analysis

North Atlantic

It’s funny, I made my start as a population geneticist championing the cause of the North Atlantic Ocean, and I don’t think about it as often these days. Our careers creep in many funny directions, sometimes pulled by funding opportunities and sometimes by fortuitous collaboration.



The above image was snared from the website of Geoff Trussell’s lab at Northeastern University. Geoff is one of my many great colleagues that I know from interactions at the CORONA meetings and every year that I can make it to the Benthic meetings on the east coast (and really, who would want to miss these meetings? Nice one, Jeremy...). Anyway, the image is primarily of the dogwhelk, Nucella lapillus. A really beautiful snail, lots of color variation, interesting genetic patterns, part of my dissertation.

The work is finally being updated, with modern statistical (ABC) approaches, by my good friend and colleague Mike Hickerson and his student and postdoc (particularly lead author Katriina Ilves). The results are clearly starting to change. There are taxonomic controls on who survived glaciation and who didn’t - on the east coast of North America, at least - rather than larval life history controls, if the statistics tell the whole story. What is amazing is how big of an impact that paper had in 2001, and I suspect this paper will have a big impact in 2010.... and yet we still clearly know so little. Most of these species have still only been assayed for mitochondrial variation. The time will come soon when we can apply for funding to tackle the same community using variation across the entire genome.

New Site

Well you are looking at v.2 of the Wares lab website. I’ve moved it all over to RapidWeaver so it is waaaaay easier to manage and expand/contract as necessary. The blog has been managed in this way for about a year, and it just took me a while to get up the courage (and the time, thank you summer) to make the switch. The previous incarnation was beautifully rendered in PHP by Carrie Bishop, and I greatly appreciate her work but this format will make it easier for me to distract myself from my “real” work.

It has been a week of banging my head against computational things in lots of ways. Turns out, for example, that MrBayes does not fully compile correctly under 64-bit architectures (like Snow Leopard OS 10.6 on my Mac Pro), so I lost a few days of work on freshwater mussel phylogenies figuring that issue out, and ultimately just snagging the compiled version off of my old G5 (32-bit) and everything works fine now, thanks. Maybe someday we’ll actually get these mussel papers out, I’d like to do it soon so I can keep working on them. Fun excuse to go splashing in a river in the summer!

Conservation of Genetics

I’m pleased to see my obsessive relationship with Tajima’s D coming to fruition: my paper will come out in Evolution in the next few months, indicating that despite our tendency to assume a data set is neutral until proven otherwise, the average mitochondrial data set does not behave the way this test of neutrality indicates it should. On the whole, there is a strong bias for negative values of Tajima’s D, suggesting we may need to re-think our nulls in evolutionary biology. However, it makes me nervous to put too much faith in this one analysis of one locus of course! Driving home from Asheville the other day I got very nervous that the effect noted in this paper: what if it is an effect of how researchers curate their data into NCBI? When I got home I checked, and there is a small “curation effect” but I think the biological effect is still strong. Hard to be confident when there are so many factors involved.

In other news, I’ve recognized just what a valuable resource is building up in my -80° freezer: several studies’ worth of DNA isolates, from seastars, isopods, barnacles, fishes, and so on. I’ve had a tendency to try and answer a question (grabbing new samples) and move on; but there is a lot more work to be done on all of those DNA samples. It was hard to get them, they are valuable, right?! So my next rotation student should expect to hear the question: “What do you want to do with all the DNA in my freezer?”