2.2 Ecological Adaptation and Disease Management
2.2.1 Adaptive Population Substructure
2.2.2 Environmental Adaptation and Tolerances
2.2.3 Disease Management
3 Future Perspectives
4 Conclusions
References
Genomics for Genetic Rescue
1 Introduction
1.1 Definitions
1.2 Genetic Rescue in Conservation and Management
1.3 Outline of the Chapter
2 Evaluating the Potential Benefits of Genetic Rescue
2.1 Inbreeding and Inbreeding Depression
2.2 Estimating Inbreeding with a Reference Genome
2.3 Estimating Inbreeding Without a Reference Genome
2.4 Inbreeding and Fitness
2.5 Quantifying Functional Variation
3 Predicting Outbreeding Depression with Genomics
3.1 Resolving Taxonomic Uncertainty
3.2 Determining Potential for Fixed Chromosomal Differences
3.3 Estimating Time and Number of Generations Since Most Recent Gene Flow
3.4 Evaluating the Extent of Adaptive Differentiation
4 Monitoring and Mechanisms
4.1 Monitoring the Outcome of Genetic Rescue
4.2 Determining the Genomic Mechanisms of Genetic Rescue
5 Future Perspectives and Conclusions
5.1 Proposed Guidelines for Using Genomics to Improve Genetic Rescue
5.2 Conclusions
References
Ex Situ Wildlife Conservation in the Age of Population Genomics
1 Introduction
2 Refining Breeding Decisions
3 Assessing Lineage Integrity and Quantifying the Extent of Hybridization/Introgression
4 Minimizing Adaptation to Captive Environment
5 Informing Interactive In Situ/Ex Situ Conservation Strategies
6 Conclusions
References
Population Genomics Advances and Opportunities in Conservation of Kiwi (Apteryx spp.)
1 Introduction
1.1 Evolutionary and Ecological Significance of Kiwi
1.2 Kiwi Are Highly Threatened and Intensively Managed
2 Review of Relevant Genomic Research
2.1 Genomic Studies of Paleognaths
2.2 Genomic Studies of Kiwi
3 Analysis of Genes Under Selection in Kiwi
3.1 Leveraging Publicly Available Data to Study Evolution in Kiwi
3.2 Genes Under Selection in the Kiwi Lineage
3.3 Genes Under Selection in Brown and Spotted Kiwi Clades
3.4 What Makes a Kiwi a Kiwi?
4 Conservation Impacts and Research Needed
4.1 Can Genomics Enhance Conservation of Kiwi?
4.2 Challenges and Opportunities
References
The Transformative Impact of Genomics on Sage-Grouse Conservation and Management
1 Introduction
1.1 Background
1.2 Conservation Status of Sage-Grouse
1.3 Sagebrush Specialist
1.4 Mating System
1.5 Why Sage-Grouse Are Good Candidates for Genetic and Genomic Research
2 How Traditional Genetics and the Shift to Genomics Help Conserve Sage-Grouse
2.1 Delineating Units for Conservation and Management
2.2 Population Connectivity and the Factors Influencing Gene Flow
2.3 Managing Genetic Diversity
3 Future Directions in Sage-Grouse Genomics
3.1 Identifying and Conserving Adaptive Genetic Variation
3.2 Exploring the Impacts of Low Genetic Diversity
3.3 Document and Better Understand Physiological Response to Stress
3.4 Incorporate Genomic Data into Comprehensive Monitoring Programs
4 Conclusion
References
Index