LANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS

LANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS

Edited by Niko Balkenhol, Samuel A. Cushman, Andrew T. Storfer, Lisette P. Waits

Landscape genetics is an exciting and rapidly growing field, melding methods and theory from landscape ecology and population genetics to address some of the most challenging and urgent ecological and evolutionary topics of our time. Landscape genetic approaches now enable researchers to study in detail how environmental complexity in space and time affect gene flow, genetic drift, and local adaptation. However, learning about the concepts and methods underlying the field remains challenging due to the highly interdisciplinary nature of the field, which relies on topics that have traditionally been treated separately in classes and textbooks.

In this edited volume, some of the leading experts in landscape genetics provide the first comprehensive introduction to underlying concepts, commonly used methods, and current and future applications of landscape genetics. Consistent with the interdisciplinary nature of the field, the book includes textbook-like chapters that synthesize fundamental concepts and methods underlying landscape genetics (Part 1), chapters on advanced topics that deserve a more in-depth treatment (Part 2), and chapters illustrating the use of concepts and methods in empirical applications (Part 3).

Aimed at beginning landscape geneticists and experienced researchers alike, this book will be helpful for all scientists and practitioners interested in learning, teaching, and applying landscape genetics.

Prof. Niko Balkenhol, Dept.of Wildlife Sciences, Georg-August-University Göttingen, Büsgenweg 3, 37077
Göttingen, Germany

Samuel Cushman, US Forest Service, Forest and Woodlands Ecosystems Program, Rockyn Mountain Research Station, Flagstaff, AZ, USA

Andrew Storfer, School of Biological Sciences, Washington State University, Pullman, WA, USA

Prof. Lisette Waits, Dept. Fish and Wildlife Sciences,University of Idaho, Moscow ID, USA

LANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS

Edited by Niko Balkenhol, Samuel A. Cushman, Andrew T. Storfer, Lisette P. Waits

Landscape genetics is an exciting and rapidly growing field, melding methods and theory from landscape ecology and population genetics to address some of the most challenging and urgent ecological and evolutionary topics of our time. Landscape genetic approaches now enable researchers to study in detail how environmental complexity in space and time affect gene flow, genetic drift, and local adaptation. However, learning about the concepts and methods underlying the field remains challenging due to the highly interdisciplinary nature of the field, which relies on topics that have traditionally been treated separately in classes and textbooks.

In this edited volume, some of the leading experts in landscape genetics provide the first comprehensive introduction to underlying concepts, commonly used methods, and current and future applications of landscape genetics. Consistent with the interdisciplinary nature of the field, the book includes textbook-like chapters that synthesize fundamental concepts and methods underlying landscape genetics (Part 1), chapters on advanced topics that deserve a more in-depth treatment (Part 2), and chapters illustrating the use of concepts and methods in empirical applications (Part 3).

Aimed at beginning landscape geneticists and experienced researchers alike, this book will be helpful for all scientists and practitioners interested in learning, teaching, and applying landscape genetics.

Inhalt

List of Contributors ix

Website xi

Acknowledgments xiii

Glossary xv

1 Introduction to Landscape Genetics Concepts Methods Applications 1
Niko Balkenhol Samuel A. Cushman Andrew Storfer and Lisette P. Waits

1.1 Introduction 1

1.2 Defining landscape genetics 2

1.3 The three analytical steps of landscape genetics 3

1.4 The interdisciplinary challenge of landscape genetics 3

1.5 Structure of this book concepts methods applications 5

References 6

Part 1: Concepts

2 Basics of Landscape Ecology: An Introduction to Landscapes and Population Processes for Landscape Geneticists 11
Samuel A. Cushman Brad H. McRae and Kevin McGarigal

2.1 Introduction 11

2.2 How landscapes affect population genetic processes 12

2.3 Defining the landscape for landscape genetic research 16

2.4 Defining populations and characterizing dispersal processes 21

2.5 Putting it together: combinations of landscape and population models 24

2.6 Frameworks for delineating landscapes and populations for landscape genetics 26

2.7 Current challenges and future opportunities 30

References 30

3 Basics of Population Genetics: Quantifying Neutral and Adaptive Genetic Variation for Landscape Genetic Studies 35
Lisette P. Waits and Andrew Storfer

3.1 Introduction 35

3.2 Overview of landscape influences on genetic variation 36

3.3 Overview of DNA types and molecular methods 38

3.4 Important population genetic models 41

3.5 Measuring genetic diversity 45

3.6 Evaluating genetic structure and detecting barriers 46

3.7 Estimating gene flow using indirect and direct methods 50

3.8 Conclusion and future directions 52

References 53

4 Basics of Study Design: Sampling Landscape Heterogeneity and Genetic Variation for Landscape Genetic Studies 58
Niko Balkenhol and Marie-Josée Fortin

4.1 Introduction 58

4.2 Study design terminology used in this Chapter 59

4.3 General study design considerations 60

4.4 Considerations for landscape genetic study design 61

4.5 Current knowledge about study design effects in landscape genetics 66

4.6 Recommendations for optimal sampling strategies in landscape genetics 71

4.7 Conclusions and future directions 73

References 74

5 Basics of Spatial Data Analysis: Linking L…