Genome 562 Spring 2007

Genome 562

Population Genetics

Spring, 2007

News
Description from the UW Course Catalog
Syllabus of lectures
Homeworks:
The course text (as a PDF), Theoretical Evolutionary Genetics by Joe Felsenstein. The version posted currently is the revised version for 2007. This course text has been reproduced locally and sold to students at cost (which this year was $21.45 -- sorry, all copies are gone).
Who is this guy who is teaching the course, anyway?
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?

These news items have the newest ones last.

The course text is still being revised. The version posted now is the 2005 text.

The 2007 course text is being printed. I will have final information by Friday, I hope. The tentative guess at the cost is $21.45. If you can, bring a check made out to me (I will post the exact amount it will cost here).

The 2007 course text is now posted. Orders have been taken for the printed version, which we hope will be available Friday.

I have now verified that the cost of the textbook will be $21.45. Checks should be made out to me as "Joseph Felsenstein". It will be available to the 19 of you who indicated that you wanted it, at the Friday lecture. Please, no one should take one that was not one of those 19 people.

There is a course mailing list. 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.
The informal "TA" for the course is Charla Lambert, whose email address starts with "clambert" and ends in the usual UW way. Thanks to her for volunteering to do this.
The homework for week 1 is posted here.
For the second problem, here are some clarifications. With microsatellite genotypes, the number of copies on individual pieces of DNA are detected by running gels. Pieces of DNA with 0 copies are not seen. So if you are am 18/0 heterozygote, the gel just sees that there seem to be 18 copies for the pieces of DNA in that region. If you are an 18/18 homozygote that also looks like 18 copies for the pieces of DNA. Those cannot be told apart. If you are an 18/19 heterozygote then the gels see both 18's and 19's, so they can tell a heterozygote for those two alleles from the homozygotes.
Also, I asked for the "genotype frequencies". I really should have asked for the "phenotype frequencies", like "18", "18/19", etc.
The homework for week 2 is posted here, a bit early.
For Homework #4, one of the students asked what "dominance" means for problem 2. It means that the Huntington's disease allele is dominant, so the fitnesses of AA : Aa : aa are 1 : 1-s : 1-s. Sorry if that was ambiguous.
My apologies for not telling you all that the room for the course was changed today (4/25), owing to the Genome Sciences Symposium needing our room. I hope not too many of you got lost. I want to emphasize that this was just for that one day. Next time we go back to our usual room.
Also, the homework assignment for today is not yet ready -- I will post it on the web site later this afternoon.
OK, now the homework (\#5) is posted.
(For homework 6) The pedigree in the homework problem is harder to do than I realized, so let me give you all a hint. The number of loops going from N to N is not 11, and it is not 12. In the second problem, in doing the equations for k you just go back to the ancestors of one of the two individuals. Be very careful to keep track of your generation subscripts (they are on the figure).
For the second problem in Homework 6, here is a key describing how one does the problem the shorter way and the longer way.
OK, I have recompiled the Windows executable, and the behavior seems to be better. It can be downloaded (as a ZIP archive) here and should be extractable if you click on it in a Windows XP system. Give it a try and see whether the results look miore reasonable. If asked, choose to Save this archive to disk. Then when you open it, choose the option to Extract All Files. After that a folder called PopG 3.1 should appear on your desktop.
The course has now been graded. I have mailed out the last homeworks, graded and with your course totals and grade written on them, to those people for whom I had UW addresses. I can mail the few others once I have addresses. A PDF of the point total distribution is available here, with the totals grouped intom two-point classes and an approximate grade scale also indicated. Thanks for your efforts -- this was a good class. Thanks particularly to Charla Lambert for her outstanding efforts as a volunteer TA.

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 this quarter by Carl Bergstrom and last quarter by Billie Swalla. Textbook last quarter was Freeman and Herron's "Evolutionary Analysis".

Genome 414 and Biology 414

Molecular evolution course by Willie Swanson, who is a very active researcher in this area.

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 Spring (even numbered years).

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 each Autumn by Elizabeth Thompson, who is a major figure (one can say a major force) in development of statistical genetics methodology.
551: Statistical Genetics II: Quantitative Traits. Offered each Winter by Bruce Weir and John Storey. 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 each Spring by Ellen Wijsman (Medical Genetics and Biostatistics) who is a well-known statistical geneticist.

Others

There are more courses and I'll gradually try to put descriptions of them here. Some other faculty members in this area (evolutionary genetics) are Bruce Weir (Biostatistics), Mary Kuhner (Genome Sciences), Josh Akey (Genome Sciences), Phil Green (Genome Sciences), Willie Swanson (Genome Sciences), Carl Bergstrom (Biology), Ben Kerr (Biology), Elizabeth Thompson (Statistics), Vladimir Minin (coming in Statistics) and Ellen Wijsman (Medical Genetics and Biostatistics).

What are some Internet resources on evolutionary biology?

There are many:

Newsgroups

There are blogs, mostly creation / evolution debating, and some Usenet newsgroups.

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

sci.bio.evolution (Usenet newsgroup): Moderated by Josh Hayes, formerly of our own Center for Quantitative Sciences, who should get some sort of award for putting up with a lot of nonsense. I think it was intended as a forum for discussion among researchers, but has tended to be filled with postings by amateurs, including some high-volume cranks. In among them are some people with serious knowledge. Not intended for evolution/creation debates: Josh screens these out.
talk.origins (Usenet newsgroup): The arena for endless debate between creationists and others, with frequent digressions into theology (or maybe it's for discussion of theology with occasional digressions into biology). Extremely high noise to signal ratio. When a decisive point is made, the opponent changes the subject or just refuses to respond. The pro-evolution posters generally do a good job.
quan_gen (Yahoo Group): Quantitative genetics and related areas in bioinformatics at a professional level.

Web Pages

Kent Holsinger's Population Biology Simulations, some Java applets to illustrate various phenomena.
The talk.origins Evolution FAQs (Frequently Asked Questions).
The Harvard Biopages evolution page, with lots of links to other evolution resources.

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, Macs, and some Unix workstations: To fetch any of these by ftp Click here It will show a page which then allows you to download the program.

this page maintained fitfully by Joe Felsenstein