Category Archives: STRUCTURE

NPR's muddled take on scientific racism and direct-to-consumer genetics

Posted on 7 Jul, 2017 by Jeremy Yoder

NPR’s science blog Cosmos & Culture has a post up about a new book on scientific racism and population genetics, particularly in connection with personal genetic ancestry reconstruction like that offered by 23andMe and other “direct-to-consumer” (DTC) genetic testing outfits. … Continue reading →

Posted in politics, STRUCTURE | Tagged , , | 1 Comment

Unbalanced population sampling and STRUCTURE

Posted on 5 Jan, 2017 by Arun Sethuraman

The utility and intuition offered by the program STRUCTURE, and more generally, the ‘admixture’ model of Pritchard et al. (2000) are unquestioned – with tens of thousands of citations, it retains its lead among the most popular population genetics software. … Continue reading →

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , | 1 Comment

On (mis)interpreting STRUCTURE/ADMIXTURE results

Posted on 5 Aug, 2016 by Arun Sethuraman

STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading →

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , , , | 1 Comment

Genomics of Hybridization – Part II, Top three of 2015

Posted on 28 Jan, 2016 by Arun Sethuraman

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading →

Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment

Genomics of Hybridization – Part 1

Posted on 21 Jan, 2016 by Arun Sethuraman

In a series of articles, I will discuss recent advances in hybridization genomics – the fundamentals of adaptive introgression, “islands of speciation”, differential gene flow, and linked selection have been discussed in my previous posts (here, here, and also at … Continue reading →

Posted in adaptation, evolution, genomics, methods, natural history, next generation sequencing, pedigree, phylogenetics, plants, population genetics, RNAseq, software, speciation, species delimitation, STRUCTURE, theory, transcriptomics | Tagged , , , , , , | Leave a comment

Earthquakes and rapid evolution

Posted on 7 Jan, 2016 by Arun Sethuraman

The 1964 Alaskan earthquake was landscape-altering in creating/uplifting numerous islands in the Gulf of Alaska, providing an ideal system to study adaptive evolution of diversification in affected species – the threespine stickleback (Gasterosteus aculeatus) being a widely studied example. In … Continue reading →

Posted in adaptation, evolution, genomics, natural history, next generation sequencing, phylogeography, population genetics, selection, STRUCTURE | Tagged , , , , , , | Leave a comment

Genomics of domestication in chicken and cattle

Posted on 29 Oct, 2015 by Arun Sethuraman

Two recent studies attempt to understand the process of adaptive evolution in domestication and artificial selection by characterizing (a) sweeps, and their association with phenotypes in extant hybrid lines (Sheng et al. 2015), and (b) phylogenomic position of an extinct … Continue reading →

Posted in adaptation, bioinformatics, domestication, evolution, genomics, natural history, Paleogenomics, phylogeography, population genetics, selection, speciation, STRUCTURE | Tagged , , , , , , | 1 Comment

Where's your wine from?

Posted on 20 Aug, 2015 by Arun Sethuraman

Human-mediated selection of yeast cultures has played a huge role in the development of numerous unique strains of Sacchromyces cerevisiae, often attributed to production of a wide variety of wines the world over. Previous studies have indicated a single domesticated … Continue reading →

Posted in domestication, evolution, genomics, horizontal gene transfer, microbiology, Molecular Ecology, the journal, next generation sequencing, phylogenetics, phylogeography, population genetics, STRUCTURE, yeast | Tagged , , , | 1 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

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