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020 |z9781118525289
035 (MiAaPQ)EBC4036063
035 (Au-PeEL)EBL4036063
035 (CaPaEBR)ebr11110812
035 (CaONFJC)MIL826460
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040 MiAaPQ|beng|erda|epn|cMiAaPQ|dMiAaPQ
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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