Table of Contents
Contents Preface Introduction
1 Historical Background
1.1 Biometricians, Saltationists and Mendelians
1.2 The Hardy–Weinberg Law
1.3 The Correlation Between Relatives
1.4 Evolution
1.4.1 The Deterministic Theory
1.4.2 Non-Random-Mating Populations
1.4.3 The Stochastic Theory
1.5 Evolved Genetic Phenomena
1.6 Modelling
1.7 Overall Evolutionary Theories
2 Technicalities and Generalizations
2.1 Introduction
2.2 Random Union of Gametes
2.3 Dioecious Populations
2.4 Multiple Alleles
2.5 Frequency-Dependent Selection
2.6 Fertility Selection
2.7 Continuous-Time Models
2.8 Non-Random-Mating Populations
2.9 The Fundamental Theorem of Natural Selection
2.10 Two Loci
2.11 Genetic Loads
2.12 Finite Markov Chains
3 Discrete Stochastic Models
3.1 Introduction
3.2 Wright–Fisher Model: Two Alleles
3.3 The Cannings (Exchangeable) Model: Two Alleles
3.4 Moran Models: Two Alleles
3.5 K-Allele Wright–Fisher Models
3.6 Infinitely Many Alleles Models
3.6.1 Introduction
3.6.2 The Wright–Fisher In.nitely Many Alleles Model
3.6.3 The Cannings In.nitely Many Alleles Model
3.6.4 The Moran In.nitely Many Alleles Model
3.7 The Effective Population Size
3.8 Frequency-Dependent Selection
3.9 Two Loci
4 Diffusion Theory
4.1 Introduction
4.2 The Forward and Backward Kolmogorov Equations
4.3 Fixation Probabilities
4.4 Absorption Time Properties
4.5 The Stationary Distribution
4.6 Conditional Processes
4.7 Diffusion Theory
4.8 Multi-dimensional Processes
4.9 Time Reversibility
4.10 Expectations of Functions of Di.usion Variables
5 Applications of Diffusion Theory
5.1 Introduction
5.2 No Selection or Mutation
5.3 Selection
5.4 Selection: Absorption Time Properties
5.5 One-Way Mutation
5.6 Two-Way Mutation
5.7 Diffusion Approximations and Boundary Conditions
5.8 Random Environments
5.9 Time-Reversal and Age Properties
5.10 Multi-Allele Diffusion Processes
6 Two Loci
6.1 Introduction
6.2 Evolutionary Properties of Mean Fitness
6.3 Equilibrium Points
6.4 Special Models
6.5 Modifier Theory
6.6 Two-Locus Diffusion Processes
6.7 Associative Overdominance and Hitchhiking
6.8 The Evolutionary Advantage of Recombination
6.9 Summary
7 Many Loci
7.1 Introduction
7.2 Notation
7.3 The Random Mating Case
7.3.1 Linkage Disequilibrium, Means and Variances
7.3.2 Recurrence Relations for Gametic Frequencies
7.3.3 Components of Variance
7.3.4 Particular Models
7.4 Non-Random Mating
7.4.1 Introduction
7.4.2 Notation and Theory
7.4.3 Marginal Fitnesses and Average Effects
7.4.4 Implications
7.4.5 The Fundamental Theorem of Natural Selection
7.4.6 Optimality Principles
7.5 The Correlation Between Relatives
7.6 Summary
8 Further Considerations
8.1 Introduction
8.2 What is Fitness?
8.3 Sex Ratio
8.4 Geographical Structure
8.5 Age Structure
8.6 Ecological Considerations
8.7 Sociobiology
9 Molecular Population Genetics: Introduction
9.1 Introduction
9.2 Technical Comments
9.3 In.nitely Many Alleles Models: Population Properties
9.3.1 The Wright–Fisher Model
9.3.2 The Moran Model
9.4 In.nitely Many Sites Models: Population Properties
9.4.1 Introduction
9.4.2 The Wright–Fisher Model
9.4.3 The Moran Model
9.5 Sample Properties of In.nitely Many Alleles Models
9.5.1 Introduction
9.5.2 The Wright–Fisher Model
9.5.3 The Moran Model
9.6 Sample Properties of In.nitely Many Sites Models
9.6.1 Introduction
9.6.2 The Wright–Fisher Model
9.6.3 The Moran Model
9.7 Relation Between In.nitely Many Alleles and Infinitely Many Sites Models
9.8 Genetic Variation Within and Between Populations
9.9 Age-Ordered Alleles: Frequencies and Ages
10 Looking Backward in Time: The Coalescent
10.1 Introduction
10.2 Competing Poisson and Geometric Processes
10.3 The Coalescent Process
10.4 The Coalescent and Its Relation to Evolutionary Genetic Models
10.5 Coalescent Calculations: Wright–Fisher Models
10.6 Coalescent Calculations: Exact Moran Model Results
10.7 General Comments
10.8 The Coalescent and Human Genetics
11 Looking Backward: Testing the Neutral Theory
11.1 Introduction
11.2 Testing in the Infinitely Many Alleles Models
11.2.1 Introduction
11.2.2 The Ewens and the Watterson Tests
11.2.3 Procedures Based on the Conditional Sample Frequency Spectrum
11.2.4 Age-Dependent Tests
11.3 Testing in the Infinitely Many Sites Models
11.3.1 Introduction
11.3.2 Estimators of è
11.3.3 The Tajima Test
11.3.4 Other "Tajima-like” Testing Procedures
11.3.5 Testing for the Signature of a Selective Sweep
11.3.6 Combining Infinitely Many Alleles and In.nitely Many Sites Approaches
11.3.7 Data from Several Unlinked Loci
11.3.8 Data from Unlinked Sites
11.3.9 Tests Based on Historical Features
12 Looking Backward in Time: Population and Species Comparisons
12.1 Introduction
12.1.1 The Reversibility Criterion
12.2 Various Evolutionary Models
12.2.1 The Jukes–Cantor Model
12.2.2 The Kimura Model and Its Generalizations
12.2.3 The Felsenstein Models
12.3 Some Implications
12.3.1 Introduction
12.3.2 The Jukes–Cantor Model
12.3.3 The Kimura Model
12.4 Statistical Procedures Appendix A: Eigenvalue Calculations Appendix B: Significance Levels for ˆ F Appendix C: Means and Variances of ˆ F References Author Index Subject Index
