Contents

Preface ix

Acknowledgements xi

1 Molecular genetics in Ecology 1

What is molecular ecology? 1

The emergence of molecular ecology 2

Protein allozymes 4

An unlimited source of data 9

Mutation and recombination 10

Polymerase chain reaction 16

Sources of DNA 20

Getting data from PCR 22

Overview 26

Chapter summary 27

Useful websites and software 28

Further reading 28

Review questions 29

2 Molecular Markers in Ecology 31

Understanding molecular markers 31

Modes of inheritance 31

Nuclear versus organelle 32

Haploid chromosomes 37

Uniparental markers: a cautionary note 41

Molecular markers 43

Co-dominant markers 44

Dominant markers 53

Overview 57

Chapter summary 57

Useful websites and software 59

Further reading 60

Review questions 60

3 Genetic Analysis of Single Populations 63

Why study single populations? 63

What is a population? 63

Quantifying genetic diversity 67

Hardy-Weinberg equilibrium 67

Estimates of genetic diversity 72

Choice of marker 75

What influences genetic diversity? 77

Genetic drift 77

Population bottlenecks 89

Natural selection 94

Reproduction 98

Overview 103

Chapter summary 104

Useful websites and software 105

Further reading 105

Review questions 106

4 Genetic Analysis of Multiple Populations 109

Why study multiple populations? 109

Quantifying population subdivision 109

Genetic distance 110

F-Statistics 112

Quantifying gene flow 117

Direct methods 117

Indirect methods 120

Assignment tests 121

Gene flow discrepancies 123

What influences gene flow? 123

Dispersal ability 127

Barriers to dispersal 129

Reproduction 131

Fragmented habitats and metapopulations 133

Interspecific interactions 136

Population differentiation: genetic drift and natural selection 138

Gene flow and genetic drift 139

Gene flow and local adaptation 142

Overview 151

Chapter summary 151

Useful websites and software 152

Further reading 153

Review questions 153

5 Phylogeography 155

What is phylogeography? 155

Molecular markers in phylogeography 155

Molecular clocks 157

Bifurcating trees 160

The coalescent 164

Applying the coalescent 166

Networks 167 Nested clade phylogeographic analysis and statistical phylogeography 170

Distribution of genetic lineages 173

Subdivided populations 173

Lineage sorting 178

Hybridization 180

Comparative phylogeography 184

Regional concordance 185

Continental concordance 188

Introduced species 193

Overview 196

Chapter summary 196

Useful websites and software 198

Further reading 198

Review questions 199

6 Molecular Approaches to Behavioural Ecology 201

Using molecules to study behaviour 201

Mating systems 202

Monogamy, polygamy and promiscuity 202

Parentage analysis 204

Mate choice 212

Social breeding 216

Manipulation of sex ratio 221

Adaptive sex ratios 222

Sex ratio conflicts 224

Sex-biased dispersal 226

Nuclear versus mitochondrial markers 227

Relatedness 228

Fst Values 228

Assignment tests 228

Concordant results 230

Foraging 232

Identifying prey 233

In search of food 238

Overview 241

Chapter summary 242

Useful websites and software 243

Further reading 243

Review questions 244

7 Conservation Genetics 247

The need for conservation 247

Taxonomy 250

Species concepts 250

Genetic barcodes 252

Subspecies 254

Conservation units 255

Population size, genetic diversity and inbreeding 257

Inbreeding depression 258

Translocations 268

Outbreeding depression 273

Captive breeding 277

Maximizing genetic diversity 278

Genetic diversity banks 280

Overview 281

Chapter summary 282

Useful websites and software 283

Further reading 283

Review questions 284

8 Molecular Ecology in a Wider Context 287

Applications of molecular ecology 287

Wildlife forensics 288

Poaching 288

Illegal trade 291

Non-human perpetrators 293

Agriculture 294

Pests and diseases 295

Law enforcement 296

Gene flow between genetically modified crops and wild relatives 297

Fishing 299

Overfishing 299

Stock enhancement 301

The future of molecular ecology 303

Chapter summary 304

Useful websites and software 305

Further reading 306

Review questions 306

Glossary 309

Answers to Review Questions 327

References 337

Index

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