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Author Archives: Arun Sethuraman
Selection scans, and the genomics of adaptive/maladaptive introgression
Natural selection, and the adaptive evolution of hybrid reproductive incompatibilities post divergence are known to be major drivers of speciation. At the phenotype level, these manifest as fitness differences between introgressing populations. At the genomic level, speciation “genes” or “islands” … Continue reading
PCA of multilocus genotypes in R
An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading
Posted in bioinformatics, genomics, howto, population genetics, R, software
Tagged data visualization, Homo sapiens, R
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IMa2p – Parallel Isolation with Migration Analyses
I figured that it was time to write an update on my post from a year ago on Bayesian MCMC in inferring ancestral demography. Recently, my postdoctoral advisor, Jody Hey and I released a version of the popular IMa2 program, … Continue reading
Posted in bioinformatics, genomics, howto, software, theory
Tagged Evolution, genomics, isolation, isolation with migration, migration, population genetics
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The Butterfly Effect
This might just take the prize for the ‘spiciest’ story in molecular co-evolution for 2015, yet. While a lot of the press coverage sounds like caterpillar thanksgiving, the science behind this study stands for the almost incredible power of molecular phylogenetics … Continue reading
Societal constructs, and Genetic diversity
While we grapple with numerous discoveries of variation in genomic diversity in humans, interest has subsequently risen in understanding their causes/results. Two recent papers describe experiments to determine (a) the effects of marital rules (who gets to marry whom) on … Continue reading
The Kennewick, and the Oase I
Last week was glorious for ancient DNA enthusiasts – here are some quick blurbs on findings from genomic analyses of the Kennewick man, and the Oase I individual. The ancestry and affiliations of Kennewick Man, Rasmussen et al. (2015) Nature DOI: … Continue reading
Posted in evolution, genomics, Paleogenomics, population genetics
Tagged gene flow, genomics, Homo sapiens, population genetics, population structure
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IBE/IBD Contour plots in R
Rob’s post from yesterday motivated me to find an alternate way of visualizing correlations between matrices of geographical or ecological data, and genetic data. I have seen plenty of Mantel, or partial Mantel tests of correlation, as well as plots … Continue reading
Posted in bioinformatics, howto, population genetics, R, software
Tagged data visualization, landscape genetics, methods, population genetics
5 Comments
Genomic history of Eurasia
The route of modern humans out of Africa has been contentious, with archaeological and genetic finds pointing towards a route through Egypt, versus one through Ethiopia. Pagani et al. (2015) analyze the genomic admixture of individuals sampled from both Egypt … Continue reading
Posted in genomics, Paleogenomics, population genetics
Tagged gene flow, genomics, Homo sapiens, population genetics, population structure
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