Instructor: Joe Felsenstein
Directions to the lecture room: from upper campus, come across the pedestrian
bridge (over Pacific Avenue) next to Kincaid Hall (the bridge nearest 15th
avenue). Walk forward
past Hitchcock Hall on the right, descending to ground level. Then turn
right on the walkway that comes out of the Health Sciences Building.
Foege (“FAY-gee”) Building is ahead of you, and the S (South) wing of it is
the left half, the downhill half. Enter it at the door which is on the left
side of that sidewalk as you reach the building. S110 is the first
room on your left as you go along this 1st floor corridor.
Alternatively, if you 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
Oh yes, and who is the building named after? Someone living:
This guy. Not bad!
News about the course
(Most recent news is first)
- The exams have been graded, the point totals in the course calculated,
and the grades assigned. A PDF showing the distribution of point totals
is available here. The grades will in a few moments
be submitted electrically via the UW's Catalyst web tools. I believe that
there is a way you can access your grade (if you are a student), once those
Thank you, all, for your large contribution to the class, especially
for asking such thoughtful questions, and so many of them.
We can send you your exam if you email me a campus address. Otherwise
you can stop by Genome Sciences any time (though best to check with me
that I am there) and I can hand the exam back to you. I have written
the point totals and grades on the exam. Please check that I have
added your points up correctly on the exam and let me know if I have
- Needless to say, there are no office hours on the 17th.
- The review session occurred and was recorded (it was 1 hour and 20 minute
long). I thought it ranged fairly widely and was a pretty good review. Here are
- The review session will be on Tuesday, December 15 at 10:30am.
It will be in the usual class lecture room, S110. I will post an
audio recording of it here soon afterwards.
- In case anyone wants to run the Muller's Ratchet program, I
have put the C source code muller.c here
and the Linux (Intel i386) executable here.
A Mac OS X Universal executable is also available, here.
It can be run by typing its name ./muller.osx in a Terminal window
(not by clicking on the executable).
I have been able to see the Muller's Ratchet
phenomenon at work with settings of a mutation rate of 0.003 and selection
coefficient of -0.1.
- To stop a run you have to type control-C (Ctrl-C) when it
asks for the number of generations. We will fix this bug
next time we use the program.
- If you save the executable to your Linux or Mac OS X machine
you may have to make the file have execute permissions by
typing "chmod +x muller" or "chmod +x muller.osx", whichever
is appropriate. That only needs to be done once.
- For homework #2, the plot of average parsimony steps versus rate of evolution is
here and the histogram of steps for different
rates is here.
- Office hours on Thursday, December 3rd are as usual: 11:30-12:30 in
- I have updated some of the page references in the Syllabus, especially
those for the coalescent, chromosome evolution, and evolution of genetic
systems material. (I think I do not yet have all the correct pages for the
Barton et. al. book for the molecular evolution material).
- Once again, I forgot to record a lecture, the one for today (11/30/2009).
Will try to remember from now on.
- Homework can be turned in any time today by email or leaving
a printout in my mailbox (which you can't get to!) or giving it to me
- (Thursday November 19) Office hours today at the usual place and time: 11:30-12:30 in
- The second computer homework, due the day before Thanksgiving, is now
posted. It is available as a PDF here.
It requires you to download and run the phylogeny simulation and
rearrangement program DNATREE. Pay close attention in the homework
assignment to the method for counting how many differences there are
between trees -- students often get that wrong.
- I have made a histogram of the midterm totals. It can be
seen here as a PDF.
- I recorded the review session. But not all of it because I forgot to
turn on the recorder until after the first 20 minutes. The recordings may be
- The review session is at 2:30pm - 3:30pm Tuesday in S040 Foege Building.
That is one floor down from the usual lecture room, and across from the
building elevators. By the way, I hope to record the review session and
post the recording here (as a link from these news items, not where the
lecture recordings are posted).
- The midterm exam is, as you all probably are well aware, in
the class lecture room at the usual class time on Wednesday.
- We voted in class to have the review session for the midterm exam
the day before the exam, Tuesday the 3rd, at 2:30pm. I will arrange a room
and post that here.
- The Office Hours this week are shifted 30 minutes earlier, owing to
a seminar I have to attend. They will be from 11:00am - 12 noon Thursday.
The room will be different too: 216 Hitchcock (one floor down from the
usual room). This room shift is just for that day. Note that there will
also be a review session some time before the exam, at a time to be
determined in class.
- Oops, forgot to push the "record" button W when I lectured today (10/21),
so there is no sound recording. I will remember from now on. Apologies.
- The first computer exercise is assigned. It a a PDF available
- It has been confirmed that we have Hitchcock 312 for the Office
Hours for the rest of this quarter.
- Office hours for me have now been moved to a small conference
room in the same building as before, Hitchcock 312. (From upper
campus, cross the bridge near Kincaid Hall, enter Hitchock
Hall which is on the right-hand side of the downhill side of the bridge,
and turn left). I do not yet know whether this holds for next week as well.
- The date of the midterm exam is now set, Wednesday, November 4.
It will be in the class room at the class time. I will do a review
session during the week before (we will agree on a time for it later).
