Introduction to Conservation Genetics, 2nd Edition
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Contents
Preface to the second edition
Preface
Copyright acknowledgments
Chapter 1 Introduction
The ‘sixth extinction’
Why conserve biodiversity?
Endangered and extinct species
What is an endangered species?
What causes extinctions?
Recognition of genetic factors in conservation biology
What is conservation genetics?
Examples of the use of genetics to aid conservation
Genetic management of threatened species
Methodology in conservation genetics
Sources of information
Summary
General bibliography
Problems
Practical exercises: categorizing endangerment of species
Chapter 2 Genetics and extinction
Genetics and the fate of endangered species
Relationship between inbreeding and extinction
Relationship between loss of genetic diversity and extinction
Summary
Further reading
Software
Problems
Practical exercises: computer projections
Section I Evolutionary genetics of natural populations
Chapter 3 Genetic diversity
Importance of genetic diversity
What is genetic diversity?
Measuring genetic diversity
Extent of genetic diversity
Low genetic diversity in threatened species and bottlenecked
populations
Variation over space and time
Genetic differences among species
Summary
Further reading
Software
Problems
Practical exercise: Measuring genetic diversity using microsatellites
Chapter 4 Characterizing genetic diversity: single loci
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
Software
Problems
Chapter 5 Characterizing genetic diversity: quantitative variation
Importance of quantitative characters
Properties of quantitative characters
Basis of quantitative genetic variation
Methods for detecting quantitative genetic variation
Partitioning genetic and environmental variation
Partitioning of quantitative genetic variation
Evolutionary potential, additive variation and heritability
Dominance variance (VD)
Measuring genetic changes over time
Correlations between molecular and quantitative genetic variation
Genotype × environment interaction
Summary
Further reading
Software
Problems
Chapter 6 Evolutionary impacts of natural selection in large populations
The need to evolve
Factors controlling the evolution of populations
Selection
Selection on quantitative characters
Summary
Further reading
Software
Problems
Practical exercises: computer simulations
Chapter 7 Evolutionary impacts of mutation and migration, and their
interactions with selection in large populations
Factors controlling the evolution of populations
Importance of mutation and migration and their interactions with
selection in conservation
Origin and regeneration of genetic diversity
Mutation
Mutation–selection balance and the mutation load
Migration
Migration–selection equilibria and clines
Summary
Further reading
Software
Problems
Chapter 8 Genetic consequences of small population sizes
Importance of small populations in conservation biology
Chance effects
Fixation
Effects of population bottlenecks
Inbreeding
Measuring population size
Selection in small populations
Mutation–selection equilibrium in small populations
Computer simulation
Summary
Further reading
Software
Problems
Practical exercises: computer simulations
Chapter 9 Maintenance of genetic diversity
Conservation of genetic diversity
Fate of different classes of mutations
Maintenance of genetic diversity in large populations
Neutral mutations under random genetic drift
Selection intensities vary among characters
Balancing selection
Reproductive fitness
Maintenance of genetic diversity in small populations
Summary
Further reading
Software
Problems
Practical exercises: Computer simulations
Chapter 10 Population genomics
Genome sequencing and population genomics
cDNA expression microarrays
What conservation benefits might be gained from genomics?
Genome organization
Insights into evolution from genomics
Insights from gene expression studies
Prospects for individual-locus genetic management
Summary
Further reading
Software
Problems
Section II Effects of population size reduction
Chapter 11 Loss of genetic diversity in small populations
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
Gene trees and coalescence
Summary
Further reading
Software
Problems
Practical exercises: computer simulations
Chapter 12 Inbreeding
What is inbreeding?
Conservation concerns with inbreeding
Measuring inbreeding: inbreeding coefficient (F)
Genetic consequences of inbreeding
Inbreeding in small random mating populations
Pedigrees
Regular systems of inbreeding
Mutation–selection balance with inbreeding
Inbreeding in polyploids
Relationships between inbreeding, heterozygosity, genetic diversity
and population size
Summary
Further reading
Software
Problems
Chapter 13 Inbreeding depression
Inbreeding depression in naturally outbreeding species
Inbreeding depression in the wild
Inbreeding depression due to small population size
Inbreeding, population viability and extinction
Characteristics of inbreeding depression
Inbreeding depression in species that regularly inbreed
Genetic basis of inbreeding depression
Purging
Detecting and measuring inbreeding depression
Genetic rescue
Summary
Further reading
Software
Problems
Chapter 14 Population fragmentation
Habitat fragmentation
Population fragmentation
Population structure
Completely isolated population fragments
Measuring population fragmentation: F statistics
Gene flow among population fragments
Measuring gene flow
Landscape genetics
Impacts of different population structures on reproductive fitness
Summary
Further reading
Software
Problems
Chapter 15 Genetically viable populations
Shortage of space for threatened species
How large?
