Category Archives: R

Models matter when linking genetic diversity to niche model predictions

Ecological niche models and the methods to create them continue to evolve. These techniques provide a tidy way to relate the distributions of taxa to environmental variables from the present, past, or future. Oh, and they are pretty too: Those pretty … Continue reading

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PCA of multilocus genotypes in R

An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 4 Comments

marmap

A couple years ago, Benoit Simon-Bouhet ended up sharing an office with Eric Pante, then a post-doc fellow in his former lab. The two quickly realized they were in a lab in which few people had the expertise or taste for coding. Thus, on … Continue reading

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IBE/IBD Contour plots in R

Rob’s post from yesterday motivated me to find an alternate way of visualizing correlations between matrices of geographical or ecological data, and genetic data. I have seen plenty of Mantel, or partial Mantel tests of correlation, as well as plots … Continue reading

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Procrustes Analyses in R

Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geographical and genetic distributions of species, following the lead of Wang et … Continue reading

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Visualizing Linkage Disequilibrium in R

Patterns of Linkage Disequilibrium (LD) across a genome has multiple implications for a population’s ancestral demography. For instance, population bottlenecks predictably result in increased LD, LD between SNP’s in loci under natural selection affect each others rates of adaptive evolution, selfing/inbreeding populations … Continue reading

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F-statistics Manhattan Plots in R

Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading

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Exploring color palettes in R

How often have you had to squint at figures with unpleasant color palettes in a manuscript online or in print, and ultimately given up on distinguishing between fifty (or maybe just around 30) shades of gray? I found the RColorBrewer … Continue reading

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , , | 8 Comments

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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