Genome Sciences 590

Evolution and Population Genetics Seminar

Autumn Quarter, 2004

topic: COALESCENTS

Tuesdays in J182 Health Sciences Building
12:30pm - 1:20pm.

We will cover the theory of the coalescent in population genetics, how evolutionary forces affect it, and how it is used in inferring population and genetic parameters. Students in the course will be expected to lead one of these sessions, to do all readings, and to participate actively. The course will expend on the coverage of coalescents in Genome 562 (Theoretical Population Genetics), Genome 541 (Computational Molecular Biology) and Genome 570 (Phylogenetic Inference).

Students registered in the course will be required to lead or co-lead one session. This will involve the leaders describing what is in the papers (the important parts anyway) for about half the session, so we can discuss the paper for the remainder of the session.

Topics

References will be listed here for each session. When a reference can be accessed by web from the UW, a link will be given here (note that it may not work from home, as you might not be recognized as being covered by the UW's subscription to an electronic journal). For the others distribution arrangements will be made in class.


October 5

Kingman's coalescent and its predecessors

I will lead this session and explain the material. The fundamental papers of Kingman, which we will not read in detail, are

A paper giving some useful methods that can be used to get close to the coalescent is my own 1971 paper (which I did not think of using to derive the coalescent):

Felsenstein, J. 1971. The rate of loss of multiple alleles in finite haploid populations. Theoretical Population Biology 2: 391-403.

In this session, we will use as our basic text a chapter from my own book Theoretical Evolutionary Genetics, which is available free as a PDF on the web (see http://evolution.genetics.washington.edu/pgbook/pgbook.html. The particular chapter is Chapter 10, which you can download as a PDF using *this link. One can also get a lot of background from my book Inferring Phylogenies, particularly chapters 26, 27, and 28.


October 12

Coalescents with population growth

Co-presenters: Joanna Kelley and Cindy Desmarais


October 19

Coalescents with migration

Co-presenters: Tom Unfried and Andrew Eckert


October 26

Recombination and coalescents

Co-presenters: Bertrand Servin and Garrett Hellenthal


November 2

Coalescents and speciation

Co-presenters: Yi-ling Chen and Yaowu Yuan


November 9

"Single-tree" inference methods

Presenter: Arindam Roy Choudhury


November 16

Presenter: Matthias Ganter

MCMC and Importance Sampling likelihood methods (I)


November 23

Co-presenters: Paul Scheet and Bill Stewart

MCMC and Importance Sampling likelihood methods (II)


November 30

Natural selection and coalescents I

Presenter: (none yet -- maybe that means me)


December 7

Natural selection and coalescents II

Co-presenters: Lisa Kim and Charla Lambert


Joe Felsenstein ( joe (at) gs.washington.edu )