Instructor: Joe Felsenstein
News about the course
- On October 5 I replaced the lecture slides projections for the October
3-7 lectures, as I updated it. Please fetch it again.
- The computer exercise is now posted. I have corrected the date (which
said "Winter, 2005"). Someone also pointed out that I had it as due
on November 1, which isn't a class day. November 2 will be fine too.
- Nervous about what kind of exams I give? Losing sleep? No need
to give your credit card number. Simply
click on these links for help! (Actually they are links to copies of
previous exams, midterm or final, visible on earlier web pages of this
1996 midterm as PDF
2004 midterm key as PDF
- Monday there will be a review session for the midterm exam. It will
be in the usual lecture room at 3:30 pm. I will answer questions on the course
- The exam on Wednesday the 2nd will be K069, which is on the ground floor
of the K wing, next door to the J wing. One way to go there is to enter the
K wing from the Rotunda eating area (it's on the southwest side) and go
down one floor on the large stairway. The room is directly in front of the
- On the genetic simulation homework: the bulleted points are not
separate questions to be answered (some aren't questions). Also, a hint: in
computing the number of new mutations per generation, all you need is
the population size N and the mutation rate u.
- On the genetic simulation homework: in asking you whether the simulated
populations spend more time waiting for mutations to arise or waiting
for them to fix once they have arisen, note that I am referring specifically
to mutations destined to be successful, that is, the copies whose
descendants will take over.
- For the exam. You might want to bring a calculator, for
multiplications and divisions and then occasional square root. If you
don't have one, you will be allowed to just leave computations in the
un-worked-out form such as (0.354 x 0.23)/2.
- The exam is graded and returned. Those students who have not got their
exams back yet can pick them up in class. In general people did well --
the totals are not as depressing as they look. Here
you will find a PDF of a histogram of totals, with some indication of roughly
what grade levels these imply.
- The second computer exercise is now posted. See the link in the
table of lecture notes and projections.
- I am nearly but not quite finished grading the first computer exercise.
It will be returned on Wednesday the 23rd.
- Some people who are running the Dnatree program on Windows xp systems
have found that it fails with a mysterious message saying that it is being
closed because there is a problem. I have tested it on several Windows xp
systems, and it has always worked for me, but I have had at least two
credible reports of this misbehavior. If it does this for you:
My apologies for this -- I think it's some kind of compiler limitation.
- One student who had this problem said "I also had the same problem that
i'm sure many others have.
However, I completely exited out of the program and then I believe I may have
restarted my computer. After that I clicked on the icon that I had saved to my
desktop and the program ran just fine."
- See if you can find another Windows system (maybe one of the University's
public access machines). It may work there.
- Try a Mac OS X or a Linux system, as those executables seem to work
- A reminder: The final exam will be on Monday, December 12, 8:30-10:30 pm in K069
Health Sciences (and for those needing more time, will continue until
at least 11:30 in the lecture room, J280).
- OUCH! I posted the wrong time for the exam. It was at 8:30am, not
8:30pm. Most of the class ignored that mistake and came at 8:30am. If there
is anyone who showed up at 8:30pm, my apologies. They should contact me and
alternative arrangements for taking the exam will be made.
- The grades are now turned in. (Thanks particularly to the three people who
were misled by my posting a wrong time for the exam, and who were very
tolerant of being made to take it at a later time). The distribution of
course totals (with indication of grade ranges) is shown here.
- If you want to pick up your final
exam (which has your grade and totals on it) see Brian Giebel in Health Sciences
K328B (the wing to the south of J wing). He has the exams available.
- The histogram of results from Computer Exercise #2 is available
here. It shows the number of partitions shared
between the estimated tree and the true tree for rate 0.4, the number for
rate 2.0, and the difference of the number shared for low rate and the number
shared for the high rate. It is evident that higher rates led to less
accuracy in the estimated tree: only one person got the reverse, and most
got a positive difference.
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:
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.
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
- 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
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".
- There are more courses and I'll gradually try to put descriptions of
What are some Internet resources on evolutionary biology?
There are many:
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
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
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
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 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
- Discussion among researchers about molecular evolution. Low
volume, high quality. Co-moderated by Jerry Learn of our Micro Department.
Very inactive lately.
- Tends to be filled with postings by fossil enthusiasts and
tends to be dinosaur-centered. Some creation/evolution debating too.
- 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.
- 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.
- 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. Weighted towards flowering plants, and
badly suffers being only sporadically updated.
- My own
PHYLIP free package of computer programs for inferring phylogenies.
Includes some web pages on all possible phylogeny programs and how to get
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
- Evonet.org, an NSF-funded
resource for evolutionary biology run by Patrick Phillips at the University
of Oregon. Mostly a list of other web pages, with a directory of
evolutionary biologists as well.
- The Population Biology, Evolution & Biomath Educational Index
posted by Carlos Lara-Moreno in 1998 (and not much updated since). Links to
population genetics courses, software, etc.
- 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.
talk.origins Evolution FAQs (Frequently Asked Questions).
- The Harvard Biopages evolution page, with lots of links to other
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
- A Windows executable version
- A Macintosh version for MacOS 8 and 9
- A MacOS X executable version
- A Linux executable version
(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
There you will find:
To read the web page which enables you to fetch any of these
- A Windows95/98/NT executable
- A PowerMac executable
- An executable for Intel-compatible machines running Linux
- An executable for Compaq/Digital Alpha processors running Compaq/Digital Unix
- Source code in C and various support files needed for compiling the program
(3) Simulation of phylogeny and inferring phylogeny
This program is also available, also from my workstation by anonymous ftp.
It is available from
evolution.gs.washington.edu. There you will find:
To read the web page which enables you to fetch any of these
- an executable for Linux on Intel-compatible processors
- a Windows 95,98,NT,2000,me,xp executable version
- a MacOS X executable that can be run in a Terminal window, Unix-style
- Some older versions for older Macs, PCs and workstations
- Source code in C that can be compiled on a Unix workstation with X windows
- A documentation file in HTML which can be read on your browser
This page maintained fitfully by Joe Felsenstein