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…mehr
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.Hinweis: Dieser Artikel kann nur an eine deutsche Lieferadresse ausgeliefert werden.
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
Inhaltsangabe
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 Landscape and Genetic Data for Landscape Genetic Studies 77 Helene H. Wagner and Marie-Josée Fortin 5.1 Introduction 77 5.2 How to model landscape effects on genetic variation 84 5.3 How to model isolation-by-distance 93 5.4 Future directions 95 Acknowledgments 96 References 96 Part 2: Methods 6 Simulation Modeling in Landscape Genetics 101 Erin Landguth Samuel A. Cushman and Niko Balkenhol 6.1 Introduction 101 6.2 A brief overview of models and simulations 101 6.3 General benefits of simulation modeling 102 6.4 Landscape genetic simulation modeling 103 6.5 Examples of simulation modeling in landscape genetics 104 6.6 Designing and choosing landscape genetic simulation models 108 6.7 The future of landscape genetic simulation modeling 111 References 111 7 Clustering and Assignment Methods In Landscape Genetics 114 Olivier François and Lisette P. Waits 7.1 Introduction 114 7.2 Exploratory data analysis and model-based clustering for population structure analysis 115 7.3 Spatially explicit methods in landscape genetics 119 7.4 Spatial EDA methods: spatial PCA and spatial factor analysis 119 7.5 Spatial MBC methods 120 7.6 Habitat and environmental heterogeneity models 121 7.7 Discussion 123 References 125 8 Resistance Surface Modeling in Landscape Genetics 129 Stephen F. Spear Samuel A. Cushman and Brad H. McRae 8.1 Introduction 129 8.2 Techniques for parameterizing resistance surfaces 133 8.3 Estimating connectivity from resistance surfaces 137 8.4 Statistical validation of resistance surfaces 139 8.5 The future of the resistance surface in landscape genetics 142 8.6 Conclusions 144 References 144 9 Genomic Approaches in Landscape Genetics 149 Andrew Storfer Michael F. Antolin Stéphanie Manel Bryan K. Epperson and Kim T. Scribner 9.1 Introduction 149 9.2 Current landscape genomics methods 150 9.3 General challenges in landscape genomics 157 9.4 Spatial autocorrelation 157 9.5 Applications of landscape genomics to climate change 159 References 160 10 Graph Theory and Network Models In Landscape Genetics 165 Melanie Murphy Rodney Dyer and Samuel A. Cushman 10.1 Introduction 165 10.2 Background on graph theory 167 10.3 Landscape genetic applications 170 10.4 Recommendations for using graph approaches in landscape genetics 175 10.5 Current research needs 176 10.6 Conclusion - potential for application of graphs for conservation 176 References 177 Part 3: Applications 11 Landscapes and Plant Population Genetics 183 Rodney J. Dyer 11.1 Introduction 183 11.2 Contemporary population genetic processes 186 11.3 Historical population genetic processes 190 11.4 Future research 192 References 194 12 Applications of Landscape Genetics to Connectivity Research In Terrestrial Animals 199 Lisette P. Waits Samuel A. Cushman and Steve F. Spear 12.1 Introduction 199 12.2 General overview of terrestrial animal study systems and research challenges 199 12.3 Detecting barriers and defining corridors 202 12.4 Evaluating population dynamics 205 12.5 Detecting and predicting the response to landscape change 206 12.6 Common limitations of landscape genetic studies involving terrestrial animals 208 12.7 Testing ecological hypotheses about gene flow in heterogeneous landscapes 208 12.8 Knowledge gaps and future directions 213 References 214 13 Waterscape Genetics - Applications of Landscape Genetics To Rivers Lakes and Seas 220 Kimberly A. Selkoe Kim T. Scribner and Heather M. Galindo 13.1 Introduction 220 13.2 Understanding marine and freshwater environments 223 13.3 Typical research questions and approaches 229 13.4 Applications of landscape genetic approaches 234 13.5 Future directions: knowledge gaps research challenges and limitations 237 Acknowledgments 238 References 238 14 Current Status Future Opportunities and Remaining Challenges in Landscape Genetics 247 Niko Balkenhol Samuel A. Cushman Lisette P. Waits and Andrew Storfer 14.1 Introduction 247 14.2 Conclusion 1: issues of scale need to be considered 248 14.3 Conclusion 2: sampling needs to specifically target landscape genetic questions 248 14.4 Conclusion 3: choice of appropriate statistical methods remains challenging 249 14.5 Conclusion 4: simulations play a key role in landscape genetics 249 14.6 Conclusion 5: measures of genetic variation are rarely developed specifically for landscape genetics 249 14.7 Conclusion 6: landscape resistance is just one of the possible landscape-genetic relationships 250 14.8 Conclusion 7: genomics provides novel opportunities but also creates new challenges 250 14.9 Conclusion 8: the scope of landscape genetics needs to expand 251 14.10 Conclusion 9: specific hypotheses are rarely stated in current landscape genetic studies 251 14.11 Conclusion 10: a comprehensive theory for landscape genetics is currently missing 252 14.12 The future of landscape genetics 252 References 253 Index 257
