November 2006 Archives

I've posted notes on AMOVA (Analysis of Molecular Variance) and rearranged the remaining lectures a bit, dropping the one originally scheduled for tomorrow and spreading the rest out. It's not clear yet whether I'll find a real data set for you to analyze for the final project, but I'll probably take time to show you how Arlequin does an AMOVA on Monday. Arlequin runs on Macs as well as PCs, so those of you with a Mac should be able to play along too -- if you're so inclined

I've posted the notes on evolution in mutigene families. I have a feeling that we won't finish everything I'd like to say about them today, so we'll probably take all or part of Friday's lecture to finish. If so, I'll just skip the stuff I'd originally planned for Friday.

I've just posted notes on Tajima's D and some related statistics. We'll start on evolution in multigene families on Wednesday.

I hope everyone had a safe and enjoyable Thanksgiving. I had a lot of work to do over the last several days, but my holiday was quite pleasant nonetheless. Of course I'm not posting this message just to give you an update on my Thanksgiving. I want to point out a couple of changes concerning the remaining assignments before I see you in lecture tomorrow. (Don't worry. It means less work, not more.)

I've just posted notes that should get us through the end of this week and into Thanksgiving vacation. I hope you used your day off Monday productively.

I've posted selected thresholds for the QTL analysis in Project #2. They're part of the table in the project assignment. I'm not entirely convinced they're the correct thresholds, but they'll be close enough for our purposes. Let me know if you run into any problems with the data. I think everything will work now.

I've uploaded some notes on topics we'll get to tomorrow, after we finish our introduction to the neutral theory.

Other items of note:

• Now that I've finished the notes, I'm going to start the permutation analysis for data set 4 (ShootDW.15). If anyone happens to have time to run data set 3 between now and tomorrow morning, that would be great. Have at it.

• In case I forget to remind you in class tomorrow, we won't have class Monday.

I've posted notes on the neutral theory of molecular evolution. Because the basic ideas are really pretty simple (even the math is simple), we may actually get through these today -- even though we first have to finish up some stuff I didn't cover on Monday. If not, we'll finish on Friday.

I've upoloaded Project #2 to the course website. It shouldn't come as a shock to you that it involves using QTL Cartographer. There's a link to the data file on the course detail page for tomorrow's lecture, but here it is again:
Fracheb1map_inp_In.mcd. As you'll see, this file contains phenotypic information on eighteen traits. I'm only asking you to analyze four of them (though you can analyze more if you feel like it). It takes about 2 1/2 hours per trait to find the appropriate threshold value, so I'll be updating a table with suggested threshold values in the assignment as I finish those analyses.

I've posted the first set of notes on molecular evolution. Before we start with them, we'll finish off a couple of things with QTL Cartographer that you need to know. As a result, we probably won't get to the Jukes-Cantor model for nucleotide sequence evolution, but we'll get there first thing on Wednesday if we don't.