Ecological Genetics

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.

Molecular ecologists finally have a text-book that deals with their discipline. Ecological Genetics fills the market-gap between general accounts of evolutionary biology and specialist texts focusing on individual research topics. The authors have brought together a useful mix of theory, practical approaches, conceptual issues, and individual case studies to provide a balanced and accessible overview of the field. Peter Hollingsworth, Royal Botanic Garden "This book is a pleasure to read: it is clearly written, well organized and leaves no ambiguity." Andre A Dhondt, Cornell University, Trends in Ecology and Evolution, August 2004 "This book is a well-written, comprehensive overview of the essential techniques underlying ecological genetics. I would certainly recommend it to any new student undertaking postgraduate study in the field of molecular ecology." Dr. Jim Provan, Queen's University Belfast

• Preface viiAbbreviations x1 Ecological genetics 1Summary 11.1 What is ecological genetics? 11.2 Why study ecological genetics? 3References 42 Markers and sampling in ecological genetics 6Summary 62.1 Introduction 62.2 Methods of data generation 72.3 Principles of sampling 152.4Practice 202.5 Within-population sampling 222.6 Among-population sampling 342.7 Power analysis 342.8 Further reading 35Essential methods information 36References 453 Genetic diversity and differentiation 52Summary 523.1 Introduction 523.2 Factors influencing diversity and differentiation 533.3 The Hardy–Weinberg equilibrium 583.4Genetic diversity 623.5 Genetic differentiation 693.6 Genetic distance 813.7 Statistical approaches 863.8 Use of genetic diversity statistics 893.9 Concluding remarks 1003.10 Further reading 100References 1004 Gene flow and mating system 106Summary 1064.1 Introduction 1064.2 Factors governing gene flow 1074.3 Considerations for measuring gene flow 1154.4 Measuring gene flow – indirect estimates 1224.5 Measuring gene flow – direct estimates 1344.6 The importance of biological and environmental factors on gene flow 143References 1455 Intraspecific phylogenies and phylogeography 150Summary 1505.1 Introduction 1505.2 Homology, gene trees, and species trees 1575.3 Tree form and building 1595.4Tree interpretation 1705.5 Organelle versus nuclear intraspecific phylogenies 1795.6 Further reading 180Essential methods information 181References 1856 Speciation and hybridization 189Summary 1896.1 Introduction 1896.2 Species 1906.3 Speciation 1946.4 Hybridization 2046.5 Analysis of speciation and hybridization 2066.6 Future developments 2336.7 Further reading 233References 2337 Case studies in ecological genetics: Lycaenid butterflies, ragworts, bears, and oaks 243Summary 2437.1 Introduction 2447.2 Lycaenid butterflies 2447.3 European ragworts 2577.4Brown bears 2657.5 European oaks 274References 292Appendix A: Data analysis software 300Appendix B: Which distance algorithm should be used and when? 306Glossary 313Index 320