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Category Archives: population genetics
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
Posted in bioinformatics, genomics, howto, population genetics, R, software
Tagged data visualization, genomics, Homo sapiens
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Killer genetic differentiation
Like most of you out there, I sometimes get bogged down in literature, and the pressure to keep up with new methods can lead to a towering “to-read” folder. I feel forced to read many of these papers no matter … Continue reading
dN(eutralist) = dS(electionist) Part 3
In a previous post, I discussed the phenomenon of background selection, which results in rapid expungement of neutral alleles linked to loci under purifying or negative selection, and conversely, the rapid fixation of neutral variants that are linked to loci of … Continue reading
Posted in adaptation, evolution, genomics, natural history, plants, population genetics, selection
Tagged genomics, population genetics
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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 data visualization, methods, population genetics
8 Comments
dN(eutralist) > dS(electionist)? Part 1
In a new series of posts, I will now proffer neutralist and selectionist reviews of recent publications. I point readers to an excellent review of the debate by Masatoshi Nei (2005). Besides being a fun exercise in PoV’s, I hope … Continue reading
Posted in evolution, genomics, mutation, population genetics, theory
Tagged Evolution, genomics, population genetics
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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
Posted in conservation, evolution, genomics, interview, methods, population genetics, software, Uncategorized
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Twice Mixed? Testing hypotheses of Neanderthal Introgression
Human migration in, and out of Africa was wrought with complex patterns of admixture (see my previous post summarizing the story so far). Of note were some recent findings on the disparity in amounts of Neanderthal introgression/ancestry between East Asians … Continue reading
Posted in adaptation, bioinformatics, evolution, genomics, mutation, Paleogenomics, population genetics
Tagged Homo sapiens, population genetics
1 Comment
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
Beauty is in the eyes of the beholder
Many animals use visual signals to scope out potential mates. In a new paper in Molecular Ecology, Sandkam et al. (2015) demonstrate that the variation underlying preference in female guppies could be explained by simple changes in expression and coding of … Continue reading