Monthly Archives: June 2015

Gene expression analysis- are we doing it wrong?

Posted on 29 Jun, 2015 by Melissa DeBiasse

In the last few weeks, three new preprints have come out suggesting that like Jack Butler dropping his kids off at school in the movie Mr. Mom, when it comes to differential gene expression analyses, we’re doing it wrong.

Posted in Uncategorized | 4 Comments

The Kennewick, and the Oase I

Posted on 25 Jun, 2015 by Arun Sethuraman

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

Posted on 18 Jun, 2015 by Arun Sethuraman

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

Adapting to the new wave of isolation by environment

Posted on 17 Jun, 2015 by Rob Denton

Isolation by environment, not distance, explains the genetic relationship between an avian taxon among Madrean Sky Islands, according to a new study appearing in Molecular Ecology by Manthey and Moyle. The authors throw the kitchen sink of new analyses at a combination … Continue reading →

Posted in adaptation, Molecular Ecology, the journal, phylogeography | Tagged , , | 1 Comment

The evolution of phylogeography in the next gen era: 20 years in review

Posted on 15 Jun, 2015 by Melissa DeBiasse

Phylogeographers have long known about the limitations of single locus studies (ie, the effects of selective sweeps, stochasticity in lineage sorting among loci) and that adding loci improves the accuracy of demographic parameter estimates. As we continue to shift towards collecting multi-locus datasets thanks to high throughput … Continue reading →

Posted in evolution, genomics, Molecular Ecology, the journal, next generation sequencing, phylogeography, Uncategorized | 3 Comments

Genomic history of Eurasia

Posted on 11 Jun, 2015 by Arun Sethuraman

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

Posted on 10 Jun, 2015 by Rob Denton

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

Old dogs, and 'carnivorous' pandas

Posted on 4 Jun, 2015 by Arun Sethuraman

It was a good fortnight for large mammals! Two recent studies attempt to date the emergence of modern canids, and offer insights into the gut microbiomes of giant pandas. Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and … Continue reading →

Posted in adaptation, evolution, genomics, metagenomics, microbiology, natural history, Paleogenomics, population genetics, speciation | Tagged , , , | Leave a comment

Live from London: reporting from "Elements, genomes, and ecosystems"

Posted on 3 Jun, 2015 by Rob Denton

Scientific meetings are great: see old friends, meet new colleagues, sow the seeds of collaboration, see interesting work from around the world, and so on. They’re fun, they really are. But they can be so big. The annual meetings of the … Continue reading →

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