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Genetic Structure and Selection in Subdivided Populations (MPB-40)
François Rousset

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List of Figures and Tables xi
Acknowledgments xiii
Preface xv
What Is and Is Not There xv
Assumed Background xv
Of Gene and Fitness xvi
1. Introduction 1
Genetic Structure in Relation to Selection 1
Plan of the Book 5
2. Selection and Drift 9
Selection in Panmictic Populations 9
Evolution in Spatially Structured Populations 11
Selection and Local Drift 12
Effective Size in Subdivided Populations 13
Measuring Population Structure 14
Genetic Identity 14
Statistical Concepts of Equilibrium and Population 19
Summary 21
3. Spatially Homogeneous Dispersal: The Island Model and Isolation by Distance 23
Island Models 24
Isolation by Distance 28
Dispersal in Natural Populations 29
The Lattice Models 32
Differentiation under Isolation by Distance 35
Summary 44
Appendix 1: General Analysis of the Lattice Model 45
Appendix 2: Miscellaneous Results 49
Diversity in a Deme 49
Average Diversity in a Population 50
Differentiation under Low Dispersal 51
4. Interpretations of Inbreeding and Relatedness Coefficients in Subdivided Populations 53
Probabilities of Coalescence in Migration Matrix Models 54
Migration Matrix Models: Formulation 54
Probabilities of Coalescence 55
Interpretations of FST 56
Coalescence before Dispersal 56
Separation of Time Scales 57
An Ancestral Reference Population? 58
Differences between Distributions of Coalescence Times 58
Properties of Inbreeding Coefficients 62
Sensitivity to Mutation and to Past Demographic Events 62
No Mutation 63
Alternative Measures of Allelic Divergence 64
5. Evolutionary Dynamics 67
Fitness in a Panmictic Population 67
Example: Resource Competition 67
Convergence Stability 68
Evolutionary Stability 71
Applicability of This Framework 74
Fitness in a Subdivided Population 81
Frequency Dependence in Subdivided Populations 82
How to Measure Selection? 84
Conclusion 87
Appendix: The Prisoner's Dilemma Game 88
Noniterated Game 88
Iterated Game 89
6. Convergence Stability in a Spatially Homogeneous Population 91
Weak Selection Effects on Probability of Fixation 92
Fixation Probability as Allele Frequency Change 92
Fitness Functions 93
Fixation Probability: Direct Fitness Expansion 97
Expression in Terms of Parameters of Population Structure 97
Practical Computation of Convergence Stability 99
Island Model 99
Isolation by Distance 100
Conclusions 101
Direct Fitness Method 101
Fitness Maximization 103
7. Inclusive Fitness, Cooperation, and Altruism 105
What Inclusive Fitness Does Measure 106
Inclusive and Direct Fitness 106
Hamilton's Derivation of Inclusive Fitness 108
Isolation by Distance 109
Altruism in Spatially Subdivided Populations 111
Cost, Benefit, and Relatedness 111
Helping Neighbors 112
Other Examples 116
The Importance of Kin Competition 117
Kin Recognition 118
Implications for Modeling Approaches 119
Inclusive Fitness Theory 119
Other Frameworks 121
Appendix: Helping Neighbors under Isolation by Distance 124
8. Diploidy (and Sex) 127
Population Structure of Diploid Populations 128
Analysis of Pollen and Seed Dispersal 129
Joint Effects of Selfing and Selection on Population Structure 136
Selection in Sexual Diploid Populations 137
Parent and Offspring Control 138
Dominance 140
Highlights 141
9. Effective Size: Concepts and Applications to Stable Populations 143
Defining Effective Size 144
Application in Diffusion Approximations 147
Computation of Effective Size of a Total Population 152
Reproductive Value 153
Deme Structure: The Strong Migration Limit 155
Deme Structure: More Accurate Results 160
Additional Factors 162
Local Effective Size 167
Concluding Remarks 168
Appendix 171
Dispersal and Class Transitions 171
Strong Migration Limit 173
10. Fluctuating Demography: Neutral Models 175
Effective Size of an Isolated Deme 175
Defining Effective Size 176
An Example 177
Structured Populations 178
A Metapopulation Model 179
Propagule Models 184
Inferences 187
11. Selection in Class-Structured Populations 189
Fitness Measures 190
Stable Demography 190
Fluctuating Demography 192
Fitness as Eigenvalue 194
Diffusion Approximations 196
Inferences 196
12. Overview and Perspectives 199
Statistical Analyses of Genetic Structure 199
All Those Data 199
Estimation Methods 201
Robustness 203
Estimation of Effective Size 203
Some Easy Improvements 204
Prospects for the Analysis of Selection 206
Current State of Theory 206
Avenues for Simplifications 208
Conclusion 209
Appendix: Algorithms for Likelihood Estimation 211
Appendix A. Mathematical Appendix 215
Notation 215
Matrix Algebra 217
Eigenvalues and Eigenvectors 217
Diagonalizable Matrices 219
Generating Functions 220
Computation of Identity in State 221
Mutation Models 221
Identity in the Different Mutation Models 222
References 227
Index 261

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File created: 11/1/2016

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