Genome 562

Population Genetics

Winter, 2011

• News
• Description from the UW Course Catalog
• Syllabus of lectures
• Homeworks (some assignments not available yet):
  • Homework 1, due January 12.
  • Homework 2, due January 19.
  • Homework 3, due January 26.
  • Homework 4, due February 2.
  • Homework 5, due February 9.
  • Homework 6, due February 16.
  • Homework 7, due February 28.
  • Homework 8, due March 2.
  • Homework 9, due March 11.
• The course text (as a PDF), Theoretical Evolutionary Genetics by Joe Felsenstein. This course text is also reproduced locally and sold to students at cost (about $27). 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
• Who is this guy who is teaching the course, anyway?
• Where is the lecture room?
• What are some other related courses?
• What are some Internet resources on evolutionary biology?
• Where can I get a copy of the genetic simulation computer program?

• The course meets in S110 Foege Building, the seminar room on the 1st floor of Foege (its door is across from the white phone in the hall). It meets at 11:30-12:20 Mondays, Wednesdays, and Fridays.
• There is a course mailing list. Registered students are on it automatically. For others, to join it or read past postings, go to this link. It requires a UW login, and past postings can be read only once you are a list member. Members can post to the mailing list. I will try to keep anyone from abusing the list and sending spam or really off-topic stuff.
• I have posted the audio file of the first lecture. I was struggling with my sound-editing software and do not have it in good enough form as a .WMA audio file but I do have it as an MP3 file. Future lectures will be posted in both forms.
• OK, I have the first lecture now also as a WMA file.
• Homework 1 is now posted. See link above.
• The course text is supposed to be ready on Friday (the 7th) by class time. Cost will be $27.10. I will take either checks made out to Joseph Felsenstein or cash. If you did not sign up on the signup sheet to get the book, you will not get one of these copies (you can of course print out your own copy or just read it on the computer). No, sorry, there are no extra copies for sale.
• Homework 2 is now posted. See link above.
• Homework 3 is now posted. See link above.
• Homework 4 is now posted. See link above.
• Homework 5 is now posted. See link above.
• Homework 6 is now posted. See link above.
• The February 23rd lecture will be given by Vladimir Minin of the Statistics Department. He is going to cover the neutral mutation theory (sections VII.1, VII.2, and VII.4 of the text).
• The February 25th lecture will be by Adam Leaché of the Biology Department. He will talk about the use of the coalescent in some real data examples in his work.
• Mary Kuhner of the Genome Sciences Department will give the lecture on the 28th. She will introduce the Markov Chain Monte Carlo method for making inferences from population samples of genotypes. This is covered in the text in section X.8. Mary works on this and has given well-received talks on it many international workshops.
• Homework 7 is now posted. See link above.
• Homework 8 is now posted. See link above.
• Homework 9 is now posted. See link above.
• Grades have been submitted -- a distribution of point totals with some indication of grades that are associated with them is available here.

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.

Where is the lecture room?

Here is a campus map showing the location.

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

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

• Bruce Weir (Biostatistics)
• Mary Kuhner (Genome Sciences)
• Josh Akey (Genome Sciences)
• Adam Leaché (Biology)
• Phil Green (Genome Sciences)
• Willie Swanson (Genome Sciences)
• Carl Bergstrom (Biology)
• Ben Kerr (Biology)
• Elizabeth Thompson (Statistics)
• Vladimir Minin (Statistics)
• Ellen Wijsman (Medical Genetics and Biostatistics).

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

• Kent Holsinger's Population Biology Simulations, some Java applets to illustrate various phenomena.
• The amazing Tree of Life , a phylogeny of all life, in the making. Trees, figures, descriptions and references at a solid professional level, each page done by a major systematist working on that group.
• TreeBASE, a database of evolutionary trees (phylogenies) from the scientific literature. Weighted towards flowering plants, and badly suffers being only sporadically updated.
• My own PHYLIP free package of computer programs for inferring phylogenies. Includes some web pages on all possible phylogeny programs and how to get them.
• But maybe you don't want to be limited to just my programs? OK, try this listing which I maintain of all known Phylogeny Programs. As of January 2010 there are 385 programs and 53 web servers listed. Many of the programs are freely downloadable.
• Want some DNA or protein sequences? How about getting them from the international database? Try the Web pages of the databases at the NCBI, the National Center for Biotechnology Information of the National Library of Medicine, in Bethesda, Maryland. Not for the faint-hearted.
• The talk.origins Evolution FAQs (Frequently Asked Questions).
• The Harvard Bio Pages evolution page, with lots of links to other evolution resources.
• The National Center for Science Education which fights the creation/evolution battle and was instrumental in providing technical resources in the Dover School Board court battle in 2005.

Computer simulations of population genetics

• See below for the one we will use in this course.
• Reed Cartwright's Red Lynx population genetics simulator runs on your browser (in Javascript) and is somewhat similar to the simulation program (see below) that we will use in this course.
• Bob Sheehy at Radford University in Virgina has another population genetics simulator (described as similar to mine but “slower and more colorful”, written in Shockwave Flash.
• A Java simulators of genetic drift, Hardy-Weinberg proportions and four other phenomena from Ted Wong at Bryn Mawr College.
• PopGen 1.0 from the University of Oulu, Finland.

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:

• Molecular Biology and Evolution
• Systematic Biology
  • 1998-present
  • 1992-2006
  • 1952-1991 as Systematic Zoology
• Evolution
  • 2000-present
  • 1947-2006
• Journal of Molecular Evolution (1997-present)
• Molecular Phylogenetics and Evolution (1993-present)
• American Naturalist
  • 1867-2004
  • 1997-present
• BMC Evolutionary Biology (Open Access) 2001-present

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.