Category Archives: population genetics

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

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Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 3 Comments

Who came first – the Paleo- or Native American?

In yet another infamous Science vs Nature race, two studies published this Tuesday toss more cans of worms at the ongoing debate about the founding of the Americas – with disparate findings. Uh oh. Skoglund et al. Nature (2015) Genetic … Continue reading

Posted in genomics, next generation sequencing, Paleogenomics, population genetics | Tagged , , , , | 2 Comments

Dozens of talks from the Evolution 2015 meetings are on YouTube

If, like me, you didn’t make it to the 2015 Evolution meetings — maybe the logistics of a trip to Brazil were beyond your financial and/or temporal means — you can make up for it with the big cache of … Continue reading

Posted in community, conferences, phylogeography, population genetics | Tagged | 1 Comment

Dispersal by land or by sea

Here, we compare and contrast the traits and selective forces influencing the evolution of dispersal in marine and terrestrial systems. From this comparison, a unifying question emerges: when is dispersal for dispersal and when is dispersal a by-product of selection … Continue reading

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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

Posted in adaptation, evolution, genomics, natural history, population genetics, selection, speciation, transcriptomics | Tagged , , , , | 1 Comment

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

Posted in evolution, genomics, natural history, population genetics, selection, societal structure | Tagged , , , , , , , | Leave a comment

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 , , , , | Leave a comment

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 , , , | 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

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Landscape genetics gets existential

I had a lot of ideas for future posts, but “landscape genetics” keeps pulling me back. Beyond the new methodology, reviews, and empirical findings, I suppose someone has to pump the brakes and get more existential. Rodney Dyer does just … Continue reading

Posted in Molecular Ecology views, Molecular Ecology, the journal, population genetics | Tagged , | 1 Comment