Tag Archives: population genetics

Visualizing Linkage Disequilibrium in R

Posted on 9 Apr, 2015 by Arun Sethuraman

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 →

Posted in bioinformatics, howto, population genetics, R | Tagged , , | 1 Comment

d(N)eutralist < d(S)electionist Part 4

Posted on 2 Apr, 2015 by Arun Sethuraman

Continuing our discussion of the neutralist-selectionist debate, recent findings by Schrider et al. (2015) bring us to the topic of selective sweeps, and their genomic signatures in a population. As we have discussed in previous posts, numerous studies (since the … Continue reading →

Posted in adaptation, evolution, mutation, population genetics, selection, theory | Tagged , , | 1 Comment

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

The imitation game: simulating the genetics of large populations

Posted on 21 Jan, 2015 by Rob Denton

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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Is genetics a requirement for restoration?

Posted on 12 Nov, 2014 by Rob Denton

The fields of conservation and genetics have relied heavily on one another for quite a while now (they even made an aptly named journal together!). Using genetic information is now an accepted, and even expected, step in recognizing and protecting … Continue reading →

Posted in community ecology, conservation, Molecular Ecology, the journal, natural history, population genetics | Tagged , , | 1 Comment