Ecological Genetics Design, Analysis, and

The use of molecular markers has revolutionized ecological genetics in the last 20 years. The fundamental problem facing new researchers is which of the many markers should be used and how the resulting data should then be analyzed. Until now, these guidelines have been hidden away in specialist journals. Ecological Genetics addresses this fundamental problem in clear, accessible language, suitable for upper-level undergraduates through to research-level professionals. The major topics in Ecological Genetics are treated within separate chapters, including: bull; bull;genetic diversity of populations and species bull;gene flow bull;phylogeography, and bull;speciation Within each chapter the potentially suitable molecular markers are described and the resulting data from each type of marker are discussed, including the underlying concepts of the various modes of analysis. These are illustrated with examples from both the plant and animal kingdoms. Researchers embarking on molecular approaches to ecological genetics (for instance, final-year undergraduates and new postgraduates) will find the book essential, and more experienced researchers will also find it of interest.

Dr Andrew Lowe recently took up a position as Research Lecturer in Ecological Genetics at the University of Queensland, Australia, after serving as a Senior Scientific Research Officer at the Centre for Ecology and Hydrology, Edinburgh, UK. He manages a global network of highly regarded research projects on speciation and hybridization, range-wide phylogeography and fine-scale population gene dynamics, and has published more than 50 articles and papers on these subjects in scientific journals and books.

Dr Stephen Harris is Druce Curator of the Oxford University Herbaria, UK. As a University Research Lecturer he teaches in plant conservation genetics, and his research interests are molecular systematics, conservation genetics, and the effects of human activities on plant genetic variation and speciation. He has published more than 50 articles and papers on these subjects in scientific journals and books.

Dr Paul Ashton is a Senior Lecturer in Botany at Edge Hill College of Higher Education, UK. He was instrumental in implementing one of the UK’s first degree programs in Conservation Biology. He is also an Associate Lecturer with the Open University and has recently developed a small research group to continue his long-held interests in plant speciation and introgression, while developing new interests in conservation genetics.

Preface

vii

Abbreviations

x

1 Ecological genetics

1

(5)

Summary

1

(1)

1.1 What is ecological genetics?

1

(2)

1.2 Why study ecological genetics?

3

(1)

References

4

(2)

2 Markers and sampling in ecological genetics

6

(46)

Summary

6

(1)

2.1 Introduction

6

(1)

2.2 Methods of data generation

7

(8)

2.3 Principles of sampling

15

(5)

2.4 Practice

20

(2)

2.5 Within-population sampling

22

(12)

2.6 Among-population sampling

34

(1)

2.7 Power analysis

34

(1)

2.8 Further reading

35

(1)

Essential methods information

36

(9)

References

45

(7)

3 Genetic diversity and differentiation

52

(54)

Summary

52

(1)

3.1 Introduction

52

(1)

3.2 Factors influencing diversity and differentiation

53

(5)

3.3 The Hardy-Weinberg equilibrium

58

(4)

3.4 Genetic diversity

62

(7)

3.5 Genetic differentiation

69

(12)

3.6 Genetic distance

81

(5)

3.7 Statistical approaches

86

(3)

3.8 Use of genetic diversity statistics

89

(11)

3.9 Concluding remarks

100

(1)

3.10 Further reading

100

(1)

References

100

(6)

4 Gene flow and mating system

106

(44)

Summary

106

(1)

4.1 Introduction

106

(1)

4.2 Factors governing gene flow

107

(8)

4.3 Considerations for measuring gene flow

115

(7)

4.4 Measuring gene flow - indirect estimates

122

(12)

4.5 Measuring gene flow- direct estimates

134

(9)

4.6 The importance of biological and environmental factors on gene flow

143

(2)

References

145

(5)

5 Intraspecific phylogenies and phylogeography

150

(39)

Summary

150

(1)

5.1 Introduction

150

(7)

5.2 Homology, gene trees, and species trees

157

(2)

5.3 Tree form and building

159

(11)

5.4 Tree interpretation

170

(9)

5.5 Organelle versus nuclear intraspecific phylogenies

179

(1)

5.6 Further reading

180

(1)

Essential methods information

181

(4)

References

185

(4)

6 Speciation and hybridization

189

(54)

Summary

189

(1)

6.1 Introduction

189

(1)

6.2 Species

190

(4)

6.3 Speciation

194

(10)

6.4 Hybridization

204

(2)

6.5 Analysis of speciation and hybridization

206

(27)

6.6 Future developments

233

(1)

6.7 Further reading

233

(1)

References

233

(10)

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

243

(57)

Summary

243

(1)

7.1 Introduction

244

(1)

7.2 Lycaenid butterflies

244

(13)

7.3 European ragworts

257

(8)

7.4 Brown bears

265

(9)

7.5 European oaks

274

(18)

References

292

(8)

Appendix A: Data analysis software

300

(6)

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

306

(7)

Glossary

313

(7)

Index

320

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Ecological Genetics Design, Analysis, and Application

Summary

Author Biography

Table of Contents

Supplemental Materials