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)
- (16 December 2013) The exams are now graded, course total points
calculated, and grades have been submitted through the University's
online system. A histogram of course point totals (in 4-point bins) is
available here. It
shows some indication of how grades correspond to totals. I have written
the exam score, the course total, and the grade on each paper and will
send the papers out to those students who have provided either an address
or an addressed envelope. The rest of you can, if you wish, email me an
address, or come by and pick up your exam.
- (2 December 2013) The second computer homework is now graded and will
be returned in class. Thanks for all the work you all did on this. A summary
of the results is given here.
- (12 November 2013) The second of the two computer homeworks is now
available. The PDF assignment will be found in the table of lecture materials
below. It is due 11/25 and involves a fair amount of work, so start early.
There are many instructions, but basically you are going to use a somewhat
clunky computer program from my PHYLIP package to manually rearrange trees and
try to find the most parsimonious tree, each student with a different data set.
- (14 October 2013) The first of the two computer homeworks has now been
assigned. The PDF assignment will be found in the table of lecture materials
below. It is due next Monday (the 21st) at the end of the day. It will not
take that long to do, but don't leave it to the last minute. It is a computer
simulation of gene frequency changes under favorable mutation.
- (7 October 2013) Owing to brain malfunction, I turned on the sound
recorder for this lecture late, so it only has the last 12 minutes of the
lecture. People wanting to hear a lecture equivalent to the missing
material should listen to the lecture of 10 October 2011 (in WMA format), or else
MP3 format), and the first 4 minutes of the lecture of 12 October 2011
WPA format), or else
MP3 format). There is some overlapping material there (on coalescent trees
of genes) which we will also cover on 9 October. I have to make this
mistake once per quarter, and will now learn my lesson.
- (4 October 2013) A new version of PopG, the genetic simulation program we will use
this quarter, is now posted.
If anyone wants to try it out, look here.
It has been rewritten in the Java language, and requires that you have Java
installed on your computer (for Windows
systems you may need to do that yourself, which can be done by following the
link on the PopG web page).
Let me know of any difficulties installing it.
- There is now a Genome 453 2013 email mailing list, to which I can post and so can all registered students in the course. We can post by emailing to email@example.com (I think you need to email from an account with the email address that is your official UW email). If people use it to ask questions of me, I will try to answer them promptly and everyone will see the questions and answers, which may be helpful. Archives of past messages should be available by going to http://mailman.u.washington.edu and searching for the list "genome453a_au13"
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, overheads and audio
These resources are of three kinds:
- Lecture outlines. These are less than a text but more than an
outline. They are PDFs of numbered lists of points covered in the lectures
(with a few points not covered but added as supplementary information).
Note that the lecture outlines this year will have some links to web
pages giving more detail, and if you are reading them on a computer
linked to the web, you can also click on those. They are labeled as
“(old)” when they are the 2011 versions that have not yet
been updated to 2013. They are fairly close to this year's, which will add
some more material.
- Lecture slides. These are the PDFs of the slides used in the
lectures. The slide PDFs are labelled “(old)”
when they are from the previous time I gave the course, in 2011, and have not
yet been revised. They are then preliminary versions of
the lecture PDFs. More will be added to these before the lectures,
but they are fairly complete.
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 choice in
the File menu on your browser to save them as PDFs.
- Audio recordings. They will posted here after each lecture.
They will be in WMA and also in
MP3 format. They have names that are the date of the lecture, so that the audio
files for the lecture of 9/29 (for example) would be called 20130929.WMA and
As the lectures are prepared (usually before or on the day they are to be
given) I will try to update the lecture outlines and the computer projection
PDFs. But sometimes I get rushed and cannot do so until after the lecture.
The projection PDFs are listed in the following table under the topic which is
being covered at the start of the talk. I may transition to the next big topic
partway through the talk, so if you want to hear about any topic, check the
last lecture of the previous topic -- it may start there.
If you want to see material from the 2011 course, just
go here. It
includes lecture outline PDFs, lecture slides, and even audio recordings of
the lectures. But keep in mind that parts of this will change for 2013.
The numbering of the lectures will also change some.
(*) This lecture's recording was started late and only has the last 12 minutes
of the lecture. See the News item (above) for alternatives for the missing
What are some other related courses?
- Biology 354 (Foundations in Evolution and Systematics)
- The main evolution course at the University, taught twice yearly.
