Data analysis and moving preps

It’s been an interesting week. After coming back from Portland, at first I thought I could do away with Structure (Pritchard) analysis completely, which was quite exciting. Then my advisor said that’s not such a good idea, so it’s back on the books. Luckily, my former undergraduate had some really good ideas about what to do. The results have been multimodal, meaning that different runs give different results. Instead of putting ALL the data in, I took some of the peripheral populations out. It was still multimodal. Then I took all the peripherals out, and it wizened up! Though I haven’t been through all the results yet, it seems like the runs are more consistent. That’s very interesting. I’m planning on adding in the peripheral populations one at a time and seeing what happens. At my advisor’s suggestion, I also took out individuals that had an identical genotype to another individual in their population, and the runs were still multimodal. I get the feeling that there’s something here that should make sense but I’m not quite grasping. I may try taking out individuals that have genotypes that are repeated ANYWHERE, not just in their populations. Just for kicks.

Does it look like I’m running around in circles with this stuff? Yes, but I’m not really, I get the feeling that (since excluding peripheral pops got rid of multimodality) I’m closing in on something. Oh – there’s another program, InStruct (Gao), based on Structure, that actually takes into account inbreeding (a big factor with Brachypodium sylvaticum, since it selfs and outcrosses). Sometime inbreeding will make Structure tell you that inbred populations are admixed (intraspecific hybrids). That’s a major concern with our data, since some of our conclusions are based on the fact that putative source populations are admixed. Well, I ran InStruct and still got admixture! Hooray! That’s a relief. I was a bit worried about that. But now, of course, I’m going to have to echo whatever analyses I run with Structure in InStruct. That’s okay, though, now that I know they won’t completely contradict each other.

My former undergraduate just used another program, SpaGeDi, to look for isolation-by-distance (IBD), where populations near each other are more similar than populations that are distant. Well, I haven’t been able to look at her results yet, but I’m getting the idea that our data presentation will look something like this:

Genetic marker information (allele freqs, etc) (Arlequin, GenePop)
IBD (mantels, SpaGeDi)
ID of source populations (GeneClass2, Structure, InStruct)

I think that makes sense. We’ll see.

On the “moving-to-India” front, my husband came in on Thursday for TM’s 2nd birthday on Friday. TM was thrilled to death! The movers are coming next Monday and Tuesday, and then we’ll be living out of suitcases until after Apr 15, when we leave for India at last. Hooray! I still have to get my husband to fill out various moving forms – don’t let me forget. He did bring the Toyota sale bill with him, so the nice couple who bought our Toyota last month finally have a legal bill of sale. My husband leaves again on Mar 6th, then comes back Apr 15 to help us get to India.

I don’t have my visa yet – if I don’t get it by mid-March, I’m going to switch my application to a tourist visa. That would be a little unfortunate, since it means I’d have to leave the country every 6 mo, but at least I’d be able to get to India. I’m hoping I could change my visa once I get there. TM has her PIO card, though, hooray! That was a major relief. It looks like a mini-passport – pretty cool. And she’s so cute!

It’s Sunday, so I don’t really want to do shopping (even online), and I’m not sure what I’ll do ‘till TM wakes up. Maybe I’ll pick up Mark Twain’s Prince and the Pauper again, but it was a little stressful, what with having the nice prince kicked out into the streets and beaten, and having the pauper in a very stressful situation as well… I may just skim it and see what the details of the plot are. I don’t always like to see nice people treated horribly...

My husband said I don’t have any classics on my Amazon wishlist, so I updated it to include a lot of classics. There ya go. I keep thinking that I might not be able to get some of my favorite movies over there, and then I remind myself that I haven’t had them for years and years over here either, and got along just fine. J.

I do need a desktop computer, though, since I live in fear of my now ageing laptop giving up the ghost. It’s out of warranty. It has several thousand dollars worth of programs that I use for my work that I don’t have the discs for. Eeeek. I’ve been trying to decide between a Mac and a PC. I may stick with a PC just ‘cause I can fix things in it myself. A Mac is better, of course, but if I’m going to India I’d rather have something I can fix myself, and a Mac is not that… Also, everyone I work with currently has PC’s and of course it would be a little tricky to interface with a Mac. Ideally, I’d have both a Mac and a PC. Hee hee hee.

Well, I’m off to entertain myself on this lovely, drippy Sunday morning. TM’s sleeping great since I begged her to drink water only at night, hooray! It took almost 2 yrs to get a good night sleep. Wow.