Introduction to Conservation Genetics

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Table of Contents

Preface

Acknowledgments

2. Genetics and extinction (back to top)

• Genetics and the fate of endangered species
• Relationship between inbreeding and extinction
• Inbreeding and extinction in the wild
• Relationship between loss of genetic diversity and extinction
• Summary
• Further reading
• Problems

• Practical Exercises: Computer projections

SECTION I EVOLUTIONARY GENETICS OF NATURAL POPULATIONS

3. Genetic diversity (back to top)

4. Characterizing genetic diversity: single loci (back to top)

• Describing genetic diversity
• Frequencies of alleles and genotypes
• Hardy-Weinberg equilibrium
• Expected heterozygosity
• Deviations from Hardy-Weinberg equilibrium
• Extensions of the Hardy-Weinberg equilibrium
• More than one locus - linkage disequilibrium
• Summary
• Further reading
• Problems

5. Characterizing genetic diversity: quantitative variation (back to top)

• Importance of quantitative characters
• Properties of quantitative characters
• Basis of quantitative genetic variation
• Methods for detecting quantitative genetic variation
• Partitioning genetic and environmental variation
• Genotype x environment interaction
• The need for contemporary comparisons and control populations
• Partitioning of quantitative genetic variation
• Evolutionary potential and heritability
• Susceptibility to inbreeding depression
• Correlations between molecular and quantitative genetic variation
• Organisation of quantitative genetic variation
• Summary
• Further reading
• Problems

6. Evolution in large populations. I. Natural selection and adaptation (back to top)

• The need to evolve
• Factors controlling the evolution of populations
• Selection
• Selection on quantitative characters
• Directional selection
• Stabilising selection
• Disruptive selection
• Summary
• Further reading
• Problems
• Practical Exercises: Computer simulations

7. Evolution in large populations. II. Mutation, migration and their interactions with selection (back to top)

• Factors controlling the evolution of populations
of mutation, migration and their interactions with selection in conservation
• Origin and regeneration of genetic diversity
• Mutation
• Selective value of mutations
• Mutation-selection balance and the mutation load
• Migration
• Migration-selection equilibria and clines
• Summary
• Further reading
• Problems

8. Evolution in small populations (back to top)

• Importance of small populations in conservation biology
• Impact of small population size: chance effects
• Inbreeding
• Measuring population size
• Selection in small populations
• Mutation in small populations
• Mutation-selection equilibrium in small populations
• Computer simulation
• Summary
• Further reading
• Problems
• Practical Exercises: Computer simulations

9. Maintenance of genetic diversity (back to top)

• Conservation of genetic diversity
• Fate of different classes of mutations
• Maintenance of genetic diversity in large populations
• Neutral mutation under random genetic drift
• Selection intensities vary among characters
• Balancing selection
• Maintenance of genetic diversity in small populations
• Summary
• Further reading
• Problems

Practical Exercises: Computer simulations

SECTION II EFFECTS OF POPULATION SIZE REDUCTION

10. Loss of genetic diversity in small populations (back to top)

• Changes in genetic diversity over time
• Relationship between loss of genetic diversity and reduced fitness
• Effects of sustained population size restrictions on genetic diversity
• Relationship between population size and genetic diversity in wild populations
• Effective population size
• Measuring effective population size
• Summary
• Further reading
• Problems
• Practical Exercises: Computer simulations

11. Inbreeding (back to top)

• What is inbreeding?
• Conservation concerns with inbreeding
• Inbreeding coefficient (F)
• Genetic consequences of inbreeding
• Inbreeding in small populations
• Pedigrees
• Breeding systems in nature
• Regular systems of inbreeding
• Mutation-selection balance with inbreeding
• Inbreeding in polyploids
• Relationship between inbreeding, heterozygosity, genetic diversity and population size
• Summary
• Further reading
• Problems

12. Inbreeding depression (back to top)

• Inbreeding depression in naturally outbreeding species
• Inbreeding depression in the wild
• Inbreeding depression due to small population size
• Inbreeding and extinction
• Characteristics of inbreeding depression
• Genetic basis of inbreeding depression
• Purging
• Detecting and measuring inbreeding depression
• Inbreeding and population viability
• Recovering from inbreeding depression
• Summary
• Further reading
• Problems

13. Population fragmentation (back to top)

• Habitat fragmentation
• Population fragmentation
• Population structure
• Completely isolated population fragments
• Measuring population fragmentation: F statistics
• Gene flow among population fragments
• Measuring gene flow
• Impacts of different population structures on reproductive fitness
• Summary
• Further reading
• Problems

14. Genetically viable populations (back to top)

• Shortage of space for threatened species
• How large?
• Retaining reproductive fitness
• Retaining evolutionary potential
• How large are threatened populations?
• What happens to species with N_e < 500?
• Retaining single locus diversity in the long-term
• Time to regenerate genetic diversity
• Avoiding accumulation of new deleterious mutations
• Genetic goals in management of wild populations
• Genetic goals in management of captive populations – a compromise
• The fallacy of small surviving populations
• Summary
• Further reading
• Problems

SECTION III FROM THEORY TO PRACTICE

15. Resolving taxonomic uncertainties and defining management units (back to top)

• Importance of accurate taxonomy in conservation biology
• What is a species?
• Sub-species
• Higher taxonomic categories
• How do species arise?
• Use of genetic markers in delineation of sympatric species
• Use of genetic markers in delineation of allopatric species
• Measuring differences between populations: genetic distance
• Constructing phylogenetic trees
• Outbreeding depression
• Defining management units within species
• Summary
• Further reading
• Problems
• Practical Exercise: Building a phylogenetic tree

16. Genetics and the management of wild populations (back to top)

• Genetic issues in wild populations
• Resolving taxonomy and management units
• Increasing population size
• Diagnosing genetic problems
• Recovering small inbred population with low genetic diversity
• Genetic management of fragmented populations
• Genetic issues in reserve design
• Introgression and hybridization
• Impacts of harvesting
• Genetic management of species that are not outbreeding diploids
• Summary
• Further reading
• Problems

17. Genetic management of captive populations (back to top)

• Why captive breed?
• Stages in captive breeding and reintroduction
• Founding captive populations
• Growth of captive populations
• Genetic management of captive populations
• Current genetic management of captive populations
• Captive management of groups
• Ex-situ conservation of plants
• Reproductive technology and genome resource banks
• Managing inherited diseases in endangered species
• Summary
• Further reading
• Problems

18. Genetic management for reintroduction (back to top)

• Reintroductions
• Genetic changes in captivity that affect reintroduction success
• Genetic adaptation to captivity
• Genetic management of reintroductions
• How successful are reintroductions?
• Supportive breeding
• Case studies in captive breeding and reintroduction
• Summary
• Further reading
• Problems

19. Use of molecular genetics in forensics and to understand species biology (back to top)

• Forensics: detecting illegal hunting and collecting
• An understanding species’ biology is critical to its conservation
• Gene trees and coalescence
• Population size and demographic history
• Gene flow and population structure
• Reintroduction
• Reproduction, parentage, founder relationships, and sexing
• Disease
• Diet
• Summary
• Further reading
• Problems

20. The broader context: Population Viability Analysis (PVA) (back to top)

• What causes endangerment and extinction?
• Predicting extinction probabilities: Population viability analysis (PVA)
• Recovering threatened populations
• How useful are the predictions of PVA?
• Lessons learned
• Minimum viable population sizes (MVP)
• Summary
• Further reading
• Problems
• Practical Exercises: Population Viability Analyses

Take home messages from this book

Revision Problems

Glossary

Answers to problems

References

Index

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