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 Landscape and Genetic Data for Landscape Genetic Studies 77 Helene H. Wagner and Marie-Josée Fortin 5.1 Introduction 77 5.2 How to model landscape effects on genetic variation 84 5.3 How to model isolation-by-distance 93 5.4 Future directions 95 Acknowledgments 96 References 96 Part 2: Methods 6 Simulation Modeling in Landscape Genetics 101 Erin Landguth Samuel A. Cushman and Niko Balkenhol 6.1 Introduction 101 6.2 A brief overview of models and simulations 101 6.3 General benefits of simulation modeling 102 6.4 Landscape genetic simulation modeling 103 6.5 Examples of simulation modeling in landscape genetics 104 6.6 Designing and choosing landscape genetic simulation models 108 6.7 The future of landscape genetic simulation modeling 111 References 111 7 Clustering and Assignment Methods In Landscape Genetics 114 Olivier François and Lisette P. Waits 7.1 Introduction 114 7.2 Exploratory data analysis and model-based clustering for population structure analysis 115 7.3 Spatially explicit methods in landscape genetics 119 7.4 Spatial EDA methods: spatial PCA and spatial factor analysis 119 7.5 Spatial MBC methods 120 7.6 Habitat and environmental heterogeneity models 121 7.7 Discussion 123 References 125 8 Resistance Surface Modeling in Landscape Genetics 129 Stephen F. Spear Samuel A. Cushman and Brad H. McRae 8.1 Introduction 129 8.2 Techniques for parameterizing resistance surfaces 133 8.3 Estimating connectivity from resistance surfaces 137 8.4 Statistical validation of resistance surfaces 139 8.5 The future of the resistance surface in landscape genetics 142 8.6 Conclusions 144 References 144 9 Genomic Approaches in Landscape Genetics 149 Andrew Storfer Michael F. Antolin Stéphanie Manel Bryan K. Epperson and Kim T. Scribner 9.1 Introduction 149 9.2 Current landscape genomics methods 150 9.3 General challenges in landscape genomics 157 9.4 Spatial autocorrelation 157 9.5 Applications of landscape genomics to climate change 159 References 160 10 Graph Theory and Network Models In Landscape Genetics 165 Melanie Murphy Rodney Dyer and Samuel A. Cushman 10.1 Introduction 165 10.2 Background on graph theory 167 10.3 Landscape genetic applications 170 10.4 Recommendations for using graph approaches in landscape genetics 175 10.5 Current research needs 176 10.6 Conclusion - potential for application of graphs for conservation 176 References 177 Part 3: Applications 11 Landscapes and Plant Population Genetics 183 Rodney J. Dyer 11.1 Introduction 183 11.2 Contemporary population genetic processes 186 11.3 Historical population genetic processes 190 11.4 Future research 192 References 194 12 Applications of Landscape Genetics to Connectivity Research In Terrestrial Animals 199 Lisette P. Waits Samuel A. Cushman and Steve F. Spear 12.1 Introduction 199 12.2 General overview of terrestrial animal study systems and research challenges 199 12.3 Detecting barriers and defining corridors 202 12.4 Evaluating population dynamics 205 12.5 Detecting and predicting the response to landscape change 206 12.6 Common limitations of landscape genetic studies involving terrestrial animals 208 12.7 Testing ecological hypotheses about gene flow in heterogeneous landscapes 208 12.8 Knowledge gaps and future directions 213 References 214 13 Waterscape Genetics - Applications of Landscape Genetics To Rivers Lakes and Seas 220 Kimberly A. Selkoe Kim T. Scribner and Heather M. Galindo 13.1 Introduction 220 13.2 Understanding marine and freshwater environments 223 13.3 Typical research questions and approaches 229 13.4 Applications of landscape genetic approaches 234 13.5 Future directions: knowledge gaps research challenges and limitations 237 Acknowledgments 238 References 238 14 Current Status Future Opportunities and Remaining Challenges in Landscape Genetics 247 Niko Balkenhol Samuel A. Cushman Lisette P. Waits and Andrew Storfer 14.1 Introduction 247 14.2 Conclusion 1: issues of scale need to be considered 248 14.3 Conclusion 2: sampling needs to specifically target landscape genetic questions 248 14.4 Conclusion 3: choice of appropriate statistical methods remains challenging 249 14.5 Conclusion 4: simulations play a key role in landscape genetics 249 14.6 Conclusion 5: measures of genetic variation are rarely developed specifically for landscape genetics 249 14.7 Conclusion 6: landscape resistance is just one of the possible landscape-genetic relationships 250 14.8 Conclusion 7: genomics provides novel opportunities but also creates new challenges 250 14.9 Conclusion 8: the scope of landscape genetics needs to expand 251 14.10 Conclusion 9: specific hypotheses are rarely stated in current landscape genetic studies 251 14.11 Conclusion 10: a comprehensive theory for landscape genetics is currently missing 252 14.12 The future of landscape genetics 252 References 253 Index 257
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