November 2008 Archives

If you tried to download the second paper for Project #3 (the one from Molecular Ecology), you will have found that the link was broken. I've fixed it now, so you should be able to get it without any trouble.

Happy Thanksgiving!

The latest issue of Nature Review Genetics has a paper by Andreas Wagner with some interesting perspective on molecular evolution. I don't plan to discuss it in class, but you might find it interesting. Here's the link.

http://www.nature.com/nrg/journal/v9/n12/full/nrg2473.html

There's also a paper in PLoS Genetics that you might find interesting. It's an alternative to QTL mapping in which all of the data are used simultaneously to predict phenotypes, and the particular loci that have an important influence on the trait emerge more naturally from the analysis.

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000231

I've just posted Project #3 to the course web site. You'll find a link to the assignment and the associated data set on the detail page for tomorrow's lecture. I'll need to introduce you to one final software package, Arlequin. The current version is only available on Windows, which is the version I'll show. But I think that the earlier version that runs on Macs will work for this project too. The interface is very similar. I may not have a chance to try the Mac version before lecture tomorrow, but I'll do my best to try it with these data by late on Monday, and I'll let you know whether you'll be able to run it on a Mac.

I've heard from a few more people about problems. If you get this message and have time before lecture this morning, please try this and let me know what happens.

I've had reports from at least two people that WinQTLCart freezes on them when they try to do an analysis, either IM or CIM. I am investigating and trying to diagnose the problem. In the meantime, if you haven't downloaded WinQTLCart and the data yet, please give it a try and let me know whether or not it works for you and what operating system you're running.

I think I know a workaround, but it's one I'd prefer to avoid using unless we have to. I'd rather fix the problem.

James F. Crow, a very distinguished and very influential population geneticist at the University of Wisconsin, has an article that's relevant to today's lecture that just appeared in Annual Review of Genetics -- literally, just appeared. I received a notice in my e-mail box this morning. I've added a link to the article under the detail page for Monday's lecture, since that's the day that has the notes I'll be starting with this morning. Here's the direct link, if you don't want to click through to Monday's notes.

If you haven't had enough quantitative genetics and you want to see a really hairy application of (a) quantitative genetics and (b) Bayesian statistics, there's a seminar in the Department of Statistics this Friday that you won't want to miss.

Hierarchical spatial modeling of additive and dominance genetic
variance for large spatial trial datasets

DATE:   Friday, November 7, 2008
TIME:    4:00 p.m.
PLACE: CLAS Building - Room 344

Professor Sudipto Banerjee
Department of Statistics
University of Minnesota

Click through for the abstract.

As promised (threatened?), I've posted the QTL problem. I'll need to show you two or three more things about  QTL Cartographer before you can do the whole analysis, but if you'd like to download the data and make sure you can read it into QTL Cartographer, everything is available from the detail page for tomorrow's lecture.

Oh, one word of warning. Each analysis for composite interval mapping is going to take a long time. I started an analysis of the %N at 25°C data this morning around 10:00am, and it's still running. I mention this as a warning. You're going to want to start your analyses fairly soon, and you'll probably want to set them to run overnight. If CIL takes inordinately long, which I'll know by lecture tomorrow, we'll settle for an interval mapping analysis instead.

I've added some additional information on using QTL Cartographer to the online notes. You can find the new version of the notes from the detail page for 29 October. The new part is the section on interpreting output files. If you've already printed the notes, you only need to print the pages in this new section if you want a copy.

I found a good QTL data set (from maize), so I'll be handing out Problem #4 on Monday. That's the bad news. The good news is that I've decided to make it due on the 14th rather than on the 10th. You'll only have one weekend available, but you'll still have a week and a half to get the analyses done.

I'll hand out the final project on the 17th rather than on the 14th as originally planned.

On a related note, we'll probably spend about half the lecture on Monday going over some more features of QTL Cartographer, and I will try to type up some supplementary notes that you're likely to find useful in doing your QTL project.