Forward-Time Population Genetics Simulations Methods, Implementation, and Applications

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Edition: 1st
Format: Paperback
Pub. Date: 2012-02-14
Publisher(s): Wiley-Blackwell
List Price: $139.94

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Summary

The rapid increase of the power of personal computers has led to the use of serious simulation programs such as easy POP in genetic studies. This book summarizes recent advances in forward-time simulation methods and demonstrates their applications in population genetics and genetic epidemiology. The authors introduce commonly used forward-time population genetics simulation methods, including some new methods, and introduce a forward-time population genetics simulation environment, simuPOP, as a powerful and flexible tool to implement these simulations. Researchers and students in population and statistical genetics will find this book useful.

Author Biography

Bo Peng, PhD, is an assistant professor in the Department of Genetics at The University of Texas MD Anderson Cancer Center. With his degrees in applied mathematics and biostatistics, he is applying advanced computational techniques such as parallel computation and larger-scale simulations to research topics in population genetics, genetic epidemiology, and bioinformatics. Marek Kimmel, PhD, is Director of the Doctoral Program in Bioinformatics and Statistical Genetics and head of the Bioinformatics Group at Rice University. He holds joint appointments as Professor of Statistics at Rice University Professor of Biostatistics and Applied Mathematics at MD Anderson Cancer Center, and Professor of Biometry, at The University of Texas School of Public Health. Christopher I. Amos, PhD, is a professor, in the Department of Genetics at The University of Texas MD Anderson Cancer Center. He also holds adjunct appointments at Rice University and in the Department of Epidemiology at The University of Texas School of Public Health.

Table of Contents

Prefacep. xiii
Acknowledgmentsp. xvii
List of Examplesp. xix
Basic Concepts and Modelsp. 1
Biological and Genetic Conceptsp. 2
Genome and Chromosomesp. 2
Genes, Markers, Loci, and Allelesp. 3
Recombination and Linkagep. 4
Sex Chromosomesp. 5
Mutation and Mutation Modelsp. 5
Population and Evolutionary Geneticsp. 7
Population Variation and Mutationp. 8
The Wright-Fisher Model and Random Matingp. 8
The Hardy-Weinberg Equilibriump. 9
Genetic Drift and Effective Population Sizep. 10
Natural Selectionp. 10
Linkage Equilibriump. 13
Population Structure and Migrationp. 15
Demographic History of Human Populationsp. 16
Coalescent and Backward-Time Simulationsp. 17
Forward-Time Simulationsp. 20
Statistical Genetics and Genetic Epidemiologyp. 21
Penetrance Modelsp. 21
Simple and Complex Genetic Diseasesp. 24
Phenotypic, Allelic, and Locus Heterogeneityp. 24
Study Designs of Gene Mappingp. 25
Referencesp. 27
Simulation of Population Genetics Modelsp. 31
Random Genetic Driftp. 31
Dynamics of Allele Frequency and Heterozygosityp. 32
Persistence Timep. 34
Demographic Modelsp. 35
The Bottleneck Effectp. 36
Mutationp. 38
A Diallelic Mutation Modelp. 38
Multiallelic Mutation Modelsp. 40
Migrationp. 42
An Island Model of Migrationp. 42
Recombination and Linkage Disequilibriump. 44
Natural Selectionp. 45
Single-Locus Diallelic Selection Modelsp. 45
Multilocus Selection Modelsp. 48
Genealogy of Forward-Time Simulationsp. 49
Genealogy of Haploid Simulationsp. 49
Genealogy of Diploid Simulationsp. 52
Referencesp. 53
Ascertainment Bias in Population Geneticsp. 55
Introductionp. 55
Methodsp. 58
Evolution of a DNA Repeat Locusp. 58
Conditional Distributions and Ascertainment Bias of Allele Sizesp. 60
Simulation Methodp. 62
Resultsp. 64
Summary of Modeling Resultsp. 64
Comparisons of Empirical Statistics Derived from Human and Chimpanzee Microsatellite Datap. 68
Discussion and Conclusionsp. 69
Referencesp. 71
Observing Properties of Evolving Populationsp. 73
Introductionp. 74
Allelic Spectra of Complex Human Diseasesp. 74
An Evolutionary Model of Effective Number of Disease Allelesp. 75
Simulation of the Evolution of ne Ip. 76
Simulation of the Evolution of Allele Spectrap. 77
Demographic Modelsp. 77
Output Statisticsp. 80
Mutation Modelsp. 84
Multilocus Selection Modelsp. 84
Evolve!p. 87
Validation of Theoretical Resultsp. 89
Extensions to the Basic Modelp. 90
Impact of Demographic Modelsp. 90
Impact of the Mutation Modelp. 92
Impact of Subpopulation Structurep. 93
Impact of Migrationp. 94
Distribution of Equilibrium Disease Allele Frequencyp. 96
Varying Selection and Mutation Coefficientsp. 97
Evolution of Disease Predisposing Loci Under Weak Selectionp. 98
Discussionp. 100
Referencesp. 102
Simulating Populations with Complex Human Diseasesp. 105
Introductionp. 106
Controlling Disease Allele Frequencies at the Present Generationp. 108
Introduction of Disease Allelesp. 108
Trajectory of Disease Allele Frequencyp. 110
Forward-and Backward-Time Simulationsp. 111
Random Mating with Controlled Disease Allele Frequencyp. 117
Forward-Time Simulation of Realistic Samplesp. 120
Methodp. 121
Drawing Population and Family-Based Samplesp. 126
Example 1: Typical Simulations With or Without Scalingp. 132
Example 2: A Genetic Disease with Two DPLp. 134
Example 3: Simulations of Slow and Rapid Selective Sweepp. 136
Discussionp. 141
Referencesp. 143
Nonrandom Mating and its Applicationsp. 147
Assortative Matingp. 148
Genetic Architecture of Traitsp. 149
Mating Modelp. 151
Simulation of Assortative Matingp. 156
More Complex Nonrandom Mating Schemesp. 158
Customized Parent Choosing Schemep. 158
Example of a Nonrandom Mating in a Continuous Habitatp. 161
Heterogeneous Mating Schemesp. 164
Simulation of Population Admixturep. 167
Simulation of Age-Structured Populationsp. 170
Simulation of Age-Structured Populationsp. 172
A Hypothetical Disease Modelp. 174
Evolution of an Age-Structured Population with Lung Cancerp. 179
Referencesp. 182
Appendix: Forward-Time Simulations Using Simupopp. 185
Introductionp. 185
What is simuPOP?p. 185
An Overview of simuPOP Conceptsp. 186
Populationp. 189
Creating a Populationp. 189
Genotype Structure of a Populationp. 192
Subpopulations and Virtual Subpopulationsp. 194
Accessing Individuals in a Populationp. 196
Population Variablesp. 198
Altering the Structure, Genotype, or Information Fields of a Populationp. 199
Multigeneration Populations and Parental Informationp. 202
Saving and Loading a Populationp. 204
Operatorsp. 204
Applicable Generationsp. 205
Operator Outputp. 206
During-Mating Operatorsp. 208
Function Form of Operatorsp. 209
Operator Statp. 210
Hybrid and Python Operatorsp. 212
Evolving One or More Populationsp. 215
Mating Schemep. 215
Conditionally Terminating an Evolutionary Processp. 217
Evolving Several Populations Simultaneouslyp. 218
A Complete simuPOP Scriptp. 219
Referencep. 226
Indexp. 227
Table of Contents provided by Ingram. All Rights Reserved.

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