Ecological Genetics

Preface vii

Abbreviations x

1 Ecological genetics 1

Summary 1

1.1 What is ecological genetics? 1

1.2 Why study ecological genetics? 3

References 4

2 Markers and sampling in ecological genetics 6

Summary 6

2.1 Introduction 6

2.2 Methods of data generation 7

2.3 Principles of sampling 15

2.4Practice 20

2.5 Within-population sampling 22

2.6 Among-population sampling 34

2.7 Power analysis 34

2.8 Further reading 35

Essential methods information 36

References 45

3 Genetic diversity and differentiation 52

Summary 52

3.1 Introduction 52

3.2 Factors influencing diversity and differentiation 53

3.3 The Hardy–Weinberg equilibrium 58

3.4Genetic diversity 62

3.5 Genetic differentiation 69

3.6 Genetic distance 81

3.7 Statistical approaches 86

3.8 Use of genetic diversity statistics 89

3.9 Concluding remarks 100

3.10 Further reading 100

References 100

4 Gene flow and mating system 106

Summary 106

4.1 Introduction 106

4.2 Factors governing gene flow 107

4.3 Considerations for measuring gene flow 115

4.4 Measuring gene flow – indirect estimates 122

4.5 Measuring gene flow – direct estimates 134

4.6 The importance of biological and environmental factors on gene flow 143

References 145

5 Intraspecific phylogenies and phylogeography 150

Summary 150

5.1 Introduction 150

5.2 Homology, gene trees, and species trees 157

5.3 Tree form and building 159

5.4Tree interpretation 170

5.5 Organelle versus nuclear intraspecific phylogenies 179

5.6 Further reading 180

Essential methods information 181

References 185

6 Speciation and hybridization 189

Summary 189

6.1 Introduction 189

6.2 Species 190

6.3 Speciation 194

6.4 Hybridization 204

6.5 Analysis of speciation and hybridization 206

6.6 Future developments 233

6.7 Further reading 233

References 233

7 Case studies in ecological genetics: Lycaenid butterflies, ragworts, bears, and oaks 243

Summary 243

7.1 Introduction 244

7.2 Lycaenid butterflies 244

7.3 European ragworts 257

7.4Brown bears 265

7.5 European oaks 274

References 292

Appendix A: Data analysis software 300

Appendix B: Which distance algorithm should be used and when? 306

Glossary 313

Index 320