Recently in Annoucements Category

I graded Project #3 on the plane ride to Auckland, and I have to say I was impressed with the quality of the answers. Most of you did a good job not only of getting numbers out of Arlequin, but also of making some biological sense of them. A few of you even tried some relevant analyses I'd only mentioned in passing or hadn't discussed at all and/or offered detailed analyses of the patterns that showed a lot of insight.

I've posted final grades for the course to PeopleSoft. I'm not sure how long they'll take to appear, but let me know if you see any problems when they do show up..

Thanks for a great semester. I hope you enjoyed it as much as I did, and I hope that you learned some things you'll find useful in the future.

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

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.

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.

Remember the t-shirt article I told you about early in the course? Well, another paper about MHC variation and mate choice in humans just appeared in Proceedings of the Royal Society. Here's the abstract:

Previous studies in animals and humans show that genes in the major histocompatibility complex (MHC) influence individual odours and that females often prefer odour of MHC-dissimilar males, perhaps to increase offspring heterozygosity or reduce inbreeding. Women using oral hormonal contraceptives have been reported to have the opposite preference, raising the possibility that oral contraceptives alter female preference towards MHC similarity, with possible fertility costs. Here we test directly whether contraceptive pill use alters odour preferences using a longitudinal design in which women were tested before and after initiating pill use; a control group of non-users were tested with a comparable interval between test sessions. In contrast to some previous studies, there was no significant difference in ratings between odours of MHC-dissimilar and MHC-similar men among women during the follicular cycle phase. However, single women preferred odours of MHC-similar men, while women in relationships preferred odours of MHC-dissimilar men, a result consistent with studies in other species, suggesting that paired females may seek to improve offspring quality through extra-pair partnerships. Across tests, we found a significant preference shift towards MHC similarity associated with pill use, which was not evident in the control group. If odour plays a role in human mate choice, our results suggest that contraceptive pill use could disrupt disassortative mate preferences. (emphasis added)

You'll want to download a copy of QTL Cartographer for the next problem. More specifically, you'll want to download a copy of WinQTLCart.¹ Although there's a version available for Linux and Mac OS X, it requires you to use a command line interface that's a lot less convenient. If you'd really like to try the analyses with that interface, I'll do what I can to help, but I have to confess to not being very familiar with it. You may be on your own.

I just ran across a very nice review article on heritability in Nature Reviews Genetics. I've added a link to it in the detail page for today's lecture, and it will also show up in the readings list for the course. Of course, if you click the link on Nature Review Genetics, you'll get there directly.

Since the data Dave Carr provided is not yet published, I've set it up in such a way that access is restricted. To retrieve it, you'll have to be inside the UConn.Edu domain. If you're retrieving the data from a computer connected to the campus network, you shouldn't have any problems. If you need to download it when you're off campus, you'll have to log on through the VPN.

I apologize for taking so long to post these solutions. I have some excuses, but I won't share them.¹ I'll just post the links.

• Problem #1 solution
• Problem #2 solution
  

I've added a link to a paper from Genetics in 1997 with the photos I described in class on Monday. You can find the link on the detail page for Monday's lecture.

You might also be interested to know that the number of loci estimated to influence height variation in humans is 54. See here for a brief discussion and a link to the papers describing the analyses. I'll mention association mapping briefly in another week or two.

Remember the t-shirt experiment I referred to? Well, a paper published today in PLoS Genetics provides evidence at the population level that mate choice in humans is influenced by the genotype at MHC loci. European American couples are significantly more dissimilar than would be expected if mating occurred at random.

I found a small error in the notes for today's genetic structure lecture. It's buried in the "Gory details" section, so you probably won't care. But if you do, and if you've printed out that page, you might want to print out a new copy.

If you're running Windows Vista, you are liable to run into permission problems when you try to install the Keys.ocf file that comes as part of your registration. To avoid this problem, I suggest installing WinBUGS in your Public directory (c:/Users/Public). It's possible to tweak the permissions, but sticking it somewhere else is easier.

If you take a look at the lecture schedule you'll notice that I didn't say anything at all about inbreeding on Friday. We'll talk about inbreeding tomorrow, and my plan is to cover both the basics of inbreeding and the basics of testing for departure from Hardy-Weinberg in lecture tomorrow. To accomplish that, I plan to skip the section on chi-squared tests in the testing Hardy-Weinberg notes, and I'll gloss over the details on self-fertilization, skipping directly to partial self-fertilization in the inbreeding notes.

It's been pointed out to me that the links on the Notes page didn't work. I think I've fixed them all now, but if you run into any that are broken, please let me know. You can also find the notes associated with any lecture by clicking on that lecture in the Schedule page. I check those links every time I upload revisions so they are (almost) guaranteed to work.

Sorry for any inconvenience.

Notes for the first two lectures have been posted. With a little luck, I hope to have notes for the first couple of weeks of class posted by the end of this week.

Before printing anything , though, please take a look at the message at the top of the Notes page.

I've just finished revising the schedule for this year's edition of the course. It's still subject to change, but the dates for the lectures and assignments should be pretty close to what we actually do now.

Although you'll find a lecture schedule if you click the link, the schedule you'll find there now is left over from Fall 2006. It will give you an idea of the topics we'll be covering, but the dates are all wrong. I'll post an announcement when they've been updated, but don't expect it until late next week.

I'm just getting things set up. If you click on the links in the title bar, they'll take you to pages from the 2006 edition of the course. They'll give you an idea of what to expect, but expect a lot of changes over the next couple of weeks as I get the site ready for Fall, 2008.