Genetics 453

Evolutionary Genetics

Winter, 2002

Instructor: Joe Felsenstein

MWF 11:30-12:20, in Fisheries Teaching and Research 034

News about the course

Description from the UW Course Catalog

GENET 453 Genetics of the Evolutionary Process (3) NW Beerli, Kuhner [they taught it in 2001]
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 GENET 371 or GENET 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 on the course newsgroup 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)

As the lectures are prepared (usually 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 3-6) (PDF)    slides for lectures 3-8 (PDF)    slides for lectures 3-8 (PDF)
Population genetics theory (lectures 7-9) (PDF)    slides for lecture 9 (PDF)    slides for lecture 9 (PDF)
Genetics of quantitative characters (lectures 9-10) (PDF)    slides for lecture 9-11 (PDF)    slides for lectures 9-11 (PDF)
Group and kin selection, punctuated equilibrium (lectures 11-13) (PDF)    slides for lecture 11-13 (PDF)    slides for lectures 11-13 (PDF)
computer exercise #1    
Electrophoretic variation and neutrality (lectures 14-16) (PDF)    slides for lectures 14-16 (PDF)    slides for lectures 14-16 (PDF)
Molecular evolution (lectures 17-19) (PDF)    slides for lectures 17-19 (PDF)    slides for lectures 17-19 (PDF)
computer exercise #2    
Coalescent trees of genes (lectures 20-21) (PDF)    slides for lectures 20-21 (PDF)    slides for lectures 20-21 (PDF)
Chromosome rearrangements (lectures 22-25) (PDF)    slides for lectures 22-25 (PDF)    slides for lectures 22-25 (PDF)
Evolution of the genetic system (lectures 26-28) (PDF)    slides for lectures 26-28 (PDF)    slides for lectures 26-28 (PDF)

What are some other related courses?

Biology 454 (Evolutionary Mechanisms)
The main evolution course at the University, taught yearly. Text in past has been Freeman and Herron's "Evolutionary Mechanisms", Futuyma's "Evolutionary Biology" or Ridley's "Evolution". This year the course is to be given by Toby Bradshaw and Jon Herron in the Spring quarter. The text is the Freeman and Herron text. What is the difference between Genetics 453 and Biology 454? Biology 454 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. Spring quarter.
Zoology 414 (Molecular Evolution)
Molecular evolution course by Scott Edwards, who is a very active researcher in that area. Texts last time were Li and Graur "Fundamentals of Molecular Evolution" and Avise "Molecular Markers". Winter quarter (Scott is on sabbatical leave in 2002 so it will resume in 2003).
Genetics 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, 2003. Text: my own notes, sold inexpensively (no royalty is paid to me).
Genetics 570 (Phylogenetic Inference)
This is a 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 2002).
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. Here are some:


Some brief descriptions of some of the major ones covering evolution. These groups have many participants who are novices to evolutionary biology. I have provided links to the groups through Google, but UW students can read them using UW's newsreading facilities too.
Discussion of systematics, including phylogeny and classification. Most postings are serious discussions by researchers. Some percentage of them are semantic issues or legalistic discussions of taxon names. There is often an endless thread about cladistic versus evolutionary-systematic approaches to classification.
Discussion among researchers about molecular evolution. Low volume, high quality. Co-moderated by Jerry Learn of our Micro Department. However, since October, 2001, this newsgroup has been inactive owing to Jerry being unable to be moderator.
Tends to be filled with postings by fossil enthusiasts and tends to be dinosaur-centered. Some creation/evolution debating too.
Originally supposed to be the forum for discussion by population biologists. But they hardly post at all there. Occasionally someone sees the "population" in the group title and starts a discussion of human overpopulation issues, which are best discussed elsewhere. This helps ensure that real population biologists will continue to avoid the group. Lots of spam.
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. Not intended for evolution/creation debates: Josh screens these out.
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 available from my workstation by anonymous ftp (see directory pub/popgen on There you will find:

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

(2) Evolution of a quantitative character

This program is available by anonymous ftp from my workstation. It is available from 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 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