Retaining reproductive fitness
Retaining evolutionary potential
How large are threatened populations?
Long-term retention of single-locus genetic diversity
Time to regenerate genetic diversity
Avoiding accumulation of new deleterious mutations
Genetic goals in the management of wild populations
Genetic goals in management of captive populations: a compromise
The fallacy of small surviving populations
Summary
Further reading
Software
Problems
Section III From theory to practice
Chapter 16 Resolving taxonomic uncertainties and defining management
units
Importance of accurate taxonomy in conservation biology
What is a species?
Sub-species
How do species arise?
Delineating sympatric species
Delineating allopatric species
Genetic distance
Constructing phylogenetic trees
Outbreeding depression
Defining management units within species
Summary
Further reading
Software
Problems
Practical exercise: building a phylogenetic tree
Chapter 17 Genetic management of wild populations
Genetic issues in wild populations
Increasing population size
Diagnosing genetic problems
Genetic rescue of small inbred populations by outcrossing
Genetic management of fragmented populations
Genetic issues in reserve design
Impacts of harvesting
Genetic management of species that are not outbreeding diploids
Summary
Further reading
Software
Problems
Chapter 18 Genetic issues in introduced and invasive species
Impact of invasive species on biodiversity
Phases in establishment of invasive species
Genetic issues in invasion biology
Evolution of native species in response to introduced species
Control of invasive species
Introgression and hybridization
Summary
Further reading
Software
Problems
Chapter 19 Genetic management of captive populations
Why captive breed?
Stages in captive breeding and reintroduction
Founding captive populations
Growth of captive populations
Genetic management during the maintenance phase
Captive management of groups
Ex situ conservation of plants
Reproductive technology and genome resource banks
Managing inherited diseases in endangered species
Summary
Further reading
Software
Problems
Chapter 20 Genetic management for reintroduction
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
Software
Problems
Chapter 21 Use of molecular genetics in forensics and to understand
species biology
Forensics: detecting illegal hunting and collecting
Understanding a species’ biology is critical to its conservation
Population size and demographic history
Gene flow and population structure
Reintroduction and translocation
Breeding systems, parentage, founder relationships and sexing
Disease
Diet
Aging and fitness from telomere lengths
Dating using molecular clocks
Summary
Further reading
Software
Problems
Chapter 22 The broader context: population viability analysis (PVA)
What causes endangerment and extinction?
Predicting extinction probabilities: population viability analysis (PVA)
Genetics and PVA
Insights into the causes of extinction from PVA
Recovering threatened populations
Using PVA to evaluate management options: case studies
How useful are the predictions of PVA?
Lessons learned
Minimum viable population sizes (MVP)
Summary
Further reading
Software
Problems
Practical exercises: population viability analyses
Take home messages from this book
Revision problems
Glossary
References
Index
Preface to the second edition
Much has changed since we began the first edition of Introduction to
Conservation Genetics 10 years ago. The human population has exceeded 6.6
billion, with consequent increased pressure on the natural world. The number
of threatened species has increased by 55% to 16 306. Over the same time,
global climate change has moved from being a somewhat abstract concern to
perhaps the pre-eminent global political focus. The impact of climate change
is now clearly discernable on the distribution and behaviour of many species.
Sea-level increases are impacting on the viability of low-lying nations and the
biota they contain. On a smaller scale, three-quarters of species of bears are
now considered to be in danger and the Yangtze River dolphin (referred to in
the first edition) has become extinct. Further, invasive species are having an
ever more important impact on biodiversity, especially with rapidly
increasing trade.
While our objectives in preparing this book are fundamentally those that
motivated the first edition, accelerating human impacts bring into even
sharper focus the need to integrate genetics into the broader conservation
effort.
Preface
The World Conservation Union (IUCN), the leading international
conservation body, recognizes the crucial need to conserve genetic diversity
as one of the three fundamental levels of biodiversity. This book provides the
conceptual background for understanding the role of genetic factors in
extinction and managing to avoid such extinctions.
Conservation genetics is the use of genetics to aid in the conservation of
populations or species
Conservation genetics encompasses:
genetic management of small populations to maximize retention of
genetic diversity and minimize inbreeding,
resolution of taxonomic uncertainties and delineation of management
units, and
the use of molecular genetic analyses in forensics and to understand
species’ biology.
Purpose of the book
We have endeavoured to make this book appealing to a wide readership.
However it is primarily directed towards those encountering the discipline for
the first time, either through formal coursework or by self-instruction.
