Applied Population Genetics Textbook Release

A short description of the post.


Center for Environmental Studies


December 17, 2015

I will be posting portions of all 10 chapters of my upcoming textbook, Applied Population Genetics, as early draft chapters to this website over the spring semester.

This book will be published in both ibook and print-on-demand versions. I prefer the ibook format because I can embed interactive content (movies, JavaScript, etc.) into the text and it will update automatically when I make revisions etc.

The drawback is that ibook is limited to OSX and iOS devices at this time—which is why I will also be making it available as a print-on-demand text (though the interactive content will not obviously be included). The complete text is scheduled to be made available by the end of the academic year and I will be using it as the primary source in my Spring courses of Population Genetics BIOL516 and Landscape Genetics ENVS 692

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Chapter 1: Learning R

  • Installation, Package Management, RStudio, Github
  • Data Types
  • Data Containers
  • Basic Programming
  • Graphical Output
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Chapter 2: Hardy-Weinberg Equilibrium

  • Theoretical Foundations & Expectations
  • Testing for Hardy-Weinberg Equilibrium
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Chapter 3: Mutation

  • Causes and Consequences
  • Equilibrium Expectations
  • Estimating Mutation Rates
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Chapter 4: Non-random Mating

  • Genetic Linkage
  • Inbreeding
  • Mixed Mating Systems & Selfing Rates
  • Relatedness
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Chapter 5: Genetic Drift

  • Drift & Structure
  • Allelic & Genotypic Diversity
  • Genetic Effective Population Size
  • Rarefaction
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Chapter 6: Population Subdivision

  • Gene Frequencies & Gene Flow
  • Genetic Distance
  • Genetic Structure
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Chapter 7: Selection

  • The Fundamental Theorem of Natural Selection
  • Neutral Theory
  • Selection on Genotypes
  • Identifying Putative Selection in Outliers & Gradients
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Chapter 8: Spatial Data

  • Spatial Autocorrelation
  • Shapefiles in R
  • Vector Data
  • Raster Data
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Chapter 9: Graph Models

  • Model Free Networks
  • Population Graphs
  • Isolation Models
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Chapter 10: Parent-Offspring Data

  • Pedigree Analyses
  • Parentage Analysis in Populations
  • Pollen Pool Analyses


  • Data sets in gstudio
  • Installing GDAL & RGEOS
  • Spatial Projections
  • Customizing the R Environment
  • About the Author