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Nature in Silico

Population Genetic Simulation and its Evolutionary Interpretation Using C++ and R

  • Textbook
  • © 2022

Overview

Authors:
  1. Ryan J. Haasl

    1. Department of Biology, University of Wisconsin-Platteville, Platteville, USA

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  • Provides numerous coding examples throughout the book
  • Contains coding problems at the end of each main chapter with solutions provided for select examples online
  • Contains 100 figures showing summaries of genetic data, results of analysis, or conceptual ideas

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Table of contents (9 chapters)

  1. Front Matter

    Pages i-xviii
    Download chapter PDF

  2. Simulation as a Form of Scientific Investigation

    • Ryan Haasl
    Pages 1-20

  3. Retrospective and Prospective Simulation

    • Ryan Haasl
    Pages 21-48

  4. Mutation and Genetic Drift

    • Ryan Haasl
    Pages 49-86

  5. Demographic Change

    • Ryan Haasl
    Pages 87-106

  6. Meiotic Recombination

    • Ryan Haasl
    Pages 107-138

  7. Population Structure and Migration

    • Ryan Haasl
    Pages 139-183

  8. Natural Selection

    • Ryan Haasl
    Pages 185-223

  9. Effects of Selection on Linked Variants

    • Ryan Haasl
    Pages 225-265

  10. Quantitative Traits

    • Ryan Haasl
    Pages 267-301

  11. Back Matter

    Pages 303-313
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Keywords

About this book

Dramatic advances in computing power enable simulation of DNA sequences generated by complex microevolutionary scenarios that include mutation, population structure, natural selection, meiotic recombination, demographic change, and explicit spatial geographies. Although retrospective, coalescent simulation is computationally efficient—and covered here—the primary focus of this book is forward-in-time simulation, which frees us to simulate a wider variety of realistic microevolutionary models. The book walks the reader through the development of a forward-in-time evolutionary simulator dubbed FORward Time simUlatioN Application (FORTUNA). The capacity of FORTUNA grows with each chapter through the addition of a new evolutionary factor to its code. Each chapter also reviews the relevant theory and links simulation results to key evolutionary insights. The book addresses visualization of results through development of R code and reference to more than 100 figures. All code discussedin the book is freely available, which the reader may use directly or modify to better suit his or her own research needs. Advanced undergraduate students, graduate students, and professional researchers will all benefit from this introduction to the increasingly important skill of population genetic simulation. 

Authors and Affiliations

  • Department of Biology, University of Wisconsin-Platteville, Platteville, USA

    Ryan J. Haasl

About the author

Ryan J. Haasl is an Associate Professor of Biology at the University of Wisconsin-Platteville. He holds an M.A. in Entomology from the University of Kansas and a Ph.D. in Genetics from the University of Wisconsin-Madison. His research focuses on the use of simulation and statistical computing to explore favorite topics such as natural selection targeting microsatellites, phylogenomics, and the consolidation of microevolutionary dynamics and macroevolutionary pattern. He is passionate about teaching genetics and evolutionary biology to undergraduate students and fostering public literacy in the biological sciences through outreach.

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