Category Archives: STRUCTURE

On (mis)interpreting STRUCTURE/ADMIXTURE results

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

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Genomics of Hybridization – Part II, Top three of 2015

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

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

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

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?

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

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