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050  4 QH456 -- .L36 2016eb 
082 0  576.5/8 
100 1  Balkenhol, Niko 
245 10 Landscape Genetics :|bConcepts, Methods, Applications 
250    1st ed 
264  1 Chicester :|bJohn Wiley & Sons, Incorporated,|c2015 
264  4 |c©2014 
300    1 online resource (287 pages) 
336    text|btxt|2rdacontent 
337    computer|bc|2rdamedia 
338    online resource|bcr|2rdacarrier 
505 0  Landscape Genetics: Concepts, Methods, Applications -- 
       Contents -- List of Contributors -- Website -- 
       Acknowledgments -- Glossary -- Chapter 1: Introduction to 
       Landscape Genetics - Concepts, Methods, Applications -- 
       1.1 Introduction -- 1.2 Defining Landscape Genetics -- 1.3
       The Three Analytical Steps of Landscape Genetics -- 1.4 
       The Interdisciplinary Challenge of Landscape Genetics -- 
       1.4.1 The Two Scopes of Landscape Genetic Research -- 1.5 
       Structure of This Book - Concepts, Methods, Applications -
       - 1.5.1 Limitations and Potential of This Book -- 
       References -- Part 1: Concepts -- Chapter 2: Basics of 
       Landscape Ecology: An Introduction to Landscapes and 
       Population Processes for Landscape Geneticists -- 2.1 
       Introduction -- 2.2 How Landscapes Affect Population 
       Genetic Processes -- 2.2.1 Area Effects -- 2.2.2 Edge 
       Effects -- 2.2.3 Isolation Effects -- 2.3 Defining the 
       Landscape for Landscape Genetic Research -- 2.3.1 What is 
       a Landscape? -- 2.3.2 Thematic Content -- 2.3.3 Thematic 
       Resolution -- 2.3.4 Spatial Extent and Grain -- 2.3.5 A 
       Priori Hypotheses should Guide Landscape Definition -- 2.4
       Defining Populations and Characterizing Dispersal 
       Processes -- 2.4.1 Panmictic Populations -- 2.4.2 
       Metapopulations -- 2.4.3 Gradient Populations -- 2.5 
       Putting It Together: Combinations of Landscape and 
       Population Models -- 2.6 Frameworks for Delineating 
       Landscapes and Populations for Landscape Genetics -- 2.6.1
       Step 1: Establish Analysis Objectives -- 2.6.2 Step 2: 
       Define the Landscape -- Define the Extent of the Landscape
       -- Establish a Model of the Landscape Structure -- 
       Establish a Relevant Grain of Analysis -- 2.6.3 Step 3: 
       Define the Population and Design the Sampling Scheme -- 
       2.6.4 Step 4: Characterize the Landscape Relative to 
       Analysis Objectives -- 2.6.5 Step 5: Conduct Analysis -- 
       2.7 Current Challenges and Future Opportunities -- 
       References 
505 8  Chapter 3: Basics of Population Genetics: Quantifying 
       Neutral and Adaptive Genetic Variation for Landscape 
       Genetic Studies -- 3.1 Introduction -- 3.2 Overview of 
       Landscape Influences on Genetic Variation -- 3.3 Overview 
       of Dna Types and Molecular Methods -- 3.3.1 Types of DNA -
       - 3.3.2 Adaptive versus Neutral Loci -- 3.3.3 Molecular 
       Methods -- 3.3.4 Unit of Analysis -- 3.4 Important 
       Population Genetic Models -- 3.4.1 Hardy-Weinberg 
       Equilibrium -- 3.4.2 Linkage Equilibrium -- 3.4.3 
       Effective Population Size and Genetic Drift -- 3.4.4 
       Mutation -- 3.4.5 Migration (Gene Flow) -- 3.4.6 Isolation
       -by-Distance and Landscape -- 3.5 Measuring Genetic 
       Diversity -- 3.5.1 Population Level -- 3.5.2 Individual 
       Level -- 3.6 Evaluating Genetic Structure and Detecting 
       Barriers -- 3.6.1 Population-Based Measures -- 3.6.2 
       Individual-Based Genetic Distance Metrics -- 3.6.3 
       Bayesian Clustering Methods -- 3.6.4 Barrier Detection 
       Methods -- 3.7 Estimating Gene Flow Using Indirect and 
       Direct Methods -- 3.7.1 Indirect Measures of Gene Flow - 
       Coalescent Approaches -- 3.7.2 Direct Measures - 
       Assignment Tests -- 3.7.3 Parentage Analysis -- 3.8 
       Conclusion and Future Directions -- References -- Chapter 
       4: Basics of Study Design: Sampling Landscape 
       Heterogeneity and Genetic Variation for Landscape Genetic 
       Studies -- 4.1 Introduction -- 4.2 Study Design 
       Terminology Used in This Chapter -- 4.2.1 Sampling Level -
       - 4.2.2 Sampling Intensity -- 4.2.3 Spatial Sampling 
       Scheme -- 4.2.4 Temporal Sampling Scheme -- 4.3 General 
