Author Archives: Arun Sethuraman

dN(eutralist) = dS(electionist) Part 3

Posted on 19 Mar, 2015 by Arun Sethuraman

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 , | Leave a comment

Exploring color palettes in R

Posted on 12 Mar, 2015 by Arun Sethuraman

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

dN(eutralist) > dS(electionist)? Part 2

Posted on 5 Mar, 2015 by Arun Sethuraman

Last week’s post dealt with the debate over differences in the efficacy of purifying selection across human genomes. This week, we’ll look at the differences in de novo mutation rates across populations. The human de novo mutation rate has gone … Continue reading →

Posted in evolution, mutation, theory | Tagged , , , | Leave a comment

dN(eutralist) > dS(electionist)? Part 1

Posted on 26 Feb, 2015 by Arun Sethuraman

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 , , | 15 Comments

Twice Mixed? Testing hypotheses of Neanderthal Introgression

Posted on 19 Feb, 2015 by Arun Sethuraman

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 , | 1 Comment

Genome-wide effects of artificial selection

Posted on 12 Feb, 2015 by Arun Sethuraman

Humans have been artificially selecting for favorable traits in crops, pets, and livestock over millennia. Years of theoretical predictions and experimental evolution studies have shown the detrimental effects of increased homozygosity, and the population-wide advantages of artificially maintaining heterozygosity. Two … Continue reading →

Posted in bioinformatics, evolution, genomics, methods, mutation, population genetics, theory | Leave a comment

Phonemes and Genomes

Posted on 5 Feb, 2015 by Arun Sethuraman

Human phonemes and genomes are thought to have evolved hand-in-glove out of Africa. Several recent studies have attempted to capture a picture of this global variation in languages and peoples, often supporting (and rejecting) a serial founder model (eg. see … Continue reading →

Posted in bioinformatics, evolution, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

Discordance in ancestry inference using human mtDNA and autosomes

Posted on 29 Jan, 2015 by Arun Sethuraman

Mitochondrial haplotypes have been used extensively over the last few decades for inference of a population structure in humans. Key findings from these studies include what has come to be known as the “Mitochondrial Eve” hypothesis (see the controversial Cann, … Continue reading →

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LaTeX hacks to save your life (and your co-authors')

Posted on 22 Jan, 2015 by Arun Sethuraman

In light of this recent study by Knauff and Nejasmic (2014) that makes a lot of presumptive leaps on the utility and effectiveness of in scientific writing, my case for the utility of for every equation, reference, table, figure, and … Continue reading →

Posted in howto, science publishing | Tagged , , | 6 Comments

SpaceMix, and a brief history of Spatial Genetics

Posted on 15 Jan, 2015 by Arun Sethuraman

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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