Category Archives: software

Battle of the Text Editors

Posted on 16 Mar, 2016 by Katie Everson

Whether you’re a coding master or a total technophobe, a good text editor is a must-have for the molecular ecology toolkit. Text editors are great for managing code, formatting input files, or jotting notes. But with so many different text … Continue reading →

Posted in bioinformatics, software | Tagged , , | 2 Comments

Geographical Heat Maps in R

Posted on 3 Mar, 2016 by Arun Sethuraman

I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading →

Posted in bioinformatics, howto, R, software | Tagged , | 2 Comments

Quick and dirty tree building in R

Posted on 26 Feb, 2016 by Ethan Linck

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading →

Posted in howto, methods, phylogenetics, R, software | Tagged , , , , , , , | 3 Comments

Finding hidden structure in uneven data

Posted on 23 Feb, 2016 by Rob Denton

If you are a population geneticist, your work might include sampling a bunch of individuals and figuring out who is related to who. Seems simple right? Before you can ask questions about differences or similarities between groups, you have to understand what … Continue reading →

Posted in software | 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

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

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

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

On false positives in Isolation with Migration analyses

Posted on 19 Oct, 2015 by Arun Sethuraman

The IM suite of tools (IM, IMa, IMa2, IMa2p, etc.) are used widely by molecular ecologists at large for the analyses and estimation of ancestral demography under an Isolation with Migration (IM) model. However, these tools come with fundamental assumptions … Continue reading →

Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory | Tagged , , , , , , , | 1 Comment