       Study Design Considerations -- 4.4 Considerations for 
       Landscape Genetic Study Design -- 4.4.1 Considerations for
       Sampling Landscape Data -- 4.4.2 Considerations for 
       Sampling Genetic Data -- 4.4.3 Matching Landscape and 
       Genetic Data -- 4.5 Current Knowledge About Study Design 
       Effects in Landscape Genetics -- 4.5.1 Sampling of 
       Landscape Heterogeneity 
505 8  4.5.2 Individual- versus Population-Based Sampling -- 
       4.5.3 Spatial Sampling Design versus Sampling Intensity --
       4.5.4 Sampling Intensity -- 4.5.5 Matching Sampling and 
       Statistical Methods -- 4.6 Recommendations for Optimal 
       Sampling Strategies in Landscape Genetics -- 4.7 
       Conclusions and Future Directions -- References -- Chapter
       5: Basics of Spatial Data Analysis: Linking Landscape and 
       Genetic Data for Landscape Genetic Studies -- 5.1 
       Introduction -- 5.2 How to Model Landscape Effects on 
       Genetic Variation -- 5.2.1 Type of Landscape Data -- 5.2.2
       Type of Genetic Data -- 5.2.3 Type of Statistical Model --
       5.2.4 Model Selection -- 5.2.5 How to Put Space into the 
       Multivariate Regression Model -- 5.2.6 Multivariate Linear
       Regression with OLS -- 5.2.7 Spatial Weights Matrix W -- 
       5.2.8 Spatial Regression -- 5.2.9 Spatial Eigenvectors -- 
       5.2.10 Multivariate Moran's I -- 5.2.11 Spatial Filtering 
       -- 5.3 How to Model Isolation-By-Distance -- 5.3.1 IBD and
       Spatial Regression with CAR -- 5.3.2 IBD and Spatial 
       Filtering with MEM -- 5.3.3 IBD and Multiple Regression of
       Distance Matrices (MRM) -- 5.4 Future Directions -- 
       Acknowledgments -- References -- Part 2: Methods -- 
       Chapter 6. Simulation Modeling in Landscape Genetics -- 
       6.1 Introduction -- 6.2 A Brief Overview of Models and 
       Simulations -- 6.3 General Benefits of Simulation Modeling
       -- 6.4 Landscape Genetic Simulation Modeling -- 6.5 
       Examples of Simulation Modeling in Landscape Genetics -- 
       6.5.1 Analytical Evaluations: (When) Do Methods Work? How 
       can we Best Quantify Landscape-Genetic Relationships? -- 
       6.5.2 Theoretical Developments: How/Why Does Landscape 
       Heterogeneity Influence Genetics? -- 6.5.3 Empirical 
       Applications: Using Simulation to Elucidate, Evaluate, and
       Explain Empirical Observations -- 6.6 Designing and 
       Choosing Landscape Genetic Simulation Models 
505 8  6.6.1 Software for Landscape Genetics Simulations -- 6.6.2
       Practical Guidelines for Conducting Landscape Genetic 
       Simulations -- 6.7 The Future of Landscape Genetic 
       Simulation Modeling -- References -- Chapter 7: Clustering
       and Assignment Methods in Landscape Genetics -- 7.1 
       Introduction -- 7.2 Exploratory Data Analysis and Model-
       Based Clustering for Population Structure Analysis -- 
       7.2.1 Exploratory Data Analysis -- 7.2.2 Model-Based 
       Clustering Approaches -- 7.2.3 Visualization of PCA and 
       STRUCTURE Results -- 7.2.4 Simulated Examples -- 7.3 
       Spatially-Explicit Methods in Landscape Genetics -- 7.4 
       Spatial Eda Methods: Spatial Pca and Spatial Factor 
       Analysis -- 7.5 Spatial Mbc Methods -- 7.6 Habitat and 
       Environmental Heterogeneity Models -- 7.6.1 Going Beyond 
       Geography -- 7.6.2 Canonical Correspondence Analysis and 
       Redundancy Analysis -- 7.6.3 Bayesian MBC Algorithms using
       Environmental Data -- 7.6.4 Ancestry Distribution Models -
       - 7.7 Discussion -- 7.7.1 From Landscape Ecology and 
       Population Genetics to Landscape Genetic Methods -- 7.7.2 
       Interpretations of EDA and MBC Outputs -- 7.7.3 Ancient 
       Events -- 7.7.4 Continuous Variation -- 7.7.5 Strengths 
       and Weaknesses of EDA and MBC Methods -- 7.7.6 Divergent 
       Selection and Population Structure -- References -- 
       Chapter 8: Resistance Surface Modeling in Landscape 
       Genetics -- 8.1 Introduction -- 8.1.1 What is a Resistance
       Surface? -- 8.1.2 Using Resistance Surfaces: A Framework -
       - 8.1.3 Selecting Variables for Resistance Surfaces: 
       Initial Questions and Assumptions -- 8.1.4 What Factors 
       Dictate the Utility of Variables for Resistance Surfaces? 