In Autumn 2013 this is given by Jon Herron, co-author of the Freeman
and Herron evolution textbook
evolutionist; I am not sure who is teaching it in Spring 2014, but in Spring
2012 and Spring 2013 it was given by Carl Bergstrom, author of the
Bergstrom and Dugatkin Evolution textbook.
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 autumn 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.
I am not sure which quarters it will be taught, but it was taught last
Winter Quarter by Jay Parrish and last Spring Quarter by Sarah McMenamin.
- Biology 449 (Applied Phylogenetics)
- A course in applied aspects of phylogenetics,
with emphasis on exercises using actual data and widely-distributed programs.
Taught by Adam Leaché, who works on coalescents and phylogenies in lizard species.
- Biology 481 (Experimental Evolutionary Ecology)
- Lecture and
lab course on evolutionary perspectives on ecology. Taught by
Benjamin Kerr, who does much research in this area.
- Genome 562 (Population Genetics)
- 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, 2015. 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 Winter, 2014). Text is my book "Inferring Phylogenies".
- Biology 550A (Evolution and Systematics Seminar)
- A seminar Fridays at 1:30pm covering various topics in evolution. Runs
Autumn, Winter, and Spring quarters.
- Biology 550B (Paleo Lunch)
- (No, the lunch is not fossilized). A
lunchtime (Thursdays at 12:30) seminar on paleobiology. Autumn, Winter,
and Spring quarters.
- 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 Facebook pages
There are blogs, mostly for creation / evolution debating. There
also used to be Usenet newsgroups such as sci.bio.evolution. The
latter are accessible through Google Groups, but they are mostly defunct now.
Some brief descriptions of some of the major ones covering evolution:
- Science writer Carl Zimmer's blog, with articles appearing frequently.
Zimmer is also co-author of an evolution textbook.
- Evolution (Facebook page)
- A Facebook page run by Elise Andrew, who works in science publishing.
Many posts about particular colorful cases of adaptations in organisms, few
about technical issues in evolutionary biology. Creationist comments are
common in the Forum section but seem to be blocked by the moderator in
the comments on the posts.
- Evolution (Facebook page)
- Yes, there are two. This one is more oriented towards arguing for
evolution. I am not sure who is running it.
- Panda's Thumb (Blog)
- Blog defending evolutionary biology against creationists and advocates of
- Uncommon Descent (Blog)
- Blog centered founded by William Dembski and Denyse O'Leary, critics of
evolutionary biology and advocates of Intelligent Design.
- Evolution News and Views
- Does the name lead you to think that this is a blog by evolutionary biologists or science reporters? Wrong.
It is a blog sponsored by the Discovery Institute, which promotes Intelligent
Design. Don't get me started ...
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. Much
more complete for some groups than others. Explore!
- The TimeTree of Life finds
estimated divergence times for many (pairs of) species. Includes a lot
of downloadable PDF material including a whole book put out by this
- 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.
- 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 2011 there are 369 programs and 53 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.
- Also not for the faint-hearted. The UCSC
Genome Browser is the central site for the assembled human genome and
comparative genomics for other mammalian species. See the genomics data
not as some textbook illustration, but as the genomic “pros” see it.
- OrthoMam is a good collection of most gene families
in mammals, aligned, and even with trees computed for each. You can get
lots of data here. A good test of the reality of common descent is to
see whether different genes give noticeably similar evolutionary trees (they
won't be exactly the same for a number of reasons, including noisy data). Do
web resources from the National Academy of Sciences
aimed at the general public or scientifically knowledgable laypersons.
talk.origins Evolution FAQs (Frequently Asked Questions). These are
FAQ pages started for the former talk.origins newsgroup, where evolution was
defended against creationism. They have been expanded since and are generally
a very complete resource for evaluating all sorts of creationist arguments.
- Kent Holsinger's
Population Biology Simulations, some Java applets to illustrate various
- The Harvard Biopages evolution page, with lots of links to other
evolution resources. But it has not been maintained and many links are broken.
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 a Java program.
You need to make sure that you have Java on your computer. Mac OS X systems
and Linux systems tend to have Java. For Windows systems Java can be
downloaded and installed from here.
To read the web page which enables you to fetch PopG
(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 quarter, is
available from its web page, for which you should
This page maintained fitfully by Joe Felsenstein