Genome 453

Evolutionary Genetics

Winter, 2005

Instructor: Joe Felsenstein

MWF 10:30-11:20, in J280 Health Sciences



News about the course


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)

The lecture PDFs for parts of the course which we have not reached are those for the previous time I gave this course (Winter 2004). In the table of links below those are marked as "(old)". This year's lecture materials for those parts of the course will be similar but not identical.

As the lectures are prepared (usually before or on the day they are to be given) I will put links here to the lecture outlines and the computer projection images. These will be available as PDFs. The computer projection images will often have blue backgrounds, so don't try to print those if you value your printer! The versions in the rightmost column have white backgrounds instead and are the ones to use when printing out the PDFs.

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 projected materials (printable)
History of genetics in evolution (PDF)    slides (PDF)    slides (PDF)
Population genetics theory (lectures 3-5) (PDF)    slides for lectures 3-7 (PDF)    slides for lectures 3-7 (PDF)
Population genetics theory (lectures 5-7) (PDF)           (ditto)           (ditto)
Genetics of quantitative characters (lectures 8-9) (PDF)    slides for lectures 8-10 (PDF)    slides for lectures 8-10 (PDF)
Group, kin selection, punctuated equilibrium (lectures 10-12) (PDF)    slides for lecture 10-12 (PDF)    slides for lectures 10-12 (PDF)
computer exercise #1    
Electrophoretic variation, neutrality (lectures 13-14) (PDF)    slides for lectures 12-14 (PDF)    slides for lectures 12-14 (PDF)
Molecular evolution (lectures 15-17) (PDF)    slides for lectures 15-17 (PDF)
   slides for lectures 15-17 (PDF)
Coalescent trees of genes (lectures 18-20) (PDF)    slides for lectures 18-20 (PDF)    slides for lectures 20-21 (PDF)
computer exercise #2    
Chromosome rearrangements (lectures 22-24) (PDF)    slides for lectures 22-24 (PDF)    slides for lectures 22-24 (PDF)
  Mary Kuhner lecture (PDF)
Carl Bergstrom lecture (Powerpoint)
Josh Akey lecture (PDF)
 
Evolution of the genetic system (lectures 25-28) (PDF)
(partly new)
   slides for lectures 25-28 (PDF)
(partly new)
   slides for lectures 25-28 (PDF)
(partly new)


What are some other related courses?

Biology 354 Foundations in Evolution and Systematics
The main evolution course at the University, taught twice yearly. Text is the 3rd edition of Freeman and Herron's "Evolutionary Analysis". In 2006 this will be given by Toby Bradshaw in the Winter quarter; in 2005 it was also given in the Spring quarter by Billie Swalla and Peter Ward in the Spring Quarter.
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 and Genome Sciences 414 (Molecular Evolution)
Molecular evolution course taught by Willie Swanson. The text has been Graur and Li's "Fundamentals of Molecular Evolution".
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 Spring, 2007. 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 Spring 2006). Text is my book "Inferring Phylogenies".
Others
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:

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. Here are some direct links to the journals:

Newsgroups

The Usenet internet news groups flourished for a while but many are now moribund. They seem to have been replaced by Yahoo Groups and by egomaniacal blogs. However few of the those actually discuss professional-level work in evolutionary biology. If you come across Yahoo Groups or blogs that seem appropriate for listing here, let me know.

Here are some of the surviving Usenet groups that are relevant: These groups have many participants who are novices to evolutionary biology. Some are former graduate students who used to work in the area but now are programmers. I have provided links to the groups through Google, but UW students can read them using UW's newsreading facilities too.

sci.bio.systematics
Discussion of systematics, including phylogeny and classification. Most postings were serious discussions by researchers. Some percentage of them were semantic issues or legalistic discussions of taxon names. There is often an endless thread about cladistic versus evolutionary-systematic approaches to classification. Lately there is little traffic: this one is almost dead.
bionet.molbio.evolution
Discussion among researchers about molecular evolution. Low volume, high quality. Co-moderated by Jerry Learn of our Micro Department. Very inactive lately.
sci.bio.paleontology
Tends to be filled with postings by fossil enthusiasts and tends to be dinosaur-centered. Some creation/evolution debating too.
sci.bio.evolution
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 others about whether humans are still evolving (answer: yes, but it's extremely slow compared to cultural change) and whether laughter is selectively advantageous. There is an endless controversy of everybody against a couple of people who think they've proven that Hamilton's formula for kin selection is wrong (they haven't). Not intended for evolution/creation debates: Josh screens these out.
talk.origins
The arena for endless debate between creationists and others, with frequent digressions into theology. Extremely high noise to signal ratio. When a decisive point is made, the opponent changes the subject or just refuses to respond.

Web Pages


Where can I get a copy of the computer programs?

There are three computer programs that students in the course will be asked to run, and submit a report of the results. The details of the assignment will be handed out later. One program simulates evolution of gene frequencies of two alleles at a single locus in the presence of genetic drift, natural selection, mutation, and migration. The second 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 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.

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 by anonymous ftp from my workstation. It is available from evolution.gs.washington.edu in directory pub/contevol. There you will find:

To read the web page which enables you to fetch any of these Click here

(3) Simulation of phylogeny and inferring phylogeny

This program is also available, also from my workstation by anonymous ftp. It is available from directory pub/dnatree on evolution.gs.washington.edu. There you will find:

To read the web page which enables you to fetch any of these Click here
This page maintained fitfully by Joe Felsenstein