Author Archives: Arun Sethuraman

Recent Ancestry of the USA and the 100k Genome Project

Posted on 8 Jan, 2015 by Arun Sethuraman

Holiday presents for pop-gen enthusiasts come in the form of data – boatloads of it! The past two weeks saw the announcements of two neat studies that spell monumental steps toward our understanding of the genetics of mixed populations. With … Continue reading →

Posted in genomics, population genetics | Tagged , , | 1 Comment

Sweeping for Sweeps

Posted on 18 Dec, 2014 by Arun Sethuraman

Reduction in genomic diversity around a site has been attributed to one of two mechanisms – (1) sites linked to positively selected mutant alleles are often `swept’ to fixation, in a process often called genetic hitchhiking, and/or (2) background selection … Continue reading →

Posted in Uncategorized | 2 Comments

Migration Circos plots in R

Posted on 11 Dec, 2014 by Arun Sethuraman

We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading →

Posted in bioinformatics, genomics, howto, R, software | Tagged , | 11 Comments

The Evolution of Recombination

Posted on 4 Dec, 2014 by Arun Sethuraman

In a recent publication, Lesecque et al (2014). provide key evidence that fills in some of the blanks to an age old question – how do recombination hotspots evolve? Their analyses of major PRDM9 (a polymorphic zinc finger protein with … Continue reading →

Posted in adaptation, genomics, mutation, population genetics, theory | Tagged , | 2 Comments

Geophylogeny plots in R for Dummies

Posted on 27 Nov, 2014 by Arun Sethuraman

Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with … Continue reading →

Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE | Tagged , | 4 Comments

#EntSoc14, a quick review

Posted on 20 Nov, 2014 by Arun Sethuraman

I have had a wonderful time at my first big bug conference – the annual meeting of the Entomological Society of America, at the Oregon Convention Center in Portland. Amid secretive (or not so secretive) break-out sessions to Voodoo Doughnuts, … Continue reading →

Posted in conferences, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

Admixture maps in R for Dummies

Posted on 13 Nov, 2014 by Arun Sethuraman

Before we get started, I’d like to point everyone to an excellent tutorial here by Kim Gilbert on making maps in R. I have been grappling with overlaying admixture plots, and migration routes on top of maps recently, and thought I’d put … Continue reading →

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , | 14 Comments

The Ust'-Ishim Genome

Posted on 6 Nov, 2014 by Arun Sethuraman

This year has been monumental in pulling together several interesting pieces in the human evolution out of Africa puzzle (Lazaridis et al., Ruiz-Linares et al., Skoglund et al., Huerta-Sanchez et al., Jeong et al., Pickrell et al., Raghavan et al., … Continue reading →

Posted in genomics, mutation, Paleogenomics, population genetics | Tagged , , | 4 Comments