
Forward-Time Population Genetics Simulations Methods, Implementation, and Applications
by Peng, Bo; Kimmel, Marek; Amos, Christopher I.Buy New
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Summary
Author Biography
Table of Contents
Preface | p. xiii |
Acknowledgments | p. xvii |
List of Examples | p. xix |
Basic Concepts and Models | p. 1 |
Biological and Genetic Concepts | p. 2 |
Genome and Chromosomes | p. 2 |
Genes, Markers, Loci, and Alleles | p. 3 |
Recombination and Linkage | p. 4 |
Sex Chromosomes | p. 5 |
Mutation and Mutation Models | p. 5 |
Population and Evolutionary Genetics | p. 7 |
Population Variation and Mutation | p. 8 |
The Wright-Fisher Model and Random Mating | p. 8 |
The Hardy-Weinberg Equilibrium | p. 9 |
Genetic Drift and Effective Population Size | p. 10 |
Natural Selection | p. 10 |
Linkage Equilibrium | p. 13 |
Population Structure and Migration | p. 15 |
Demographic History of Human Populations | p. 16 |
Coalescent and Backward-Time Simulations | p. 17 |
Forward-Time Simulations | p. 20 |
Statistical Genetics and Genetic Epidemiology | p. 21 |
Penetrance Models | p. 21 |
Simple and Complex Genetic Diseases | p. 24 |
Phenotypic, Allelic, and Locus Heterogeneity | p. 24 |
Study Designs of Gene Mapping | p. 25 |
References | p. 27 |
Simulation of Population Genetics Models | p. 31 |
Random Genetic Drift | p. 31 |
Dynamics of Allele Frequency and Heterozygosity | p. 32 |
Persistence Time | p. 34 |
Demographic Models | p. 35 |
The Bottleneck Effect | p. 36 |
Mutation | p. 38 |
A Diallelic Mutation Model | p. 38 |
Multiallelic Mutation Models | p. 40 |
Migration | p. 42 |
An Island Model of Migration | p. 42 |
Recombination and Linkage Disequilibrium | p. 44 |
Natural Selection | p. 45 |
Single-Locus Diallelic Selection Models | p. 45 |
Multilocus Selection Models | p. 48 |
Genealogy of Forward-Time Simulations | p. 49 |
Genealogy of Haploid Simulations | p. 49 |
Genealogy of Diploid Simulations | p. 52 |
References | p. 53 |
Ascertainment Bias in Population Genetics | p. 55 |
Introduction | p. 55 |
Methods | p. 58 |
Evolution of a DNA Repeat Locus | p. 58 |
Conditional Distributions and Ascertainment Bias of Allele Sizes | p. 60 |
Simulation Method | p. 62 |
Results | p. 64 |
Summary of Modeling Results | p. 64 |
Comparisons of Empirical Statistics Derived from Human and Chimpanzee Microsatellite Data | p. 68 |
Discussion and Conclusions | p. 69 |
References | p. 71 |
Observing Properties of Evolving Populations | p. 73 |
Introduction | p. 74 |
Allelic Spectra of Complex Human Diseases | p. 74 |
An Evolutionary Model of Effective Number of Disease Alleles | p. 75 |
Simulation of the Evolution of ne I | p. 76 |
Simulation of the Evolution of Allele Spectra | p. 77 |
Demographic Models | p. 77 |
Output Statistics | p. 80 |
Mutation Models | p. 84 |
Multilocus Selection Models | p. 84 |
Evolve! | p. 87 |
Validation of Theoretical Results | p. 89 |
Extensions to the Basic Model | p. 90 |
Impact of Demographic Models | p. 90 |
Impact of the Mutation Model | p. 92 |
Impact of Subpopulation Structure | p. 93 |
Impact of Migration | p. 94 |
Distribution of Equilibrium Disease Allele Frequency | p. 96 |
Varying Selection and Mutation Coefficients | p. 97 |
Evolution of Disease Predisposing Loci Under Weak Selection | p. 98 |
Discussion | p. 100 |
References | p. 102 |
Simulating Populations with Complex Human Diseases | p. 105 |
Introduction | p. 106 |
Controlling Disease Allele Frequencies at the Present Generation | p. 108 |
Introduction of Disease Alleles | p. 108 |
Trajectory of Disease Allele Frequency | p. 110 |
Forward-and Backward-Time Simulations | p. 111 |
Random Mating with Controlled Disease Allele Frequency | p. 117 |
Forward-Time Simulation of Realistic Samples | p. 120 |
Method | p. 121 |
Drawing Population and Family-Based Samples | p. 126 |
Example 1: Typical Simulations With or Without Scaling | p. 132 |
Example 2: A Genetic Disease with Two DPL | p. 134 |
Example 3: Simulations of Slow and Rapid Selective Sweep | p. 136 |
Discussion | p. 141 |
References | p. 143 |
Nonrandom Mating and its Applications | p. 147 |
Assortative Mating | p. 148 |
Genetic Architecture of Traits | p. 149 |
Mating Model | p. 151 |
Simulation of Assortative Mating | p. 156 |
More Complex Nonrandom Mating Schemes | p. 158 |
Customized Parent Choosing Scheme | p. 158 |
Example of a Nonrandom Mating in a Continuous Habitat | p. 161 |
Heterogeneous Mating Schemes | p. 164 |
Simulation of Population Admixture | p. 167 |
Simulation of Age-Structured Populations | p. 170 |
Simulation of Age-Structured Populations | p. 172 |
A Hypothetical Disease Model | p. 174 |
Evolution of an Age-Structured Population with Lung Cancer | p. 179 |
References | p. 182 |
Appendix: Forward-Time Simulations Using Simupop | p. 185 |
Introduction | p. 185 |
What is simuPOP? | p. 185 |
An Overview of simuPOP Concepts | p. 186 |
Population | p. 189 |
Creating a Population | p. 189 |
Genotype Structure of a Population | p. 192 |
Subpopulations and Virtual Subpopulations | p. 194 |
Accessing Individuals in a Population | p. 196 |
Population Variables | p. 198 |
Altering the Structure, Genotype, or Information Fields of a Population | p. 199 |
Multigeneration Populations and Parental Information | p. 202 |
Saving and Loading a Population | p. 204 |
Operators | p. 204 |
Applicable Generations | p. 205 |
Operator Output | p. 206 |
During-Mating Operators | p. 208 |
Function Form of Operators | p. 209 |
Operator Stat | p. 210 |
Hybrid and Python Operators | p. 212 |
Evolving One or More Populations | p. 215 |
Mating Scheme | p. 215 |
Conditionally Terminating an Evolutionary Process | p. 217 |
Evolving Several Populations Simultaneously | p. 218 |
A Complete simuPOP Script | p. 219 |
Reference | p. 226 |
Index | p. 227 |
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