Genome 453
Evolutionary Genetics
Autumn, 2007
Instructor: Joe Felsenstein
Directions to the lecture room: from upper campus, come across the pedestrian
bridge that goes to the central part of Health Sciences Center. Go to the
main corridor of that building (not the main corridor of Health Sciences)
and then up three floors. We're somewhere near there.
News about the course
(Most recent news is first)
- As our building's crazy security system makes it very difficult for people
to individually come to our department office to pick up their exams,
we have decided to make them available at the beginning of next quarter.
On January 9 (a Wednesday) Brian Giebel of the Genome Sciences department
office will be in the first floor hallway of Foege Building with the
exams, which can be picked up then. He will be there from 4:00-5:00pm. We
will try to post here if these plans change.
- The distribution of point totals and a rough indication of the grades
these correspond to are available here.
- Just a suggestion to bring a calculator capable of not only adding and
subtracting, but even of multiplying and dividing.
And reminder that the exam is at 8:30am in the course lecture room, not
at the usual course time.
- I have now posted here a PDF of the 2002 final.
I seem to recall it was too hard and a little confusing.
- I have succeeded in booking a room in Health Sciences for the
review session instead of the one in Foege Building. In fact, it is
Hogness Auditorium! This is the huge auditorium in Health Sciences
(capacity over 300). So bring 260 of your friends. To get there
go to the fourth floor of the T-wing, then go to the main corridor
of the Health Sciences Building. Walk toward the hospital. The
entry to Hogness Auditorium will be on the left (there are signs).
I will lead a procession there after class.
- A distribution of numbers of differences in branches between the
most parsimonious trees and the true trees, over 34 class members, is
shown in this PDF.
- As we decided in class last time, the review session will be at 11:30am on
Monday (tomorrow). I have tried to get a room for it. So far I have
got S110 Foege Building. This is the new building to the west of Health
Sciences. If you can reach the walkway leading out of the J wing of
Health Sciences, continue westward from there: the building is ahead of you,
and the S (South) part of it is the downhill, canalward half. The room is on
the first floor to the left after you enter the building.
If you go across the footbridge that is near Kincaid Hall, you should walk
straght ahead until you pass Hitchcock Hall, then turn right, then follow
the directions above.
However Monday morning I am going to make an emergency effort to get the
review session into one of the T wing lecture halls (as we did last time).
If I succeed I will post that here and try to put up signs on the lecture
room doors as well.
The review session is this early because I was not available on either
Wednesday or Thursday, so we had to choose between Monday, Tuesday, or
Friday. The exam is in our lecture room at 8:30-10:30 Monday the 10th.
- In doing the Dnatree runs, I ask you to set the "rate of evolution".
This is *not* the "Transition/Transversion ratio" (as some have thought)
but is the quantity that you are asked for with the question: "prob of change per unit time?" which comes after you have dismissed the first menu and provided the random number seed.
- The score distribution on the midterm is now plotted and can be fetched
(as a PDF) here.
- The exam is now graded and will be returned in class tomorrow (Friday the
9th).
- The review session for the midterm exam will be held on 10/31 at
11:30-12:20 (the hour after class). It will be in HSB T739, which is the
lecture hall next door to our usual one.
- The first computer assignment is assigned and is due 10/31. See the
link in the table of lecture notes below.
- Woops, those links didn't work. Now they do.
- 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
course):
1996 midterm as PDF
2004 midterm key 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:
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
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 (Autumn 2005). 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.
In Winter 2007 this was given by Billie Swalla in the
Winter quarter; in Spring 2007 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 and Genome Sciences 414 (Molecular Evolution)
- Molecular evolution course
Taught by Willie Swanson. Taught last autumn but not on schedule for this
autumn, and uncertain when it will next be offered.
- 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 a well-known researcher in this area. Last year it was
given in the Spring quarter.
- Biology 481 (Experimental Evolutionary Ecology)
- Lecture and
lab course on evolutionary perspectives on ecology. Taught by Toby Bradshaw,
Ben Kerr, and Josh Tewksbury. 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 Spring, 2009. 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 Spring 2008). Text is my book "Inferring Phylogenies".
- 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:
Blogs, Yahoo groups, and Newsgroups
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
me know.
Some brief descriptions of some of the major ones covering evolution:
I have provided links to the newsgroups through Google, but UW students
can read them using UW's newsreading facilities too.
-
sci.bio.evolution
(Usenet newsgroup)
- 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.
-
talk.origins (Usenet newsgroup)
- 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.
Lately everybody is being dismissive of everyone else's arguments.
- quan_gen (Yahoo Group)
- Quantitative genetics and related areas in bioinformatics at a professional
level. Run by Bruce Walsh of the University of Arizona.
- Panda's Thumb (Blog)
- Blog defending evolutionary biology against creationists and advocates of
Intelligent Design.
- Uncommon Descent (Blog)
- Blog centered around William Dembski and Denyse O'Leary, critics of
evolutionary biology and advocates of Intelligent Design.
-
sci.bio.systematics (Usenet newsgroup)
- Discussion of systematics, including phylogeny and classification.
Very little traffic. Most postings lately have been meeting announcements.
-
bionet.molbio.evolution
(Usenet newsgroup)
- Discussion among researchers about molecular evolution. Very low
volume (almost defunct), but was high quality.
-
sci.bio.paleontology
(Usenet newsgroup)
- Tends to be filled with postings by fossil enthusiasts and
tends to be dinosaur-centered. Some creation/evolution debating too.
Electronic journals
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:
Web Pages
- 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
them.
- But maybe you don't want to be limited to just my programs? OK,
try this listing which I maintain of all known
Phylogeny
Programs. As of September 2007 there are 332 programs and 47 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
fossils.
- The
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.
- The
talk.origins Evolution FAQs (Frequently Asked Questions).
- The Harvard Biopages evolution page, with lots of links to other
evolution resources.
- Kent Holsinger's
Population Biology Simulations, some Java applets to illustrate various
phenomena.
- 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.
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 Windows executable version
- A Macintosh version for MacOS 8 and 9
- A MacOS X executable version. (At the moment it will not work in
native mode on Intel Macs, but it will run well in emulation mode).
- A Linux executable version (Small glitch: if you enter a number in
a box in the menu of parameters, before leaving the menu click your mouse on
one of the other boxes to make sure it takes the new value).
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
Click here
(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
directory pub/contevol.
There you will find:
- 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
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
evolution.gs.washington.edu. There you will find:
- 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
To read the web page which enables you to fetch any of these
Click here
This page maintained fitfully by Joe Felsenstein