 |
Molecular ecology / by Joanna R. Freeland, Heather Kirk, Stephen Petersen. — 2nd ed. — Chichester : Wiley-Blackwell, c2011. – (58.181/F854/2nd ed.) |
Contents
Contents
Preface
Acknowledgements
1 Molecular Genetics in Ecology
What is molecular ecology?
The emergence of molecular ecology
Protein allozymes
Allozymes as genetic markers
An unlimited source of data
Mutation and recombination
Is genetic variation adaptive?
Polymerase chain reaction
Primers
Sources of DNA
Getting data from PCR
DNA sequencing
Second-generation sequencing
Third-generation sequencing
Quantitative PCR
Overview
Chapter summary
Useful websites and software
Further reading
Review questions
2 Molecular Markers in Ecology
Understanding molecular markers
Modes of inheritance
Nuclear versus organelle
Animal mitochondrial DNA
Plant mitochondrial DNA
Plastids， including chloroplast DNA
Haploid chromosomes
Identifying hybrids
Uniparental markers: A cautionary note
Molecular markers
Co-dominant markers
Allozymes
RFLPs
DNA sequences
SNPs
Microsateflites
Dominant markers
RAPDs
AFLPs
Overview
Chapter summary
Useful websites and software
Further reading
Online activities
Review questions
3 Genetic Analysis of Single Populations
Why study single populations?
What is a population?
Quantifying genetic diversity
Hardy-Weinberg equilibrium
Estimates of genetic diversity
Haploid diversity
Choice of marker
What influences genetic diversity?
Genetic drift
What is effective population size?
Quantifying census population size
Quantifying effective population size
Single-Sample Estimators
Temporal method
Demographic influences on Ne
Sex ratios
Variation in reproductive success
Fluctuating population size
Ne， genetic drift and genetic diversity
Population bottlenecks
Founder effects and invasive species
Natural selection
The major histocompatibility complex
Reproduction
Inbreeding
Polyploidy
Overview
Chapter summary
Useful websites and software
Further reading
Online activities
Review questions
4 Genetic Analysis of Multiple Populations
Why study multiple populations?
Quantifying population subdivision
Genetic distance
F-statistics
Interpreting FST
Non-a priori identification of populations
Quantifying gene flow
Direct methods
Indirect methods
Assignment tests
What influences gene flow?
Barriers to dispersal
Landscape genetics
Metapopulations
Interspecific interactions
Hybridization
Population differentiation: genetic drift and natural selection
Gene flow and genetic drift
Gene flow and local adaptation
Drift versus selection
Patterns of molecular evolution
Discordant genetic differentiation
Clinal variations in allele frequencies: FsT versus QsT
Overview
Chapter summary
Useful websites and software
Further reading
Online activities
Review questions
5 Studying Ecologically Important Traits: Ecogenomics， QTL Analysis， and Reverse Genetics
Studying ecologically important traits
cDNA libraries and ESTs
Microarrays
How do microarrays work?
Probes
Verifying differences in gene expression
Microarray applications
Variation within individuals
Variation between species
Sequence differences
Differences in gene expression
Microarrays and community ecology of microorganisms
Microorganism functions
Microarrays and genotyping
Connecting genotype to phenotype
Reverse genetics
QTL analysis
Linkage mapping
QTL mapping
QTL mapping of ecologically important traits
Overview
Chapter summary
Useful websites and software
Further reading
Review questions
6 Phylogeography
What is phylogeography?
Molecular markers in phylogeography
Organelle versus nuclear markers
Repetitive versus non-repetitive markers
Neutral versus adaptive markers
Molecular clocks
Bifurcating trees
The coalescent
Applying the coalescent
Networks
Nested Clade Phylogeographic analysis and statistical phylogeography 244
The distributions of genetic lineages
Subdivided populations
Dispersal and vicariance
Comparative phylogeography
Regional concordance
Continental concordance
European post-glacial recolonization routes
Dispersal and invasive species
Allele sharing between species
Lineage sorting
Hybrid zones
Overview
Chapter summary
Useful websites and software
Further reading
Online activities
Review questions
7 Behavioural Ecology
Why use molecules to study behaviour?
Mating systems
Parentage analysis
Extra-pair fertilizations
Who achieves EPFs?
Does environment influence EPFs?
Mate choice
Post-copulatory mate choice
Social breeding
Social insects
Manipulating sex ratios
Sex ratio conflicts
Sex-biased dispersal
Nuclear and mitochondrial markers
Relatedness
Fsx values
Assignment tests
Spatial autocorrelation
Concordant results
Predators and prey
Identifying prey
Predation and conservation
Overview
Chapter summary
Useful websites and software
Further reading
Online activities
Review questions
8 Conservation Genetics
The need for conservation
Taxonomy
Species concepts
DNA barcoding
Subspecies
Conservation units
Hybrids
Population size， genetic diversity and inbreeding
Inbreeding depression
Heterozygosity fitness correlations
Self-fertilization
Inbreeding avoidance
Outbreeding depression
Translocations
Genetic rescue
Source populations
Restoration genetics
Captive breeding
Maximizing genetic diversity
Captive inbreeding and outbreeding
Genetic diversity banks
Overview
Chapter summary
Useful websites and software
Further reading
Online activities
Review questions
Glossary
Answers to Review Questions
References
Index
