Category Archives: bioinformatics

The 2016 Workshop on Genomics summary

Posted on 29 Feb, 2016 by Elin Videvall

I recently had the pleasure to spend two and a half weeks in the beautiful medieval town of Český Krumlov, Czech Republic. The reason was the popular Workshop on Genomics that was running and I was one of the TAs … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing | Tagged , , , , , , | Leave a comment

The Neanderthal admixture plot thickens…

Posted on 25 Feb, 2016 by Arun Sethuraman

Previous studies of archaic admixture from Altai Neanderthals and Denisovans into modern humans outside of Africa have put forth several lines of evidence for gene flow from Neanderthals into common ancestors of Eurasian populations, from Denisovans into ancestors of modern … Continue reading →

Posted in bioinformatics, evolution, genomics, mutation, natural history, next generation sequencing, Paleogenomics, population genetics, speciation | Tagged , , , | 2 Comments

There and back again: an angiosperm's tale

Posted on 19 Feb, 2016 by Stacy Krueger-Hadfield

Eelgrass (Zostera marina) is the dominant seagrass in the northern hemisphere and provides the foundation of highly productive ecosystems that rival tropical rain forests and coral reefs in ecosystem services. Zostera isn’t really a grass, but a monocot, like a … Continue reading →

Posted in adaptation, bioinformatics, community ecology, evolution, genomics, plants | Tagged , , , , | Leave a 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

An Oedipus complex in mosses?

Posted on 11 Dec, 2015 by Stacy Krueger-Hadfield

Nannandrous … phyllodioicous … gotta love botanical terms and these will most definitely find their way into this week’s list of favorite words! Both refer to the tiny epiphytic nature of males situated on much larger female shoots. There may be many … Continue reading →

Posted in bioinformatics, evolution, genomics, haploid-diploid, plants, population genetics | Tagged , , , | Leave a comment

Pre-adapted algal ancestors colonized land

Posted on 7 Dec, 2015 by Stacy Krueger-Hadfield

The colonization of land by plants 450 Mya marked a major transition on Earth and was one of the critical events that led to the emergence of extant terrestrial ecosystems. Chief among the challenges the terrestrial environment presented for these … Continue reading →

Posted in adaptation, bioinformatics, Coevolution, evolution, genomics, haploid-diploid, next generation sequencing, phylogenetics, plants, transcriptomics | Tagged | Leave a comment

Bees brought to their knees

Posted on 27 Nov, 2015 by Stacy Krueger-Hadfield

As regular readers of TME will have read, this past summer was a whirlwind of sampling in which I took the briefest of holidays in the Southwest of England before attending the European Phycological Congress (read about the congress here and here). … Continue reading →

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2D Posterior Density Plots in R

Posted on 6 Nov, 2015 by Arun Sethuraman

I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading →

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

A Nice opinion on confronting uncertainty and modeling it for GBS data

Posted on 3 Nov, 2015 by Stacy Krueger-Hadfield

Just over a week ago, I had the opportunity to work in Chris Nice‘s lab at Texas State University. I was accompanied by one of our MS students, Ben, and my colleague, Erik Sotka, to prep libraries for a genomic … Continue reading →

Posted in bioinformatics, genomics, interview | Tagged , , , | 1 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