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.
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!
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.
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).
(*) 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 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.
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):
Note that Yang's book is also available through the UW Library web pages, in an
electronic book format.
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 are the homeworks assigned (so far):
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:
Where is the lecture room?
Course email mailing list
Lecture projections and audio recordings
The course text and how to get it
Books on Reserve
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.
Computer exercises (homeworks)
Some data sets you can download and use
Turbeville. J. McC., Schulz, J .R. and R. A. Raff.
1994. Deuterostome phylogeny and the sister group of the chordates: evidence from
molecules and morphology. Molecular Biology and Evolution 11: 648-655.
Alignment is by them. These are chordates, protochordates, echinoderms,
thisachordates, and thatachordates. Heavy-duty industrial-strength data.
These sequences are in interleaved format.
Click here to download.
I will be putting up some more datasets and web sites of aligned
sequences.
What are some other related courses?
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:
There are also relevant papers on population genetics in genetics and genomics journals such as Genetics, Genome Biology, Genome Research, Nature Genetics, PLoS Genetics, BMC Genomics and Theoretical Population Biology.
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:
Web Pages