Genome 570

Phylogenetic Inference

Winter, 2010

Monday, Wednesday, and Friday


S110 Foege Building

News about the course

Description from the UW Course Catalog

GENOME 570 Phylogenetic Inference (3) Felsenstein
Methods for inferring phylogenies (evolutionary trees) - biological assumptions, statistical foundations, and computational methods. A comprehensive introduction for graduate students in the biological sciences to phylogenetic methods using data from molecular sequences, continuous and discrete characters, and gene frequencies. Prerequisite: introductory courses in evolution and in statistics. Offered: alternate years; Sp.

Lecture projections

Here are the lecture projections. The ones marked “(preliminary)” are this year's, but may have some more material added later.

Audio recordings

I will be making audio recordings of my lectures. They will be posted here in two forms, as WMA files and as MP3 files. They will be recorded at a medium quality (to reduce file size) and should be about 5 Megabytes each. Watch for them here. Their names indicate the date of the lecture: thus the lecture for February 13th would be files 20100213.WMA and 20100213.mp3. The 4-digit year is followed by the 2-digit month and the 2-digit day.

week 1 week 2 week 3 week 4 week 5 week 6
week 7 week 8 week 9 week 10
Ouch! forgot to record the lecture of 3/05!
(see Chapter 26 of the book and maybe
also this (this) recorded lecture from
Genome 541 in Spring.
Review Session (WMA)
Review Session (MP3)

Where is 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 the bay.

Here is a campus map showing the location.

Oh yes, and who is the building named after? Someone living: This guy. Not bad!

The course text and how to get it

The course text is my book, Inferring Phylogenies, published by Sinauer Associates. The University Book Store (South Campus Center branch) will have copies. It can also be ordered from Sinauer Associates, from Amazon, from Barnes and Noble, etc. The first printing of the book has many typos. A web page listing the typos is available. Many of these were corrected in the second printing, and some more in the third printing. If there is a box on the back cover with reviews of the book, that is the second or third edition.

Computer exercises

There will be several computer exercises that you will be asked to do. These will use either data sets accessible here, or data of your own choosing. The exercises can use my own PHYLIP programs or any other phylogeny program you want to use. For an extensive list of available programs, with links to their web pages, look

The results of the exercises are to be handed in as homeworks.

Here are the homeworks assigned (so far):

Some data sets you can download and use

Almost all the data sets used in the book can be downloaded from its data sets web site.

These additional data sets are so that we can discuss common examples when people try out various programs. They are in PHYLIP formats, but these can often be read by other programs such as PAUP and MacClade. These data sets can be downloaded by clicking on the appropriate words. If clicking on them happens to display the file rather than open a window that asks you where to put the file, you may be able to get your browser to save it by using a "Save As" function (on most browsers that's in the Files menu).

Here are some other sources of aligned sequence data:

I will be putting up some more datasets and web sites of aligned sequences.
What are some other related courses?

Biology 354 (Foundations in Evolution and Systematics)
The main evolution course at the University, taught twice yearly (Winter and Spring). Texts are “Evolution” by Barton et al. and Weiner's “The Beak of the Finch”. This year's course is being taught by Peter Ward in the Winter quarter, and is also being taught by Gregory Wilson in the Spring Quarter. Ward, a paleontologist, is noted for his work on mass extinctions and has written many books on evolution for the general public. Wilson, who works on fossil mammals, is also a paleontologist.
Genome 453 (Evolutionary Genetics)
This is an undergraduate-level course on evolution and genetics. Given every Autumn, it overlaps somewhat with Biology 354 but covers the genetic aspects of evolution with less emphasis on ecology and paleontology than the first, less emphasis on molecular evolution than the second. In even-numbered years the course is given by Mary Kuhner, in odd-numbered years by me. It should be understood that this is basically an undergraduate course.
Biology 550 (Evolution and Systematics Seminar)
Weekly seminar with readings, presentations, and lots of discussion, the main seminar for biology graduate students to discuss evolutionary biology. Run by Toby Bradshaw, who keeps interest stirred up. Fridays at 1:30, this quarter in Hitchcock 320. Every quarter during the regular academic year.
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 notes, downloaded as a PDF for free or sold as printed copies in the course inexpensively (no royalty is paid to me).

What are some Internet resources on evolutionary biology?

There are many:

Electronic journals

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. If you are at another institution, you may be able to access a different run of years of each journal. Here are some direct UW links to the leading journals covering evolution:

Blogs and Newsgroups

There are blogs, mostly creation / evolution debating, and some Usenet newsgroups. The latter are accessible through Google Groups. Blogs have taken over from newsgroups, which are basically nearly dead now. I do not have enough understanding of Facebook to know what is available there.

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

Dechronization (Blog)
Named after a science fiction novel written by the famous evolutionary biologist George Gaylord Simpson, this is a technically oriented blog run by about 6 young phylogeny-oriented evolutionary biologists. Aside from occasional natural history it is mostly devoted to phylogenetic methods.
Panda's Thumb (Blog)
Blog defending evolutionary biology against creationists and advocates of Intelligent Design, run by Reed Cartwright, a phylogeny postdoc.
Uncommon Descent (Blog)
Blog centered around William Dembski and Denyse O'Leary, critics of evolutionary biology and advocates of Intelligent Design. (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. Lately traffic has declined, as newsgroups are disappearing. (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.

Web Pages

This page maintained fitfully by Joe Felsenstein