Category Archives: methods

Dishing out Art: “Soiling” our microbiology curriculum

Sarah Adkins wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. She is a MS student working with Dr. Jeffrey Morris at UAB. They are looking at how microbes (i.e., phytoplankton and E. … Continue reading

Posted in blogging, Coevolution, evolution, methods, microbiology, natural history, selection | Tagged , , , , , | Leave a comment

An Update on the Great BAMM Controversy

Update, 01 August 2016, 2:50PM. This post has been updated to include information contained in the supplemental material of Rabosky et al. 2017, and clarify the difference between branch-specific and tree-wide rate variation. Back in August, I summarized the main … Continue reading

Posted in blogging, evolution, methods, phylogenetics, science publishing, software, speciation | Tagged , , , | Leave a comment

Unbalanced population sampling and STRUCTURE

The utility and intuition offered by the program STRUCTURE, and more generally, the ‘admixture’ model of Pritchard et al. (2000) are unquestioned – with tens of thousands of citations, it retains its lead among the most popular population genetics software. … Continue reading

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , | 1 Comment

The road ahead

It’s been almost two weeks since we woke up to the reality that Donald Trump — the failed casino mogul, the virtuoso tax-dodger, the reality-show star, the self-described serial sexual assailant, the Ku Klux Klan endorsee and darling of white … Continue reading

Posted in citizen science, community, funding, NIH, NSF, politics, United States | 19 Comments

Divergence and Linked Background Selection

We have widely discussed the reduction in neutral diversity due to demography and linked selection effects (e.g. selective sweeps and hitchhiking, or background selection) in several previous posts (e.g see here, here, and here). However, how linked selection affects neutral divergence … Continue reading

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The almighty CRISPR-Cas9 technology: The future of conservation?

In the first post on CRISPR-Cas9, I’ve explained how bacteria and archaea create a “database” of infections and use it as a form of prokaryotic immunization. This time, I’m going to concentrate on how biotechnology turns this natural phenomenon into … Continue reading

Posted in conservation, evolution, methods, theory | Tagged , , , | 1 Comment

When your programming may be inadequate to the task: new options for metagenome analysis

There’s a lot of data in the form of metagenomes out there, and picking apart those mountains of data to uncover meaningful results is difficult. Recently, we received a suggestion from a reader to discuss a recent program (CLARK-S) developed … Continue reading

Posted in bioinformatics, community ecology, metagenomics, methods | Tagged , , , , , | Leave a comment