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


Notes posted for week of 5 November

I've got this week's notes posted on the web site. We still have a few things to finish up from last week, since Sandy took away some of our time together. But by the end of the week, I expect to be fully caught up.

The 1000 Genomes Project

They surveyed 1092 genomes, but 1000 is a nice round number, and that's the name of the project. Here's an abstract of a report from today's Nature.

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38|[thinsp]|million single nucleotide polymorphisms, 1.4|[thinsp]|million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.