- The class syllabus (linked above) now has the dates correct for
- The Office Hours will occur on Thursdays from 11:30-12:30. They
will be Hitchock Hall room 346 (one of the big labs, in fact). I will
not be able to do this on the 8th of October, as I will be out of town
- The class lecture on the 9th of October will be given by
Mary Kuhner, as I have to be away that day.
- The final exam will be at the time specified by the University for
courses that are given at our time slot. This will be Wednesday,
December 16, at 2:30-4:30. The room will be announced later. The midterm
exam will occur during a class period, and its date will be announced later.
I have the PDF links to two old midterm exams, so that they now work.
- Office hours will be 11:30-12:30 on Thursdays. We are working on a
room, and I will post it here and email to the class mailing list about
where it will be. Until we settle on one, I will be outside the class
lecture room at that time, starting today.
- There is a class mailing list that mails to all registered students
in the class. It is genome453a_au09 with the usual suffix,
u.washington.edu, You are welcome to email questions there and
I will email announcements and answers.
- Swine Flu Policy: we may all get sick with it this quarter, including
me. Anyone who is sick is urged not to come to class until you are free of
fever for 24 hours (when not taking anti-fever medication). We will be
making lecture materials available on the course web site, I will try to
be available by phone to help you work from home to keep up. I also am making
plans to post audio files of my lectures on the web site, so people who have to
stay at home can look at the slides and also hear what I say. If I get sick
I will stay away and the course will be taught during that period by
Mary Kuhner, who teaches it even-numbered years and is a highly-rated teacher.
She knows her stuff.
- On the first day we will try to find a congenial time slot for me to
have office hours, where I will be available in S110 or S040 or some
publicly accessible area of the building. Come prepared to help us
find a time that works for you.
- The room has a big table you will be able to sit at. You are more
than welcome to bring lunch and eat it during class. The Vista Cafe
is next door to the room and food can be purchased there. The Rotunda
Cafe is on the 1st floor of I wing, not too far away. Then there's
our neighborhood restaurant which has a take-out window, on Boat Street very
near our building.
- 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
exam as PDF
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)
Preliminary versions of
the lecture PDFs. More will be added to these before the lectures,
but they are fairly complete. Then lecture outlines are labelled ``old''
when they are from last year and have not yet been revised.
Again, they are fairly close. The numbering of the lectures will
The audio files will be posted here too. They will be in WMA and also in MP3
As the lectures are prepared (usually before or on the day they are to be given)
I will update the lecture outlines and the computer projection
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.
In Winter 2009 this was given by Billie Swalla;
in Spring 2009 it was given by Carl Bergstrom.
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 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. Taught by Billie
Swalla, who is an active researcher in this area. Given this quarter, and last
year it was also given in the Spring quarter, taught by David Parichy.
- Biology 481 (Experimental Evolutionary Ecology)
- Lecture and
lab course on evolutionary perspectives on ecology. Taught by
Josh Tewksbury and Ben Kerr. Autumn quarters.
- 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 Winter, 2011. 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 Winter, 2010). 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:
Blogs and Newsgroups
There are blogs, mostly creation / evolution debating, and some Usenet
newsgroups. The latter are accessible through Google Groups.
Some brief descriptions of some of the major ones covering evolution:
- Panda's Thumb (Blog)
- Blog defending evolutionary biology against creationists and advocates of
- Uncommon Descent (Blog)
- Blog centered around William Dembski and Denyse O'Leary, critics of
evolutionary biology and advocates of Intelligent Design.
- 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 amateurs, including some high-volume
cranks. In among them are some people with serious knowledge. Not intended for
evolution/creation debates: Josh screens these out. Lately traffic has
declined, as newsgroups are disappearing.
- The arena for endless debate between creationists and others, with
frequent digressions into theology (or maybe it's for discussion of theology
with occasional digressions into biology). Extremely high noise to signal ratio.
When a decisive point is made, the opponent changes the subject or just
refuses to respond. The pro-evolution posters generally do a good job.
- Tends to be filled with postings by fossil enthusiasts and
tends to be dinosaur-centered. Some creation/evolution debating too.
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:
- The amazing Tree of Life , a phylogeny of all life, in the
making. Trees, figures, descriptions and references at a solid professional
level, each page done by a major systematist working on that group.
- 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
- But maybe you don't want to be limited to just my programs? OK,
try this listing which I maintain of all known
Programs. As of September 2009 there are 385 programs and 52 web servers
listed. Many of the programs are freely downloadable.
- The Paleontology Portal run by
professional societies, the US Geological Survey, and the University of
California Museum of Paleontology gives information on many groups and their
University of California Museum of Paleontology
pages, which a number of evolution and phylogeny electronic exhibits. This is
a sort of "virtual museum".
- 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
- Kent Holsinger's
Population Biology Simulations, some Java applets to illustrate various
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
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 Mac OS X executable version
- A Linux executable version
- A Macintosh version for MacOS 8 and 9
(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
(3) Simulation of phylogeny and inferring phylogeny
This program, which we will probably use later in the quarterm, is
available from its web page, for which you should
This page maintained fitfully by Joe Felsenstein