Genetic structure & competition in subdivided populations

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