Genome 570

Phylogenetic Inference

Winter, 2014

Monday, Wednesday, and Friday

11:30am-12:20pm

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.


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!


Course email mailing list

The course now has an email mailing list, to which all registered students have been subscribed. You can view past mailings here). To send mail to the whole mailing list, email to  genome570a_wi14@u.washington.edu"  Everyone on the list can email to the whole list. I will also post announcements about the course and answer questions there. If people email me questions at my own email address about the course, if they are of general interest I will often use the mailing list to answer them, after anonymizing who asked the question.


Lecture projections and audio recordings

Here are the lecture projections. The ones marked “(old)” are from the 2012 course; they will be similar in 2014 but will have some more material added later.

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 20140213.WMA and 20140213.mp3. The 4-digit year is followed by the 2-digit month and the 2-digit day. The audio recordings are organized according to the topic being covered at the beginning of the talk (so to find a given topic you may need to start in the last recording of the previous group).

Week   Lecture projections (PDFs)      Lecture recordings      
      (WMA format)
      
      Lecture recordings      
      (MP3 format)
      
Week 1   Parsimony, tree enumeration 20140106.WMA
20140108.WMA
20140110.WMA
20140106.mp3
20140108.mp3
20140110.mp3
Week 2   Searching for trees, ancestral states 20140113.WMA
20140115.WMA
20140117.WMA
20140113.mp3
20140115.mp3
20140117.mp3
Week 3   Parsimony variants, compatibility 20140122.WMA
20140124.WMA
20140122.mp3
20140124.mp3
Week 4    Statistics and parsimony. History and philosophy. Distance methods. 20140127.WMA
Sorry, 1/29 lecture not recorded
20140131.WMA
20140127.mp3
Sorry, 1/29 lecture not recorded
20140131.mp3
Week 5   Distance methods, DNA models 20140203.WMA
20140205.WMA
20140207.WMA
20140203.mp3
20140205.mp3
20140207.mp3
Week 6   Protein and codon models, Likelihood methods, rate variation 20140210.WMA
20140212.WMA
20140214.WMA
20140210.mp3
20140212.mp3
20140214.mp3
Week 7   Bayesian inference 20140219.WMA
20140221.WMA
20140219.mp3
20140221.mp3
Week 8   Testing trees, bootstraps, jackknifes, gene frequencies 20140224.WMA
20140226.WMA
20140228.WMA
20140224.mp3
20140226.mp3
20140228.mp3
Week 9   Covariances, comparative methods, coalescents 20140303.WMA
20140305.WMA
20140307.WMA
20140303.mp3
20140305.mp3
20140307.mp3
Week 10   Likelihoods on coalescents, consensus trees, tree distances. tests on tree shape 20140310.WMA
20140312.WMA
20140314.WMA
20140310.mp3
20140312.mp3
20140314.mp3
Review session(18 March 2014 at 10am in the classroom) ReviewSession.WMA ReviewSession.mp3


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.


Books on Reserve

Three other textbooks have been placed on 4-hour reserve at the Health Sciences Library (T wing of Health Sciences Library):

These are well worth looking at. Yang's book is a well-organized and carefully thought-out introduction to molecular phylogenetics. Semple and Steel's book is an introduction from the point of view of mathematicians, with lots of definitions, theorems, and proofs. Baum and Smith's book is intended as an accessible introduction at an undergraduate level, and it is worth seeing how they accomplish that.


Computer exercises (homeworks)

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

here
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 File 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. In Autumn 2011 this was given by Charlotte Konikoff, a molecular evolutionist; in Spring 2012 it will be 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.
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 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 David Parichy, who s a developmental biologist. Given this quarter; last academic year it was given in both Autumn and Spring quarters.
Biology 449 (Applied Phylogenetics)
A new course in applied aspects of phylogenetics, with emphasis on exercises using actual data and widely-distributed programs. Taught in Winter quarter of odd-numbered years by Adam Leaché, who works on coalescents and phylogenies in lizard species. This course can be viewed as complementary to Genome 570.
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. 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, 2013. Text: my own extensive lecture notes, downloaded as PDF's for free or sold inexpensively (no royalty is paid to me).
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 food is not fossilized, nor is it provided, but participants can bring food). A lunchtime (Thursdays at 12:30) seminar on paleobiology. Autumn, Winter, and Spring quarters.
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:

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:

Blogs

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:

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.
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 ...

Web Pages


This page maintained fitfully by Joe Felsenstein