Genome 570

Phylogenetic Inference

Winter, 2016

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?

Directions to the lecture room:The building used to be reachable from upper campus using the overpass near Kincaid Hall. But alas, that route is impossible owing to construction. From upper campus, 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. Enter it at the door which is to the right as you pass through the opening in the building. S110 is the first room on your left as you go along this 1st floor corridor.

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_wi16@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 2014 course; they will be replaced by the lecture dates in 2016 by ones which are similar but which will have some more material added.

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 10-12 Megabytes each. Watch for them here. Their names indicate the date of the lecture: thus the lecture for February 13th would be files 20160213.WMA and 20160213.mp3. The 4-digit year is followed by the 2-digit month and the 2-digit day.

I will put the audio files here as soon after the lecture as I can. In the meantime, if you want to hear the corresponding lectures from 2014, you will find them at the 2014 course web page.

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 20160104.WMA
20160106.WMA
20160108.WMA
20160104.mp3
20160106.mp3
20160108.mp3
Week 2   Searching for trees, ancestral states, parsimony variants 20160111.WMA
20160113.WMA
20160115.WMA
20160111.mp3
20160113.mp3
20160115.mp3
Week 3   Character weighting, compatibility 20160120.WMA
20160122.WMA
20160120.mp3
20160122.mp3
Week 4    Statistics and parsimony. History and philosophy 20160125.WMA
20160127.WMA
20160129.WMA
20160125.mp3
20160127.mp3
20160129.mp3
Week 5   Distance methods, DNA models 20160201.WMA
20160203.WMA
20160205.WMA
20160201.mp3
20160203.mp3
20160205.mp3
Week 6   Protein and codon models, Likelihood methods, rate variation 20160208.WMA
20160210.WMA
20160212.WMA
20160208.mp3
20160210.mp3
20160212.mp3
Week 7   Bayesian inference 20160217.WMA
20160219.WMA
20160217.mp3
20160219.mp3
Week 8   Testing trees, bootstraps, jackknifes, gene frequencies 20160222.WMA
20160224.WMA
20160226.WMA
20160222.mp3
20160224.mp3
20160226.mp3
Week 9   Covariances, comparative methods, coalescents 20160229.WMA (*)
20160302.WMA (*)
20160304.WMA
20160229.mp3 (*)
20160302.mp3 (*)
20160304.mp3
Week 10   Likelihoods on coalescents, consensus trees, etc. 20160307.WMA
20160309.WMA
20160311.WMA
20160307.mp3
20160309.mp3
20160311.mp3
Review session(Given 15 March) Review.WMA Review.mp3

(*) on 29 February 2016 the sound recorder ran out of space after 33 minutes of recording, just as the section on Quantitative Characters was starting. The reason for the problem was not understood until 15 minutes into the next lecture, the one for 2 March 2016. For similar material covering the gap, see the 2014 web page (here) and the recording of the lecture of 3 March 2014 from about time 13 minutes and 40 seconds to almost the end of that lecture.


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, third or fourth printing.


Books on Reserve

Two other textbooks have been placed on 24-hour reserve at the Health Sciences Library (which is at the east end of the 3rd floor of the T wing of Health Sciences):

One other textbook that I requested be placed there turned out to be on "closed reserve" at the Odegaard Undergraduate Library (OUGL), so it can be read there: 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.

Note that Yang's book is also available through the UW Library web pages, in an electronic book format.


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. Last quarter (Autumn 2015) the course was given by Jon Herron, co-author of the Freeman and Herron evolution textbook. In Winter 2015 this is given by Robert Bryson, a postdoctoral fellow who works on phylogeography and biogeography.
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, a highly knowledeable population geneticist. It should be understood that this is basically an undergraduate course.
Biology 414 Molecular Evolution
Theoretical and empirical study of molecular evolution. Taught Winter, 2016 by Vladimir (Volodymyr) Minin of the Department of Biology and the Department of Statistics, who is actively involved in developing methods for statistical and computationally analyzing molecular evolution. One 2-hour lab session of Biology 414 overlaps with Genome 570 by 20 minutes.
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. It was given in 2014; I am not sure when it will next be taught.
Biology 449 and Biology 553 (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. To be offered in Winter, 2016. This course can be viewed as complementary to Genome 570.
Biology 469 (Evolution and medicine)
A new course on ways in which evolution provides insights and is applied in medicine. Taught this quarter by Daniel Promislow, an experienced evolutionary geneticist working in the Department of Pathology in the School of Medicine.
Biology 481 (Experimental Evolutionary Ecology)
Lecture and lab course on evolutionary perspectives on ecology. Taught by Jake Cooper, who works in this area. It will be given this quarter.
Genome 562 (Population Genetics)
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. The next time it will be given is in Winter, 2017, which may be the last time it is given. 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 lunch is not fossilized). A lunchtime (Thursdays at 12:30) seminar on paleobiology. Autumn, Winter, and Spring quarters.
Biology 550C (Phylogenetics - Theory, Methods and Empirical Data Seminar)
A seminar run by Adam Leaché Thursday at 2:30pm covering various topics in evolution. Runs 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