Genetics 453

Evolutionary Genetics

Winter, 1999

Instructor: Joe Felsenstein

MWF 11:30-12:20, in Health Sciences J280

News about the course

My office hours for Winter, 1999 are 1:30-2:30 Thursdays in J253 Health Sciences (down the hall from the classroom).
There will be a new computer simulation exercise this year, in addition to the one on population genetics. It will involve simulating the molecular evolution of a piece of DNA and analyzing it by parsimony. The programs are now available.

Description from the UW Course Catalog

GENET 453 Genetics of the Evolutionary Process
Credits: 3
Quarters: W
Instructor: Felsenstein
Gen. Educ.: NW
Course Desc.: 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: 371 or 372. Offered: W.

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 am trying to compensate by handing out copies of my overheads each time.

What are some other related courses?

Biology 454 (Evolutionary Mechanisms): The main evolution course at the University, taught yearly by Joel Kingsolver (Zoology Department) and Doug Schemske (Botany Department). Both are well-known researchers in evolutionary biology. Text in past has been Futuyma's "Evolutionary Biology" or Ridley's "Evolution". This year it is Freeman and Herron's "Evolutionary Analysis". 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. Winter quarter.
Zoology 414 (Molecular Evolution): Molecular evolution course by Scott Edwards, who is an active researcher in that area. Texts are Li and Graur "Fundamentals of Molecular Evolution" and Avise "Molecular Markers". Winter quarter. Note -- This is an undergraduate course.
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, 1999. Text: my own notes, sold inexpensively (no royalty is paid to me) by ASUW Publications in the HUB.
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 (starting Spring, 1998).
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:

Newsgroups

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

sci.bio.systematics: 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.
bionet.molbio.evolution: Discussion among researchers about molecular evolution. Low volume, high quality. Co-moderated by Jerry Learn of our Micro Department.
sci.bio.paleontology: Tends to be filled with postings by fossil enthusiasts and tends to be dinosaur-centered. Some creation/evolution debating too.
bionet.population-biology: Supposed to be the forum for discussion by population biologists. But they don't post much 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.
sci.bio.evolution: Moderated by Josh Hayes 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.
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.

World Wide Web Pages

The amazing Tree of Life , a phylogeny of all life, in the making. A professional data base system of systematics, in effect.
TreeBASE, a database of evolutionary trees (phylogenies) from the scientific literature. Mostly contains angiosperm plants now, and badly suffers from not being effectively updated.
EP-GED the Evolution and Population-Genetics Educational Database, pages maintained by Patrick Phillips at the University of Texas at Arlington which have many links to people, departments, software, etc in evolutionary genetics.
My own PHYLIP free package of computer programs for inferring phylogenies. Includes some web pages on all possible phylogeny programs and how to get them.
The University of California Museum of Paleontology pages, which include a substantial evolution and phylogeny section. This is a sort of "virtual museum".
Our own Burke Museum has a Vertebrate Paleontology Page that leads on to many images of vertebrate fossils.
Want some DNA or protein sequences? How about getting them from the international database? Try the Web pages of the databases at the NCBI, the National Center for Biotechnology Information of the National Library of Medicine, in Bethesda, Maryland. Not for the faint-hearted.
The journal Systematic Biology is the major journal of systematics. These are the Web pages of the Society of Systematic Biology, which publishes the journal. Its pages include tables of contents with abstratcs of many papers.
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 computer programs?

There are two 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 other 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.

(1) Simulation of gene frequency evolution

This program is freely distributable. It is available from my workstation by anonymous ftp (see directory pub/popgen on evolution.genetics.washington.edu. There you will find:

a 386 DOS executable version which can be run under Windows as well
a pre-386 DOS version for those who have PC/XT or PC/AT-compatible machines
a Macintosh version for non-PowerMac (680x0) processors
a Macintosh version for PowerMacs
Source code in C that can be compiled on a Unix workstation with X windows
an executable for DEC Alpha (OSF1)
an executable for Sun SPARCstations
an executable for DECstations
an executable for IBM RS6000 AIX systems

To fetch any of these by ftp Click here Try reading the README file from that directory first.

(2) Simulation of phylogeny and inferring phylogeny

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

a Windows 95,98,NT executable version
a self-extracting Binhexed Macintosh version for PowerMacs
a self-extracting Binhexed Macintosh version for 68k Macs
an executable for DEC Alpha (Digital Unix)
an executable for Sun SPARCstations
an executable for IBM RS6000 AIX systems
an executable for Linux on Intel-compatible processors
Source code in C that can be compiled on a Unix workstation with X windows
A documentation file in Postscript
A documentation file in PCL (for HP-compatible printers)
A documentation file in HTML which can be read on your browser

To fetch any of these by ftp Click here Try reading the README file from that directory first.

This page maintained fitfully by Joe Felsenstein