Genome 453

Evolutionary Genetics

Autumn, 2009

Instructor: Joe Felsenstein

MWF 11:30-12:20, in S110 Foege Building

Directions to 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.

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

News about the course

(Most recent news is first)

Description from the UW Course Catalog

GENOME 453 Genetics of the Evolutionary Process (3) NW
Contributions of genetics to the understanding of evolution. Processes of mutation, selection, and random genetic events as they affect the genetic architecture of natural populations and the process of speciation. Emphasis on experimental data and observation, rather than mathematical theory. Prerequisite: either GENOME 371 or GENOME 372.

Instructor course description: Joseph Felsenstein

Why don't we have a textbook?

(I know it makes everyone insecure, but at the graduate level it is standard not to have a textbook. If you go to grad school you'll have to get used to it.) Mostly it's because I can't come up with one that covers adequately the particular mix of topics I give. Make a suggestion and we'll discuss it. I have considered or even used Futuyma, Maynard Smith's "Evolutionary Genetics", and others but they don't work. I will be handing out detailed outlines of the material covered in lecture, and see below for electronically accessible lecture outline and projection materials.

Lecture materials (outlines and overheads)

Preliminary versions of the lecture PDFs. More will be added to these before the lectures, but they are fairly complete. Then lecture outlines are labelled ``old'' when they are from last year and have not yet been revised. Again, they are fairly close. The numbering of the lectures will change. The audio files will be posted here too. They will be in WMA and also in MP3 format.

As the lectures are prepared (usually before or on the day they are to be given) I will update the lecture outlines and the computer projection images.

If the PDFs display on your computer rather than offer you the ability to download them, you should be able to use the Save As option on your browser to save them as PDFs.

Outline of material projected materials audio of lectures
   (lecture of 10/21 was not
    recorded. Oops.)
lecture of 10/23 (WMA)
lecture of 10/23 (MP3)
lecture of 11/25 (WMA)
lecture of 11/25 (MP3)
(Oops. The lecture of 11/30
was not recorded)

What are some other related courses?

Biology 354 Foundations in Evolution and Systematics
The main evolution course at the University, taught twice yearly. In Winter 2009 this was given by Billie Swalla; in Spring 2009 it was given by Carl Bergstrom.
What is the difference between Genome 453 and Biology 354? Biology 354 is a fine course with a somewhat different emphasis. It is more oriented to covering issue such as evolutionary ecology, speciation, fossil record, and so on, while we spend more time than they do on genetic effects -- particularly molecular evolution, chromosome evolution, and population genetics. There is some substantial overlap. The syllabus of 354 for the winter quarter indicates that it will cover some particular topics in more depth rather than attempt a broad survey.
Biology 415 (Evolution and development)
Advanced undergraduate course, requiring an introductory evolution course as a prerequisite, on "Evo-devo", the intersection of developmental biology and evolution. This has been an area where there have been a lot of recent advances. Taught by Billie Swalla, who is an active researcher in this area. Given this quarter, and last year it was also given in the Spring quarter, taught by David Parichy.
Biology 481 (Experimental Evolutionary Ecology)
Lecture and lab course on evolutionary perspectives on ecology. Taught by Josh Tewksbury and Ben Kerr. Autumn quarters.
Genome 562 (Population Genetics)
Now given every other year, this is the graduate theoretical evolutionary genetics course that I give. Lots of equations, though mostly at a low mathematical level. No pictures of cute furry animals. Next time it's given will be Winter, 2011. Text: my own extensive lecture notes, downloaded as PDF's for free or sold inexpensively (no royalty is paid to me).
Genome 570 (Phylogenetic Inference)
This is my graduate-level course on evolutionary trees. Methods for inferring phylogenies, and methods for doing things with them. Some background in statistics necessary. It will be given every other Spring (next time is Winter, 2010). Text is my book "Inferring Phylogenies".
There are more courses and I'll gradually try to put descriptions of them here.

What are some Internet resources on evolutionary biology?

There are many:

Blogs and Newsgroups

There are blogs, mostly creation / evolution debating, and some Usenet newsgroups. The latter are accessible through Google Groups.

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.
Uncommon Descent (Blog)
Blog centered around William Dembski and Denyse O'Leary, critics of evolutionary biology and advocates of Intelligent Design. (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. Lately traffic has declined, as newsgroups are disappearing. (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. (Usenet newsgroup)
Tends to be filled with postings by fossil enthusiasts and tends to be dinosaur-centered. Some creation/evolution debating too.

Electronic journals

There is of course, the professional literature in evolutionary biology. Contrary to popular belief, scientists don't publish their works primarily by writing books. They publish papers in scientific journals. 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. Here are some direct links to the leading journals covering evolution:

Web Pages

Where can I get a copy of the computer programs?

There are three computer programs available. Students in the course will be asked to run two of them, and submit a report of the results. The details of the assignments will be handed out later. One program, PopG, simulates evolution of gene frequencies of two alleles at a single locus in the presence of genetic drift, natural selection, mutation, and migration. The first computer exercise will consist of running this. The second program, ContEvol, is presented here in case you might want to play with it -- it will not be used in an assignment. It simulates the evolution of a quantitative character which is controlled by 5 loci, under the action of natural selection towards an optimum phenotype. The third program, Dnatree, simulates the branching of a phylogeny, the evolution of a DNA sequence along those branches, and allows the user to search by manually rearranging the tree for the most parsimonious tree, and see whether this recovers the true tree. This will be used for the second computer assignment.

The first program is available in newly updated form. The other two are older and have a clunkier interface.

(1) PopG -- Simulation of gene frequency evolution

This program is freely distributable. It is distributed as

We also distribute source code for all of these versions, which you can use to compile moidified versions if you want. But you will probably not need to do this. To read the web page which enables you to fetch any of these Click here

(2) Evolution of a quantitative character

(We probably won't use this program this quarter, but feel free to play with it as a learning tool) This program is available from its web page, for which Click here

(3) Simulation of phylogeny and inferring phylogeny

This program, which we will probably use later in the quarterm, is available from its web page, for which you should Click here

This page maintained fitfully by Joe Felsenstein