FORWARD-TIME POPULATION GENETICS SIMULATIONS: Methods, Implementation, and Applications -- CONTENTS -- PREFACE -- ACKNOWLEDGMENTS -- LIST OF EXAMPLES -- 1 BASIC CONCEPTS AND MODELS -- 1.1 Biological and Genetic Concepts -- 1.1.1 Genome and Chromosomes -- 1.1.2 Genes, Markers, Loci, and Alleles -- 1.1.3 Recombination and Linkage -- 1.1.4 Sex Chromosomes -- 1.1.5 Mutation and Mutation Models -- 1.2 Population and Evolutionary Genetics -- 1.2.1 Population Variation and Mutation -- 1.2.2 The Wright-Fisher Model and Random Mating -- 1.2.3 The Hardy-Weinberg Equilibrium -- 1.2.4 Genetic Drift and Effective Population Size -- 1.2.5 Natural Selection -- 1.2.6 Linkage Equilibrium -- 1.2.7 Population Structure and Migration -- 1.2.8 Demographic History of Human Populations -- 1.2.9 Coalescent and Backward-Time Simulations -- 1.2.10 Forward-Time Simulations -- 1.3 Statistical Genetics and Genetic Epidemiology -- 1.3.1 Penetrance Models -- 1.3.2 Simple and Complex Genetic Diseases -- 1.3.3 Phenotypic, Allelic, and Locus Heterogeneity -- 1.3.4 Study Designs of Gene Mapping -- References -- 2 SIMULATION OF POPULATION GENETICS MODELS -- 2.1 Random Genetic Drift -- 2.1.1 Dynamics of Allele Frequency and Heterozygosity -- 2.1.2 Persistence Time -- 2.2 Demographic Models -- 2.2.1 The Bottleneck Effect -- 2.3 Mutation -- 2.3.1 A Diallelic Mutation Model -- 2.3.2 Multiallelic Mutation Models -- 2.4 Migration -- 2.4.1 An Island Model of Migration -- 2.5 Recombination and Linkage Disequilibrium -- 2.6 Natural Selection -- 2.6.1 Single-Locus Diallelic Selection Models -- 2.6.2 Multilocus Selection Models -- 2.7 Genealogy of Forward-Time Simulations -- 2.7.1 Genealogy of Haploid Simulations -- 2.7.2 Genealogy of Diploid Simulations -- References -- 3 ASCERTAINMENT BIAS IN POPULATION GENETICS -- 3.1 Introduction -- 3.2 Methods -- 3.2.1 Evolution of a DNA Repeat Locus.

3.2.2 Conditional Distributions and Ascertainment Bias of Allele Sizes -- 3.2.3 Simulation Method -- 3.3 Results -- 3.3.1 Summary of Modeling Results -- 3.3.2 Comparisons of Empirical Statistics Derived from Human and Chimpanzee Microsatellite Data -- 3.4 Discussion and Conclusions -- References -- 4 OBSERVING PROPERTIES OF EVOLVING POPULATIONS -- 4.1 Introduction -- 4.1.1 Allelic Spectra of Complex Human Diseases -- 4.1.2 An Evolutionary Model of Effective Number of Disease Alleles -- 4.1.3 Simulation of the Evolution of ne -- 4.2 Simulation of the Evolution of Allele Spectra -- 4.2.1 Demographic Models -- 4.2.2 Output Statistics -- 4.2.3 Mutation Models -- 4.2.4 Multilocus Selection Models -- 4.2.5 Evolve! -- 4.2.6 Validation of Theoretical Results -- 4.3 Extensions to the Basic Model -- 4.3.1 Impact of Demographic Models -- 4.3.2 Impact of the Mutation Model -- 4.3.3 Impact of Subpopulation Structure -- 4.3.4 Impact of Migration -- 4.3.5 Distribution of Equilibrium Disease Allele Frequency -- 4.3.6 Varying Selection and Mutation Coefficients -- 4.3.7 Evolution of Disease Predisposing Loci Under Weak Selection -- 4.3.8 Discussion -- References -- 5 SIMULATING POPULATIONS WITH COMPLEX HUMAN DISEASES -- 5.1 Introduction -- 5.2 Controlling Disease Allele Frequencies at the Present Generation -- 5.2.1 Introduction of Disease Alleles -- 5.2.2 Trajectory of Disease Allele Frequency -- 5.2.3 Forward- and Backward-Time Simulations -- 5.2.4 Random Mating with Controlled Disease Allele Frequency -- 5.3 Forward-Time Simulation of Realistic Samples -- 5.3.1 Method -- 5.3.2 Drawing Population and Family-Based Samples -- 5.3.3 Example 1: Typical Simulations With or Without Scaling -- 5.3.4 Example 2:AGenetic Disease with Two DPL -- 5.3.5 Example 3: Simulations of Slow and Rapid Selective Sweep -- 5.4 Discussion -- References.

6 NONRANDOM MATING AND ITS APPLICATIONS -- 6.1 Assortative Mating -- 6.1.1 Genetic Architecture of Traits -- 6.1.2 Mating Model -- 6.1.3 Simulation of Assortative Mating -- 6.2 More Complex Nonrandom Mating Schemes -- 6.2.1 Customized Parent Choosing Scheme -- 6.2.2 Example of a Nonrandom Mating in a Continuous Habitat -- 6.3 Heterogeneous Mating Schemes -- 6.3.1 Simulation of Population Admixture -- 6.4 Simulation of Age-Structured Populations -- 6.4.1 Simulation of Age-Structured Populations -- 6.4.2 A Hypothetical Disease Model -- 6.4.3 Evolution of an Age-Structured Population with Lung Cancer -- References -- APPENDIX: FORWARD-TIME SIMULATIONS USING simuPOP -- A.1 Introduction -- A.1.1 What is simuPOP? -- A.1.2 An Overview of simuPOP Concepts -- A.2 Population -- A.2.1 Creating a Population -- A.2.2 Genotype Structure of a Population -- A.2.3 Subpopulations and Virtual Subpopulations -- A.2.4 Accessing Individuals in a Population -- A.2.5 Population Variables -- A.2.6 Altering the Structure, Genotype, or Information Fields of a Population -- A.2.7 Multigeneration Populations and Parental Information -- A.2.8 Saving and Loading a Population -- A.3 Operators -- A.3.1 Applicable Generations -- A.3.2 Operator Output -- A.3.3 During-Mating Operators -- A.3.4 Function Form of Operators -- A.3.5 Operator Stat -- A.3.6 Hybrid and Python Operators -- A.4 Evolving One or More Populations -- A.4.1 Mating Scheme -- A.4.2 Conditionally Terminating an Evolutionary Process -- A.4.3 Evolving Several Populations Simultaneously -- A.5 A Complete simuPOP Script -- Reference -- INDEX.