Wednesday, March 19, 2008

FSTAT analyses make a pretty picture

I should probably have a blog for different parts of my life – kids, healthcare etc, and PhD work. But I’ll just stick with this one.

My advisor sent me a paper (Waples & Gaggiotti 2006) that talked about the definitions of a population, and included some cool tests to see whether a group of samples were panmictic or not. How did I miss it? I’d read it before, but didn’t put the analysis together with what I wanted to do. It’s exactly what I’ve been looking for! Structure couldn’t do it, and Geneclass2 wasn’t quite it either.

The Structure analyses were a mess – Brachypodium sylvaticum has high inbreeding (really high, like FIS=0.7), and the source populations for the small area we’re working on right now are really admixed. Or so it seems. Whatever the problem, Structure identified the peripheral populations as belonging to distinct clusters, while the source populations were a big huge mess. GeneClass2 was fun, but the picture it painted wasn’t clear – I could easily tell which populations were sources for a lot of other pops, but it was hard to figure out a way to draw it out graphically.

Then I re-read Waples & Gaggiotti 2006 and found that they did a pairwise test (in FSTAT) for population differentiation, and when the tests were insignificant, they concluded that the populations were, well, effectively a single population. That’s just what I was looking for! We had sampled about every mile along three roads, and I wanted to see which populations (sample sites, really) were similar, thinking that would give a good idea of dispersal patterns in the area. I probably should have mapped out all the individuals, and it wouldn’t have been too hard, but I didn’t, so now estimating neighborhood size is out of the question. That would have been ideal. But this pairwise test for differentiation works pretty well! I’m happy with it, at any rate.

I drew up a picture on a map with sample sites connected that were not different, and sent it off to my advisor and other coauthor (the former undergraduate). I haven’t heard from them yet, but I’m hoping they’ll like it.

Meanwhile, the move to India is moving apace. My husband will come back to “collect” us on Apr 10th or so, then we’ll spend a few days in MD with TM so she can have a break from flying. Then we’ll fly to Frankfurt and from there to Bangalore. The last leg will be the worst, ‘cause she’ll be awake. Yoikes. Well, we’ll do our best.

In India, we’ll stay in a temporary apartment provided by my husband’s job until I can find an apartment we like, then we’ll move. Hooray! I really look forward to having a place of our own. Thank goodness his work is paying for the move, ‘cause it’s costing an arm and a leg. Anyway, then TM will have her toys and books again, and we’ll have more than one room to live in! What fun! I hope to find a school for her quickly, so she can get back to playing with friends and I can get back to work. I figure that after about a year of living there, we’ll be enjoying ourselves immensely.

My grandpa’s visiting this week, and I’m in charge of entertainment today and Friday, so there’s work down the drain, but it may be the last time I see him, so I’d better aprovechar, as they say in Spain.