I've posted notes (and a link to a paper) on analysis of molecular variance. One way or the other we'll get started on AMOVA tomorrow -- even if I have to cut the discussion of evolution in multigene families a little short. It would be a disservice to you not to give you a little exposure to AMOVA and nested clade analysis before the course is over.
The notes on multigene families are now complete. You'll notice that I've revised the lecture schedule (a little) to reflect where we stand. The lecture last Friday is labeled as "Tajima's D." We'll finish our discussion of Tajima's D on Monday and start our discussion of evolution in multigene families. I don't expect that we'll finish it. But we will finish it on Wednesday. And we'll finish off the course with a discussion of phylogeography on Wednesday and Friday.
Three other organizational items of which you should be aware:
Preliminary notes on multigene families are now posted. They aren't complete, and we probably won't get to them on Friday anway, so I suggest waiting for a while before printing them.
I've posted the solution to Problem #4. In addition to the link from here, you'll find links on the detail page of the lecture for the 14th of April, when it was due, and from the "Notes" page. In fact, I've collected notes for all WinBUGS related problems at the bottom of the notes page, so it will be easy for you to find them if you ever want to refresh your memory.
I hope to have some notes posted on evolution in multigene families late tonight or early tomorrow morning, but there's a good chance we won't start talking about that until Monday anyway. So don't worry if they're not there (as if you would anyway).
This press release from the National Science Foundation describes work on hemoglobin that is relevant to the discussion of evolution in multigene families that we'll start soon.
I just noticed a problem with the data file associated with Problem #5 (and I am shocked, shocked to find that none of you noticed it). I've corrected the problem and uploaded a new data file. Unfortunately, that means that if you already have some results, you'll need to start your analyses over again. Sorry about that.
Oh, if you're wondering what the problem was, it had to do with the map information. The first two markers on each chromosome were both situated at map position 0. Come to think of it, I'm sure the reason that no one pointed out my mistake was that you're all too polite.
Notes on detecting selection associated with nucleotide polymorphisms are now posted. I hope to get started discussing the Adh example on Monday, but I know we'll be continuing it and some others into Wednesday. We're taking a little longer to get through this than I expected, but that's OK.
On a related note, we plan to return Out of Africa papers and Problem #4 papers on Monday. The slow turnaround on the OoA papers is my fault not Robynn's. I'll be grading this weekend, instead of enjoying the weather (unless you count grading papers on my deck as "enjoying the weather").
Notes on patterns of nucleotide and amino acid substitution are now available on the detail page for the 16 April lecture. We won't finish them, but I hope at least to get started on the topics they deal with.
Notes on the neutral theory of molecular evolution are now posted. I've also posted the next problem -- which does not involve WinBUGS. (OK. You can stop cheering now.)
I finally posted notes on my solution to problem #3 (the effective population size problem) to the web site. You can find them in one of two ways:
I expect to have notes on the neutral theory of molecular evolution posted late this afternoon (or maybe late tonight, if I get a lot of interruptions). I'll post another notice as soon as they're available.
The first set of molecular evolution notes are now available. We'll be using them at least part of the day on Wednesday too. Enjoy!
The hint I provided in the notes was correct. Unfortunately, I uploaded an old version of the data file. I've uploaded a new one and verified with my own WinBUGS runs that it now works correctly. The problem is that I shouldn't have included the sire ID.
Now if you have difficulties with the problem they're a little less attributable to me. Sorry for the confusion.
Nature Genetics released a "Users guide to the human genome" last fall that I just discovered. We (probably) won't be using it directly in the course, but it's relevant to our current discussions about QTL mapping. You might want to take a look. It's available on-line at http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v35/n1s/index.html.
Notes for the lectures on quantitative trait locus analyses are now posted. I plan to spend the first part of Monday's lecture wrapping up a few loose ends from traditional quantitative genetics and dealing with any questions you've managed to formulate. We'll spend the rest of Monday's lecture and most or all of Wednesday's lecture going over the notes outlining the basic principles of QTL analysis. On Friday, I'll give you a whirlwind tour of QTL Cartographer.
Oh, if you're wondering where Robynn is. It seems she's in New Orleans. I guess there's some basketball being played there.
Kent will be assigning Problem 4 on Mon., and it is due on the 14th. I will plan to be available in the TLS computer room after class on Mon., the 12th, and will stop by Beach Hall on Tues. (13th) at 1:00 if that works for the Beach Hall gang.
As always, you can e-mail me or make an appointment to get together with me about the assignment any time.