Category Archives: The Molecular Ecologist

The Molecular Ecologist: Tallying differences between species — across the whole genome

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Muchárik bielokrký (Ficedula albicollis); Collared Flycatcher A collared flycatcher. Photo by Photo Nature.

This week at the Molecular Ecologist, I discuss a new, genome-wide study of genetic differentiation between two closely related species — the collared flycatcher and the pied flycatcher.

Equipped with the core genome sequence, the team collected still more sequence data from ten male flycatchers of each species, and aligned these additional sequences to the genome sequence, identifying millions of sites that vary within the two species, and millions of sites where they share variants. They scanned through all these sites to identify points in the genome where differences between the two small samples of flycatchers were completely fixed — that is, sites where all the collared flycatcher sequences carried one variant, and all the pied flycatcher sequences carried a different variant. The frequency of these fixed differences varied considerably across the genome, but there are dozens of spots where they’re especially concentrated, forming peaks of differentiation.

To learn what all those “islands of divergence” could tell us about how the two flycatchers came to be different species, go read the whole thing.◼

The Molecular Ecology Online Forum

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Remember the Molecular Ecologist symposium I attended as part of the 2012 Evolution meetings in Ottawa? Well, there’s going to be a sequel, launching Wednesday in convenient online format.

The Molecular Ecologist will be hosting speakers from the Ottawa symposium in a live-chat on the blog, starting at 9 a.m. US Central Time and running until noon (that’s 3-6 p.m. GMT, for those of us located outside North American). We’re trying out a live-chat service called CoverItLive, which will let readers follow the coversation and submit questions and/or comments directly from the blog — test runs have gone pretty smoothly, and I’m excited to see how this works as a medium for scientific discussion.

If you want to review the Ottawa symposium beforehand, check out the archived material at the Molecular Ecology websited. To indicate your interest and submit questions in advance, e-mail Molecular Ecology Managing Editor Tim Vines; otherwise, just join us Wednesday morning at The Molecular Ecologist.◼

The Molecular Ecologist: Genes … in … space!

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(A) Geography, and (B) genetics. Figure 2 from Wang et al. (2012).

I’ve got a new post up over at The Molecular Ecologist, discussing a new paper that tries to take a quantitative approach to a phenomenon that keeps turning up in human population genomic datasets, in which genetic data mirrors the geography of the places it was collected.

It’s something of a classic result in human population genomics: Go out and genotype thousands of people at thousands of genetic markers. (This is getting easier to do every day.) Then summarize the genetic variation at your thousands of markers using Principal Components Analysis, which is a method for transforming that genetic data set into values on several statistically dependent “PC axes.” Plot the transformed summary values for each of your hundreds of samples on the first two such PC axes, and you’ll probably see that the scatterplot looks strikingly like the map of the places where you collected the samples.

Of course “looks strikingly like” is not a very quantitative statement. To see how the new study deals with that problem, go read the whole thing. And yes, I manage to shoehorn in a reference to the Muppets.◼

The Molecular Ecologist: ABC, quick as A-B-C

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If I said you had a nice posterior Reverend Bayes, would you take offense? Photo via WikiMedia Commons.

Over at The Molecular Ecologist, new contributor Peter Fields—a Ph.D. student studying plant-pathogen coevolution at the University of Virginia—writes about approximate Bayesian computation and a new approach to this still-developing method of statistical inference that can make it quite a bit faster.

ABC functions upon the rationale that the likelihood might be approximated through the use of simulation and simulation summary statistics2, and that the evaluation of model fit to a dataset can be identified through a comparison of Ss derived from simulated scenarios and calculation of those same summaries on an observed, empirical dataset. In theory, simulation summaries are selected to provide maximal distinction amongst competing models. In practice, identifying these summaries isn’t always easy, and is the object of continued research3

For an introduction to ABC, and a description of the new approach, go read the whole thing.◼

Big, bloggy news

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Starting today, I’m officially part of the crew at the Molecular Ecologist, the group blog associated with the journal Molecular Ecology, as both a contributor and a sort of coordinator/administrator.

Molecular Ecology‘s managing editor Tim Vines first approached me about joining the site back at Evolution 2012, and I’m excited to start talking about the many wonderful uses of molecular genetic data with Holly Bik, Mark Christie, Nick Crawford, and Peter Fields. We’re hoping to bring in lots of guest posters as well. (And if you’re interested, send me an e-mail.) Although the Molecular Ecologist is affiliated with Molecular Ecology, the vision of the site is not to promote the journal itself, but to build a space for the community of scientists interested in the journal’s subject matter. As part of that effort, we’ve launched a Molecular Ecologist page on Facebook, and I’m taking over @molecologist on Twitter.

This doesn’t mean I’ll stop posting at Nothing in Biology Makes Sense!, much less here at D&T; the Molecular Ecologist is aimed at a somewhat different audience than either of my other online locales, and while this may spread me a little thinner, I expect I’ll be covering different topics at each site.◼

The Molecular Ecologist

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The journal Molecular Ecology Resources, a methods-focused offshoot of Molecular Ecology, has just launched an official blog, The Molecular Ecologist. One of the contributors is Dilara Ally, who until quite recently was one of my colleagues at the University of Idaho Department of Biological Sciences. From the first few posts, it looks like TEM will be a good resource for working biologists, who are the target audience.