Applied Population Genetics Textbook Release
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
Chapter 1: Learning R
Installation, Package Management, RStudio, Github
Data Types
Data Containers
Basic Programming
Graphical Output
Chapter 2: Hardy-Weinberg Equilibrium
Theoretical Foundations & Expectations
Testing for Hardy-Weinberg Equilibrium
Chapter 3: Mutation
Causes and Consequences
Equilibrium Expectations
Estimating Mutation Rates
Chapter 4: Non-random Mating
Genetic Linkage
Inbreeding
Mixed Mating Systems & Selfing Rates
Relatedness
Chapter 5: Genetic Drift
Drift & Structure
Allelic & Genotypic Diversity
Genetic Effective Population Size
Rarefaction
Chapter 6: Population Subdivision
Gene Frequencies & Gene Flow
Genetic Distance
Genetic Structure
Chapter 7: Selection
The Fundamental Theorem of Natural Selection
Neutral Theory
Selection on Genotypes
Identifying Putative Selection in Outliers & Gradients
Chapter 8: Spatial Data
Spatial Autocorrelation
Shapefiles in R
Vector Data
Raster Data
Chapter 9: Graph Models
Model Free Networks
Population Graphs
Isolation Models
Chapter 10: Parent-Offspring Data
Pedigree Analyses
Parentage Analysis in Populations
Pollen Pool Analyses
Appendices
Data sets in gstudio
Installing GDAL & RGEOS
Spatial Projections
Customizing the R Environment
About the Author
#Araptusattenuata #landscapegenetics #geneflow #populationgraphs #phylogeography #theory #R #geneticstructure #cGD #BajaCalifornia