Sunday, February 24, 2008

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.

Sunday, February 10, 2008

Quick 1-night visit to Portland for committee meeting

I just got back from a whirlwind visit to Portland, Oregon. I loved flying in on the plane from Burbank, seeing the green trees. There were no leaves, no, the trees were green with moss, lichens and fungus. It was cloudy and drizzly. I love it! Nothing against Southern Cal, which I admit has quite a bit of charm with its snuggly warm sunny days, but I love the Northwest.

I flew in, then helped a visiting prospective graduate student find her way around, then had a meeting with my committee. Those meetings simply scare me for some reason. I don’t seem to be able to express myself well in front of them. They had a lot of helpful comments, though, and were not necessarily antagonistic, just, oh what’s the word, intense. It’s great to have a group of people intensely interested in what you’re doing, but for some reason I always feel like I’m about to do something wrong. Silly me. They agreed with my dissertation plan, which goes something like this:

Chapter 1: Introduction to dispersal and gene flow, from an article I have in press with Elsevier in their upcoming Encyclopedia of Ecology.

Chapter 2: Genetic marker development methods paper for my project, in press with Molecular Ecology Notes

Chapter 3: Oregon-wide dispersal/gene flow patterns for Brachypodium sylvaticum

Chapter 4: A small-scale analysis of a group of populations near Sweet Home (this is the one I’m currently getting ready to publish)

Chapter 5: Outcrossing data. I haven’t looked at this data much in-depth yet, but we have data from field-collected progeny that could be quite interesting. We’ll see.

I’m glad they liked my plan, and they’re not against me continuing to work long-distance, even if it’s from India. They’re very supportive, which is great! I’d like to meet with them again before we leave, maybe on a 1&1 basis. We’ll see if I can pull that off.

We had a fun lab party in the greenhouse and some of the other faculty showed up. I simply love our lab parties! Hot Lips pizza, which is simply scrumptious, some sushi made by a lab member, salad, chocolate, beer (Sprite for me), and wonderful company.

I spent Saturday morning with my former undergraduate, hacking away at some analyses for the paper we're working on. There's so much more to do! But we'll just keep working at it and hope for the best. Flew out in the afternoon after a lovely buffet lunch at House of India or something like that, and got home around 9pm to an ecstatic TM.

TM did great staying with my aunt and uncle. My mom even came to play with her on Saturday, which she really loved. But it was very very difficult for me to be away from her for so long, knowing that neither my husband nor I would be around. For some reason that just made it very difficult. I still have a tic in my right eyelid from the combined stress of everything. Hopefully it’ll go away soon.

Now all I have to do is manage to get our visas so we can ship our stuff to India (I didn’t know we had to have visas before shipping), get our current manuscript submitted to a journal for publication, and finish the 3 native plant garden projects that are jumbling around in my head.