Genome 562

Population Genetics

Winter, 2011


News about the course

These news items have the newest ones last.


Lecture materials

The derivations will mostly be done on the whiteboard, not on lecture projections (with a few exceptions, mostly of figures from tbe course text). The derivations are shown step-by-step in the text.

For the use of people who cannot make it to a lecture, WMA and MP3 audio files of the lectures will be linked here (as they are given). You should be able to use these together with the appropriate pages of the book to get some sense of what was done in the lecture. The files are recorded at medium quality, and are about 6 Mb in size. Their names indicate the date: the files for the lecture for January 5, 2011 will be called 20110105.WMA and 20110105.mp3. As the recordings are made and posted here these names will become links to the files. Thanks to Ben Vernot for recording the 02/18 talk and making it available to me when I forgot to bring my recorder.

Week 1Week 2Week 3Week4Week 5
20110103.WMA
20110103.mp3
20110105.WMA
20110105.mp3
20110107.WMA
20110107.mp3
20110110.WMA
20110110.mp3
20110112.WMA
20110112.mp3
20110114.WMA
20110114.mp3
20110119.WMA
20110119.mp3
20110121.WMA
20110121.mp3
20110124.WMA
20110124.mp3
20110126.WMA
20110126.mp3
20110128.WMA
20110128.mp3
20110131.WMA
20110131.mp3
20110202.WMA
20110202.mp3
20110204.WMA
20110204.mp3
Week 6Week 7Week 8Week9Week 10
20110207.WMA
20110207.mp3
20110209.WMA
20110209.mp3
20110211.WMA
20110211.mp3
20110214.WMA
20110214.mp3
20110216.WMA
20110216.mp3
20110218.WMA
20110218.mp3
(recordings not
available for lectures
by Vladimir Minin
and Adam Leaché)
Mary Kuhner's
  lecture PDF

20110302.WMA
20110302.mp3
20110304.WMA
20110304.mp3
20110307.WMA
20110307.mp3
20110309.WMA
20110309.mp3
20110311.WMA
20110311.mp3


Where is the lecture room?

From upper campus, come across the pedestrian bridge (over Pacific Avenue) next to Kincaid Hall (the bridge nearest 15th avenue). Walk forward past Hitchcock Hall on the right, descending to ground level. Then turn right on the walkway that comes out of the Health Sciences Building. Foege (“FAY-gee”) Building is ahead of you, and the S (South) wing of it is the left half, the downhill half. Enter it at the door which is on the left side of that sidewalk as you reach the building. S110 is the first room on your left as you go along this 1st floor corridor.

Alternatively, if you come down 15th avenue, Foege Building is on your left after you cross Pacific Avenue. To reach the S (South) wing, go halfway along the outside of the building and enter through the opening in the building, entering the part of the building closer to the bay.

Here is a campus map showing the location.

Oh yes, and who is the building named after? Someone living: This guy. Not bad!


Description from the UW Course Catalog

GENOME 562 Population Genetics
Credits: 4
Quarters: Sp
Instructor: Felsenstein
Course Desc.: Mathematical and experimental approaches to the genetics of natural populations, especially as they relate to evolution. Emphasis on theoretical population genetics. Prerequisite: permission of instructor. Offered: Sp.


What are some other related courses?

The UW has great strength is evolutionary genetics and statistical genetics. Some relevant courses are:

Biology 354
The main evolution course at the University, taught last Autumn quarter by Gregory Wilson, a paleontologist and expert on early mammals. Textbook most recently was Barton et al. Evolution and Jeffrey Weiner's The Beak of the Finch.
Genome 453 (Evolutionary Genetics)
This is an undergraduate-level course on evolution and genetics. Given every Autumn, it overlaps somewhat with Biology 354 but covers the genetic aspects of evolution with less emphasis on ecology and paleontology than the first, less emphasis on molecular evolution than the second. In even-numbered years the course is given by Mary Kuhner, in odd-numbered years by me. It should be understood that this is basically an undergraduate course.
Biology 550 (Evolution and Systematics Seminar)
Weekly seminar (“EvolSyst”) run Autumn, Winter and Spring by the inimitable Toby Bradshaw. Discussion of many topics in evolution, with presentations by the participants. Its course mailing list postings can be publicly viewed (search for EvolSyst on the UW mailing list system). Fridays at 1:30, this quarter in Hitchcock 320. Every quarter during the regular academic year.
Genome 570
This is my graduate-level course on Phylogenetic Inference. Methods for inferring phylogenies, and methods for doing things with them. Some background in statistics necessary. It will be given every other Winter (in even-numbered years). Textbook is my own book Inferring Phylogenies.
Statistics/Biostatistics 550-551-552
The core course series for the UW's outstanding Statistical Genetics program. The three courses are:
550
Statistical Genetics I: Mendelian traits. Offered in Spring, recently by Elizabeth Thompson, who is a major figure (one can say a major force) in development of statistical genetics methodology, and by Vladimir Minin, a rising star in areas overlapping statistical genetics and molecular evolution.
551
Statistical Genetics II: Quantitative Traits. Offered each Autumn by Bruce Weir. Bruce has had a long and distinguished career in statistical genetics (formerly at North Carolina State University).
552
Statistical Genetics III: Design and Analysis. Offered some Winters by Ellen Wijsman (Medical Genetics and Biostatistics) who is a well-known statistical geneticist. Not offered this year.
Others
There are more courses and I'll gradually try to put descriptions of them here. Some faculty members in this area (evolutionary genetics) are

What are some Internet resources on evolutionary biology?

There are many:

Blogs

There are blogs, mostly creation / evolution debating, and some Usenet newsgroups (which I have not listed here as they have become too inactive). I do not have enough understanding of Facebook to know what is available there.

Some brief descriptions of some of the major ones covering evolution:

Panda's Thumb (Blog)
Blog defending evolutionary biology against creationists and advocates of Intelligent Design, run by Reed Cartwright, a phylogeny postdoc.
Uncommon Descent (Blog)
Blog owned by William Dembski and Denyse O'Leary, critics of evolutionary biology and advocates of Intelligent Design.
Dechronization (Blog)
Named after a science fiction novel written by the famous evolutionary biologist George Gaylord Simpson, this is a technically oriented blog run by about 6 young phylogeny-oriented evolutionary biologists. Aside from occasional natural history it is mostly devoted to phylogenetic methods. However it is very rarely updated these days, alas.

Web Pages

Computer simulations of population genetics

There are quite a few more. Search using a search engine with the phrase “Population genetics simulation”

Electronic journals

There is of course, the professional literature in evolutionary biology. Some of these journals (links given below) are available in electronic versions for UW people. If these links don't give you access you should use the Electronic Journals links in the University Library site, and type in the name of the journal. If you are at another institution, you may be able to access a different run of years of each journal. Here are some direct UW links to the leading journals covering evolution:


Where can I get a copy of the genetic simulation program?

The program is freely distributable. It is available from my server. There you will find source code, documentation and executables for Windows, Mac OS X, and Unix workstations: To fetch any of these Click here. It will show a page which then allows you to download the program.


this page maintained fitfully by Joe Felsenstein