The only book available in the area of forward-time population genetics simulations--applicable to both biomedical and evolutionary studiesThe rapid increase of the power of personal computers has led to the use of serious forward-time simulation programs in genetic studies. Forward-Time Population Genetics Simulations presents both new and commonly used methods, and introduces simuPOP, a powerful and flexible new program that can be used to simulate arbitrary evolutionary processes with unique features like customized chromosome types, arbitrary nonrandom mating schemes, virtual subpopulations, information fields, and Python operators.The book begins with an overview of important concepts and models, then goes on to show how simuPOP can simulate a number of standard population genetics models--with the goal of demonstrating the impact of genetic factors such as mutation, selection, and recombination on standard Wright-Fisher models. The rest of the book is devoted to applications of forward-time simulations in various research topics.Forward-Time Population Genetics Simulations includes:* An overview of currently available forward-time simulation methods, their advantages, and shortcomings* An overview and evaluation of currently available software* A simuPOP tutorial* Applications in population genetics* Applications in genetic epidemiology, statistical genetics, and mapping complex human diseasesThe only book of its kind in the field today, Forward-Time Population Genetics Simulations will appeal to researchers and students of population and statistical genetics.

Preface ixAcknowledgments xiiiList of examples xxiii1. Basic concepts and models 11.1 Biological and genetic concepts 21.2 Population and evolutionary genetics 61.3 Statistical genetics and genetic epidemiology 172. Simulation of population genetics models 252.1 Random genetic drift 252.2 Demographic models 292.3 Mutation 312.4 Migration 342.5 Recombination and linkage disequilibrium 362.6 Natural selection 372.7 Genealogy of forward-time simulations 413. Ascertainment bias in population genetics 473.1 Introduction 473.2 Methods 493.3 Results 543.4 Discussion and Conclusions 584. Observing properties of evolving populations 634.1 Introduction 644.2 Simulation of the evolution of allele spectra 664.3 Extensions to the basic model 785. Simulating populations with complex human diseases 895.1 Introduction 895.2 Controlling disease allele frequencies at the present generation 915.3 Forward-time simulation of realistic samples 1025.4 Discussion 1196. Nonrandom mating and its applications 1256.1 Assortative mating 1266.2 More complex non-random mating schemes 1326.3 Hetergeneous mating schemes 1406.4 Simulation of age structured populations 145Appendix: Forward-time simulations using stimulPOP 157A.1 Introduction 157A.2 Population 160A.3 Operators 172A.4 Evolve on or more populations 181A.5 A complete stimuPOP script 185