       -- 8.2 Techniques for Parameterizing Resistance Surfaces -
       - Expert Opinion -- Empirical Parameterization -- 8.3 
       Estimating Connectivity From Resistance Surfaces -- 8.4 
       Statistical Validation of Resistance Surfaces 
505 8  8.4.1 Applications of Resistance Surfaces in Landscape 
       Genetics -- 8.4.2 Concise Considerations for Effective 
       Uses of Resistance Surfaces -- 8.5 The Future of the 
       Resistance Surface in Landscape Genetics -- 8.5.1 Advances
       in Remote Sensing -- 8.5.2 Development of Model Selection 
       and Optimization Methodologies -- 8.5.3 Resistance 
       Surfaces in Adaptive Landscape Genomics -- 8.6 Conclusions
       -- References -- Chapter 9: Genomic Approaches in 
       Landscape Genetics -- 9.1 Introduction -- 9.2 Current 
       Landscape Genomics Methods -- 9.2.1 Population Genomics --
       9.2.2 QTL to Genome-Wide Association Studies -- 9.2.3 
       Candidate Gene Approaches -- 9.2.4 Exomes and 
       Transcriptomes -- 9.3 General Challenges in Landscape 
       Genomics -- 9.3.1 Spatial Data Collection -- 9.4 Spatial 
       Autocorrelation -- 9.4.1 Isolation-by-Adaptation -- 9.5 
       Applications of Landscape Genomics to Climate Change -- 
       References -- Chapter 10: Graph Theory and Network Models 
       in Landscape Genetics -- 10.1 Introduction -- 10.2 
       Background on Graph Theory -- 10.2.1 What is a Graph? -- 
       10.2.2 What are the Assumptions of Graph Theoretic 
       Approaches? -- 10.2.3 What Edges are Relevant? -- 10.3 
       Landscape Genetic Applications -- 10.3.1 Describing 
       Population Structure -- Theoretical Background -- 
       Conceptual Framework -- Data Requirements -- Software -- 
       Case Study -- 10.3.2 Hypothesis of Connectivity -- 
       Theoretical Background -- Implementation -- Case Studies -
       - 10.3.3 Functional Connectivity -- Theoretical Background
       -- Modeling Framework -- Data Requirements and Assumptions
       -- Software Implementation -- Case Study -- 10.4 
       Recommendations for Using Graph Approaches in Landscape 
       Genetics -- 10.4.1 Recommendation 1: Clearly Identify 
       Research Questions -- 10.4.2 Recommendation 2: Choosing an
       Adequate Study Design -- 10.4.3 Recommendation 3: Testing 
       Underlying Assumptions -- 10.5 Current Research Needs 
505 8  10.6 Conclusion - Potential for Application of Graphs for 
       Conservation 
588    Description based on publisher supplied metadata and other
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590    Electronic reproduction. Ann Arbor, Michigan : ProQuest 
       Ebook Central, 2020. Available via World Wide Web. Access 
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650  0 Ecological genetics 
655  4 Electronic books 
700 1  Cushman, Samuel 
700 1  Storfer, Andrew 
700 1  Waits, Lisette 
776 08 |iPrint version:|aBalkenhol, Niko|tLandscape Genetics : 
       Concepts, Methods, Applications|dChicester : John Wiley & 
       Sons, Incorporated,c2015|z9781118525289 
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