Category Archives: software

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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Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 2 Comments

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

Toying with eigenvectors

There are few things I enjoy more than when someone takes the time to clearly communicate a complex idea. The whole “you don’t know it until you teach it” phenomenon gives me the utmost respect for those who put effort into … Continue reading

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Show me the power

Describing the patterns of genetic structure and mating system variation in presents challenges from the outset of sample collection to data analysis (see this post and this post). At the beginning of February, I had the pleasure to collaborate with Sean … Continue reading

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Comparing runs and counting K

If you are someone who has any interaction with population genetics, the letter K may cause you a distinct feeling of uneasiness. Identifying the number of distinct genetic clusters (often represented as K) in a data set is a primary component in … Continue reading

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Estimating the ticks and tocks of molecular clocks

M Like many undergraduate students, I learned about the linear, universal molecular clock: the homogeneous rate of nucleotide change over time. When I sat down to actually do analyses of molecular data, I was confounded by the array of options to treat … Continue reading

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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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haploidy, diploidy, polyploidy … not a problem

Investigating pairwise relatedness is fundamental to the characterization of the mating system and inferring genetic structure. If no pedigree exists, then relatedness is estimated from genetic markers (e.g., microsatellite loci) using method-of-moment or maximum-likelihood methods. However, not all individuals in … Continue reading

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