Genome 562

Population Genetics

Winter, 2015


News about the course

These news items have the newest ones last.


About the course text:

The course text (as a PDF), Theoretical Evolutionary Genetics by Joe Felsenstein. (An early 2015 version is the one currently available there. Some corrections will be made in a few days but it is almost at the 2015 version.) This course text will also be reproduced locally and sold to students at cost (at a cost of about $25). Students who want new printed copies should commit at the second class session to buy them. If you can't make the second class session and want to be signed up to buy the text, email me.


Lecture materials (audio recordings, etc.)

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 9 Mb in size. Their names indicate the date: the files for the lecture for January 5, 2015 will be called 20150105.WMA and 20150105.mp3. As the recordings are made and posted here these names will become links to the files.

The lecture on 7 January was recorded only for the first 28 minutes, owing to inadequate file space on the recorder.

Week 1Week 2Week 3Week4Week 5
20150105.WMA
20150105.mp3
20150107.WMA (partial)
20150107.mp3 (partial)
20150109.WMA
20150109.mp3
20150112.WMA
20150112.mp3
20150114.WMA
20150114.mp3
20150116.WMA
20150116.mp3
  (holiday)

20150121.WMA
20150121.mp3
20150123.WMA
20150123.mp3
20150126.WMA
20150126.mp3
20150128.WMA
20150128.mp3
20150130.WMA
20150130.mp3
20150202.WMA
20150202.mp3
20150204.WMA
20150204.mp3
20150206.WMA
20150206.mp3
Week 6Week 7Week 8Week9Week 10
20150209.WMA
20150209.mp3
20150211.WMA
20150211.mp3
20150213.WMA
20150213.mp3
  (holiday)

20150218.WMA
20150218.mp3
(Lecture of Friday, February 20
not recorded. See News above
for other recordings of this material).
20150223.WMA
20150223.mp3
20150225.WMA
20150225.mp3
20150227.WMA
20150227.mp3
20150302.WMA
20150302.mp3
20150304.WMA
20150304.mp3
20150306.WMA
20150306.mp3
20150309.WMA
20150309.mp3
20150311.WMA
20150311.mp3
20150313.WMA
20150313.mp3

... and here are the projections from the course, as PDFs:

Week 1 (PDF)
Week 2 (PDF)
Week 3 (PDF)
Week 5 (PDF)
Week 6 (PDF)
Week 7 (PDF)
Week 8 (PDF)
Week 9 (PDF)
Week 10 (PDF)


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.

However ... partway through the quarter the area between Foege and Health Sciences Building will start turning into a huge construction pit, so after that you could come down 15th avenue, or do some other roundabout route.

Here is a campus map showing the location. Unfortunately the campus maps system puts on the map a big box showing a photo of the building, which manages to obscure all the stuff nearby and thus probably confuse everyone as to where the building is. Notice where the little pointer tip is below that box, then use the X button to dismiss that irritating box.

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.


Note: below this point the material is from the 2013 course web page and has not yet been revised.

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 Jon Herron, who is author of a major evolution textbook, and last Spring quarter by Carl Bergstrom, a major researcher in evolutionary genetics (and on information networks in science). I believe that it will also be taught in Autumn and Spring quarters but it is not yet announced who will be teaching it.
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 in Winter, 2016. 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 or Tim Thornton. Bruce has had a long and distinguished career in statistical genetics (formerly at North Carolina State University). Thornton is a statistical geneticist who is in the Biostatistics Department.
552
Statistical Genetics III: Design and Analysis. Offered some Winters by Ellen Wijsman (Medical Genetics and Biostatistics) who is a well-known statistical geneticist.
AFS 497
Advanced Population Genetic Analyses. Discusses computer programs for various kinds of population genetics inferences, with labs in their use. Taught by Lorenz Hauser of the School of Aquatic and Fisheries Sciences.
BIO A 482
Human Population Genetics. Taught by Daryl Holman of the Department of Anthropology's program in Biocultural Anthropology.
Other courses and people:
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, many involved in creation / evolution debating, and some Usenet newsgroups (which I have not listed here as they have become mostly 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:

Carl Zimmer's blog
Zimmer is one of the best, and best-known science journalists specializing in evolution (you will find his pieces in many places, including the New York Times). He is also an author of an evolution textbook.
John Hawks's weblog
(that's where the word "blog" came from: they were originally web-logs). John Hawks is a physical anthropologist at the University of Wisconsin who blogs informatively and entertainingly.
Genomicron
T. Ryan Gregory's interesting blog covers evolutionary genomics and some other evolutionary issues. He works on transposon genomics and is at McMaster University in Canada.
Cryptogenomicon
The blog of the Eddy / Rivas lab, soon to be at Harvard University. Sean Eddy is well-known in computational genomics. In addition to lab business his blog has hosted some of the most aiuthoritative and trenchant criticism of the hype surrounding the recent release of Encode data on function of genomic elements.
Sandwalk
Named after the walking path where Darwin did a lot of his thinking, this is written by Larry Moran, professor of Biochemistry at the University of Toronto and author of a major biochemistry textbook. In it he hammers creationists, argues that natural selection is invoked too much, and promotes his views on (actually, mostly against) religion.
Panda's Thumb
Blog defending evolutionary biology against creationists and advocates of Intelligent Design, run by Reed Cartwright, a young phylogeneticist at Arizona State University.
Uncommon Descent
Blog started by William Dembski and Denyse O'Leary, critics of evolutionary biology and advocates of Intelligent Design. Now run by lawyer Barry Arrington, it regularly features O'Leary's endlessly astonishing take on why "Darwinism" is obviously wrong.
Skeptical Zone
Elizabeth Liddle, a neuroscientist in Manchester, England, was one of the most patient, most polite, and most telling critics of Intelligent Design in comments at Uncommon Descent. She was banned from it in early 2012 in a remarkable shoot-oneself-in-the-foot mass purge by the site's owner, Barry Arrington. So she went out and opened up discussion on her own site, which encourages supporters and critics of Intelligent Design to examine each others' arguments without getting too rancorous. Most of the creationists and ID advocates avoid posting at TSZ now, but a few still do and others come by from time to time. The remaining commenters tend to spend a lot of time discussing philosophy, but occasional postings about biology do occur.
Pharyngula
P. Z. Myers, who teaches biology at the University of Minnesota at Morris, is one of the most entertaining bloggers. He originally concentrated on destroying creationist arguments and explaining new developments in evolutionary biology. More recently his blogging effort has been concentrated on attacking religion, and his blog Pharyngula has become one of the most highly cited in the world. The link here is to the limited copy of his blog content at Scienceblogs, which highlights the postings on science from his full blog and omits the posts on religion.
Tree of Life
Jonathan Eisen's blog. He teaches at University of California, Davis. It covers "phylogenomics" of microbial systems and microbial metagenomics, with authority and vigor.
Dechronization (defunct)
Named after a science fiction novel written by the famous evolutionary biologist George Gaylord Simpson, this was a technically oriented blog run by about 6 young phylogeny-oriented evolutionary biologists. Aside from occasional natural history it was mostly devoted to phylogenetic methods. However it is never updated these days, alas. The last posting was in mid-2011.

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