What we're reading: Bayesian phylogenetics for whole genomes and coevolutionary interactions in epidemiology

In the journals
Aberer A.J., K. Kobert, and A. Stamatakis. 2014. ExaBayes: Massively parallel Bayesian tree inference for the whole-genome era. Mol. Biol. Evol. 31(10): 2553-2556. doi: 10.1093/molbev/msu236.

Modern sequencing technology now allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary trees. We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on data sets of arbitrary size.

Kodaman N., R.S. Sobota, R Mera, B.G. Schneider, and S.M. Williams. 2014. Disrupted human–pathogen co-evolution: a model for disease. Frontiers in Genetics. 5:290. doi: 10.3389/fgene.2014.00290.

We suggest that disrupted co-evolution between a pathogen and its human host can explain variation in disease outcomes, and that genome-by-genome interactions should therefore be incorporated into genetic models of disease caused by infectious agents

In the news
“There is a fundamental and culturally learned power imbalance between men and women, and it follows us into the workplace. The violence born of this imbalance follows us also. We would like to believe that it stops short of following us into the laboratory and into the field — but it does not.”
“Our students are counting on us to create an environment that enables their success. Safety always comes first. Safety requires an aware environment and respectful attitude in the workplace. *The workplace includes the field*.”
“Amid a wave of recent journal article retractions, researchers are taking to social media to discuss a perennial favourite: a three-year-old paper looking at the relationship between a journal’s impact factor and its retraction frequency.”
“I recommend that we drop the preproposals, go to a single full proposal a year, and as a community commit to careful review of the adhoc proposals we receive.”

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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