Genome 453

Evolutionary Genetics

Autumn, 2015

Instructor: Joe Felsenstein

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

Directions to the lecture room:The building used to be reachable from upper campus using the overpass near Kincaid Hall. But alas, that route is impossible owing to construction. From upper campus, 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. Enter it at the door which is to the right as you pass through the opening in the building. S110 is the first room on your left as you go along this 1st floor corridor.

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, overheads and audio recordings)

These resources are of three kinds:

As the lectures are prepared (usually before or on the day they are to be given) I will try to update the lecture outlines and the computer projection PDFs. But sometimes I get rushed and cannot do so until after the lecture. The projection PDFs are listed in the following table under the topic which is being covered at the start of the talk. I may transition to the next big topic partway through the talk, so if you want to hear about any topic, check the last lecture of the previous topic -- it may start there.

If you want to see material from the 2013 course, just go here. It includes lecture outline PDFs, lecture slides, and even audio recordings of the lectures. But keep in mind that parts of this will change for 2015. The numbers of lectures in each part of the course will also change some.

Outline of material projected materials audio of lectures (WMA) audio of lectures (MP3)
(Review sessions)
(Review sessions)
(Second review session)
(Second review session)

What are some other related courses?

Biology 354 (Foundations in Evolution and Systematics)
The main evolution course at the University, taught twice yearly. This quarter (Autumn 2015) the course is given by Jon Herron, co-author of the Freeman and Herron evolution textbook. In Winter 2015 this is given by Robert Bryson, a postdoctoral fellow who works on phylogeography and biogeography.
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 autumn quarter indicates that it will cover some particular topics in more depth rather than attempt a broad survey.
Biology 414 Molecular Evolution
Theoretical and empirical study of molecular evolution. Taught Winter, 2016 by Vladimir (Volodymyr) Minin of the Department of Biology and the Department of Statistics, who is actively involved in developing methods for statistical and computationally analyzing molecular evolution.
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. I am not sure when it will next be taught.
Biology 449 (Applied Phylogenetics)
A course in applied aspects of phylogenetics, with emphasis on exercises using actual data and widely-distributed programs. Taught by Adam Leaché, who works on coalescents and phylogenies in lizard species. To be offered in Winter, 2016.
Biology 481 (Experimental Evolutionary Ecology)
Lecture and lab course on evolutionary perspectives on ecology. Taught by Jake Cooper, who works in this area. I do not know when this will next be taught.
Genome 562 (Population Genetics)
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, 2017. 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, 2016). Text is my book "Inferring Phylogenies".
Biology 550A (Evolution and Systematics Seminar)
A seminar Fridays at 1:30pm covering various topics in evolution. Runs Autumn, Winter, and Spring quarters.
Biology 550B (Paleo Lunch)
(No, the lunch is not fossilized). A lunchtime (Thursdays at 12:30) seminar on paleobiology. Autumn, Winter, and Spring quarters.
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 Facebook pages

There are blogs, mostly for creation / evolution debating. There also used to be Usenet newsgroups such as The latter are accessible through Google Groups, but they are mostly defunct now.

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

The Loom (Blog)
Science writer Carl Zimmer's blog, with articles appearing frequently. Zimmer is also co-author of an evolution textbook.
Evolution (Facebook page)
A Facebook page run by Elise Andrew, who works in science publishing. Many posts about particular colorful cases of adaptations in organisms, few about technical issues in evolutionary biology. Creationist comments are common in the Forum section but seem to be blocked by the moderator in the comments on the posts.
Evolution (Facebook page)
Yes, there are two. This one is more oriented towards arguing for evolution. I am not sure who is running it.
Panda's Thumb (Blog)
Blog defending evolutionary biology against creationists and advocates of Intelligent Design.
Uncommon Descent (Blog)
Blog centered founded by William Dembski and Denyse O'Leary, critics of evolutionary biology and advocates of Intelligent Design.
Evolution News and Views
Does the name lead you to think that this is a blog by evolutionary biologists or science reporters? Wrong. It is a blog sponsored by the Discovery Institute, which promotes Intelligent Design. Don't get me started ...

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 a Java program. You need to make sure that you have Java on your computer. Mac OS X systems and Linux systems tend to have Java. For Windows systems Java can be downloaded and installed from here. To read the web page which enables you to fetch PopG 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 quarter, is available from its web page, for which you should Click here

This page maintained fitfully by Joe Felsenstein