Category Archives: R

The imitation game: simulating the genetics of large populations

Computational simulations of genetic data are such a powerful and flexible tool for carrying out studies in molecular ecology. Do you want to know how much explanatory power your data provides? Simulate it! Predict the future response of species to … Continue reading

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SpaceMix, and a brief history of Spatial Genetics

Incorporating spatial data to inform studies of the population demography of a species has a long history of interest. From inferring geographical clines in Principal Components Analyses (Menozzi et al. 1978), using location data as “informative priors” during model-based estimation … Continue reading

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A population genetic R-evolution

Uphill, both ways, in the snow, without shoes … quite apt when thinking of the dark days, in the not too distant past, in which a separate input file was needed for each popgen analysis in order to use a … Continue reading

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Migration Circos plots in R

We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading

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Geophylogeny plots in R for Dummies

Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with … Continue reading

Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE | Tagged , | 2 Comments

Admixture maps in R for Dummies

Before we get started, I’d like to point everyone to an excellent tutorial here by Kim Gilbert on making maps in R. I have been grappling with overlaying admixture plots, and migration routes on top of maps recently, and thought I’d put … Continue reading

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , | 11 Comments

Calculating genetic differentiation with R

As molecular ecologists, it is often necessary and useful to calculate some measure of genetic differentiation. This is often accomplished with metrics such as Wright’s Fst an or an unbiased analog (e.g., Weir & Cockerham’s Fst; G’st etc.). In addition … Continue reading

Posted in population genetics, R, software | 12 Comments

Using GitHub with R and RStudio

A few weeks back, the Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading

Posted in bioinformatics, howto, R, software | 16 Comments

Random drift and phenotypic evolution

This week we have a guest post from Markku Karhunen. Markku’s research at the University of Helsinki included the development and implementation of a number of very interesting and useful population genetics methods. In his guest post Markku discusses these … Continue reading

Posted in adaptation, methods, population genetics, quantitative genetics, R, software, Uncategorized | 2 Comments

Using R to run parallel analyses of population genetic data in STRUCTURE: ParallelStructure

In this guest post, Francois Besnier explains how to use ParallelStructure, his new R package for running STRUCTURE analyses in parallel computing environments. To start with, thanks to The Molecular Ecologist blog team (Tim and Jeremy) for the invitation to … Continue reading

Posted in howto, population genetics, R, software, STRUCTURE | 4 Comments