EEB 348 -- Population Genetics

Population Genetics and Microevolutionary Theory

I just got a copy of Alan Templeton's new book, Population Genetics and Macroevolutionary Theory (Wiley, published September 2006), and it looks pretty good. It's also pretty pricey ($99.95 on Amazon.com, $79.96 for members on Barnes & Noble.com, and $99.95 on Wiley's site). But if you want a good one-volume reference, this would be my current recommendation.

Final grades posted

I've posted final grades to PeopleSoft. A few of you will find incompletes, but I think you're all expecting them. If you have any questions, please e-mail me. Have a wonderful winter break, and travel safely. Thanks for a great semester. I hope you enjoyed it as much as I did.

Course evaluations

I'll be stopping lecture about 10 minutes early for the usual course evaluations. I don't have a way for those of you at Avery Point to fill out the formal evaluations (unless there's something going on down there that I haven't heard about), but if you have comments you'd like to share, please send them to Kathy Tebo indicating that they are instructor evaluations for EEB 348. She will hold onto them until some time early in Spring semester -- well after I've filed grades.

In addition to that evaluation, there are two more I hope you'll participate in. The first is an evaluation of the distance learning aspects of the course through the Institute for Teaching and Learning. Please return the Word document directly to Steve Fletcher at the address indicated in the document. Please notice that the folks at ITL are interested in your assessment of the distance learning environment regardless of whether you participated in the course from Avery Point or from Storrs.

The second is your chance to evaluate Uzay. Please return your evaluation directly to Kathy Tebo. Neither Uzay nor I will see his evaluation until after the first of the year. I'm not sure if I'll ever see the results of the survey from ITL.

More on NCA

I've just posted revised notes on Nested Clade Analysis. I haven't changed anything. I've only added a description of how to produce the “nested” set of haplotypes that are used for the next phase of the analysis. You'll find the new material at the beginning of the section entitled “Nested clade analysis”

I've also posted links to three papers (two on NCA, one on statistical phylogeography) that you may find interesting/useful.

Nested clade analysis

I've posted the notes for nested clade analysis. As noted in the detail page for tomorrow's lecture, I don't think we'll finish everything in these notes tomorrow. I expect to spend more time on it on Friday. As a result, I will barely be able to say the words "statistical phylogeography." If you're interested, talk to me, and I'll be happy to provide pointers to some relevant papers.

Project #3

I've posted Project #3.You'll be please to know that you don't have to fight with any software for this project. All you have to do is to read a few papers and apply what you know to a critical analysis of them. Easy, right?

]]> By the way, we'll be focusing almost entirely on AMOVA on Monday. Depending on how things go, I may decide to drop the last lecture on phylogeny reconstruction and focus on phylogeography instead. Let me know if you have strong preferences one way or the other.

AMOVA

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

Evolution in multigene families

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.

Tajima's D

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

Welcome back!

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.)

]]> You'll see on the Overview page of the course website, I've eliminated one of the short projects I was originally planning to assign, and I've adjusted the weight assigned to each project and problem a little to compensate for the missing eleven points.

You'll also see on the course schedule page that I've changed the date when I plan to assign the final project to Monday, 4 December (from Wednesday, 6 December). The final project will still be due on Wednesday, 13 December.

It's also possible that the final project will be a bit different from those you've done so far. In particular, I'm thinking that I may ask you to read and evaluate a paper on molecular phylogeography or on analysis of selection at the molecular level. If I can, I'll get at a copy of at least some of the original data so that you can reanalyze it if you want to, but the emphasis will be on evaluating work that others have done rather than doing a problem yourself. If you're interested, you can refer to Project #3 from Spring 2004 for an example of what you might be in for.

Notes

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.

Thresholds -- finally!

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.

More notes

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.

Neutral theory of molecular evolution

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.

Project #2

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 had to fight with this data set quite a bit to get it to run. I suggest trying a preliminary analysis to make sure you can get it to run. That way there will be more time for me to help you solve any problems you may encounter. Enjoy!