Registering for EEB 5895

I mentioned yesterday that you'll need to register for EEB 5895, section 9 in addition to EEB 5348. What I failed to mention is that you're going to need a permission number from me to register for EEB 5895. Drop me a line at Don't worry if it takes me a while to respond. As you may know, in addition to being a faculty member in EEB, I am Vice Provost for Graduate Education and Dean of The Graduate School. So long as you plan your schedule around EEB 5895 as well as EEB 5348, we have plenty of time to get you enrolled.

Registering for Spring 2015

If you are visiting this page before registering for EEB 5348 in Spring 2015, I congratulate you on planning ahead. I also want to let you know that in addition to registering for EEB 5348, you should register for EEB 5895, section 9. That's a 1-credit special topics course that will be the "lab" for the course. That's where you'll get hands-on experience with the software you'll need to do the projects assigned during the course.

I'll be checking the class roster for both courses periodically and sending e-mails to anyone who hasn't signed up for both, but if you happen to see this message and sign up for both from the start, it will save us both a bit of trouble.

Final grades posted

I just posted the final grades to PeopleSoft. They should appear in your record by 7:00pm or 8:00pm tonight. If you don't see them by noon on Thursday, December 20, drop me a line, and I'll try to figure out where the hang up is.

Thank you for a great semester. If you are traveling over the holidays, travel safely. And whether you're traveling or staying close by, have a wonderful holiday season.

Population genomics notes posted

I just posted my last set of notes for this semester, my notes on population genomics. I've also finished compiling the entire set of notes (including a lecture or two that I didn't give this year) into a single PDF volume. It's ready to be printed double-sided and bound into a notebook if you'd like to have a permanent printed reference (sort of like a textbook). If you're interested click the link entitled "Lecture notes in population genetics" at the to of the Notes page.

study group today, Nov 27, is cancelled

Due to a family emergency I will not be at the study group this morning for Problem 6.  Feel free to go to talk to your fellow students, but unfortunately I won't be able to make it.
A few hints: 
Population names
Grevena = Perivoli
Ontria = Ondria

Determine if Valade used Fst-like or Rst-like AMOVAs when doing their analyses.  Use Rst AMOVA when you do your analyses and make sure you are comparing Rst values with your groupings and the paper's.

feel free to email me any questions you may have


Notes posted

I've posted notes for the lectures on Monday and Wednesday. I hope you had a wonderful Thanksgiving week, and I look forward to seeing you tomorrow morning.

Fst outliers

I've uploaded two files to the course web site:

  • Fst-outlier.txt contains the Arlequin output
  • Fst-outlier.pdf contains a simple plot showing
    • The probability distribution of Fst derived from the simulation.
    • The observed values of Fst at each locus (dashed lines in the order noted)
    • The mean value of Fst (red line)

Problem 6 study groups

Back by popular demand... Study groups
There will be 2 study groups for Problem 6
Thursday November 15,  2-3pm
Tuesday November 27, 10-11am

I will be available by email from now until the problem is due except for Nov 22 to 24 for Thanksgiving.


Notes posted for week of 12 November

I posted the notes for this week late yesterday afternoon. We have a few things left to say about Tajima's D and related statistics, but we should finish that discussion in the first 10-15 minutes of class on Monday.That being said, I realized on Friday that I've been doing a lot of talking and not getting a lot of questions, so please come prepared to ask questions on anything we've covered in the last week or so. If we happened to spend the whole hour dealing with your questions, I'd be delighted.

Problem 5 study groups

Study groups for Problem 5 and using R  were/ will be held this week 
Tuesday 10-11
Wednesday 2-3
Thursday 2-3

There will also be a study group next Tuesday 10-11am, November 13

Problem 5 is another large project, so your response should be 4-5 pages.

The primary paper is available via advanced access at