Genetics 570

Phylogenetic Inference

Spring, 2000

News about the course

The exams have now been graded and the grades turned in. Class members who want to see their exams (which have the point totals and grades written on them) should see the front desk secretary in the Genetics Department office, J205 Health Sciences Building. That is the same floor as my office and as the original lecture room, but turn right out of the elevator. The term papers are also attached to the exams (they counted 100 points, the exam 200 points).

By agreement with the class, two extra sessions were scheduled, to help us keep up with the material. They are on Monday, May 22 at 2:30 pm and on Wednesday, May 31, at 1:30 (i.e. right after the regular lecture time). Both have been scheduled in J112 HSB. The topics we hope to cover in the rest of the course are:

May 24: Trees from gene frequencies and quantitative characters
May 26: Comparative methods
May 31 (lecture 1): Coalescents
May 31 (lecture 2): Likelihood on coalescents
June 2: Consensus trees and tree distances

With luck we will get a bit ahead of this schedule.

The class will meet in a different room Wednesday and Friday for the rest of the quarter. We will meet in J112 HSB which is one floor down from the original lecture room. On Mondays we will continue to meet in the original lecture room, J280 HSB. The new room is smaller and more conducive to interaction (alas, we can't get it on Mondays).

Joe will be away at a previously scheduled meeting Friday, April 28 through Monday, May 1. The lectures on those two days will be given by (respectively) Dick Olmstead (Botany Department) and Scott Edwards (Zoology Department). Both have been asked to present an example, from their work, of the inference and use of phylogenies. Although they may use some methods (such as the bootstrap or maximum likelihood) that have not yet been discussed in our course, these lectures should help make the methods that we have been examining more real.
Joe has to be out of town to attend to a sick relative from Friday, April 7 to (perhaps) Thursday, April, 13. He will try to read e-mail from there. Lectures those three times will be given by Mary Kuhner or Peter Beerli. Apologies for the short notice.
The course textbook is now available at ASUW Publishing, 113 HUB. It costs $20.
There is a course newsgroup, which is called uwash.class.genet570. It can be read and posted to from within the U.W.
The room for the course has been changed to Health Sciences J280. I will post a notice of this on the room that is listed in the old Time Schedule. If attendance is small enough, we may also move to a smaller seminar room.
If you are told you need an entry code from us, graduate students can get one from the Genetics Department office, J205 Health Sciences, and they don't need to see me. Undergraduates should see me.

Description from the UW Course Catalog

GENET 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.

The course text and how to get it

The course text is the preliminary version of my book, Inferring Phylogenies. It will be sold by ASUW Publishing, 113 HUB, starting the first day of classes. Price is about $20 (I do not get any royalty).

Books on reserve at Health Sciences Library


612.0151   Doolittle, R. F. (ed.).  1996.   Computer methods for
M566       macromolecular sequence analysis. Methods in
v.266      Enzymology, vol. 266.  Academic Press, San Diego.
   
QA292      Sankoff, D. and J. B. Kruskal.  1983.   Time warps, string edits,
.T55       and macromolecules: the theory and practice of sequence comparison.
1983       Addison-Wesley, Reading, Massachusetts.
   
QH83       Funk, V. A. and D.R Brooks.  1981.   Advances in cladistics:
.A43       proceedings of the first meeting of the Willi Hennig Society.
1981       New York Botanical Garden, Bronx, New York. 
   
QH83       Platnick, N. I. and V. A. Funk, (eds.). 1983.   Advances in
.A43       cladistics, volume 2: proceedings of the second meeting of the
1983       Willi Hennig Society.  Columbia University Press, New York.
   
QH83       Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996.
.M665      Phylogenetic inference.  pp. 407-514 in Molecular Systematics,
1996       2nd ed., ed.  D. M. Hillis, C. Moritz, and B. K. Mable.
           Sinauer Associates, Sunderland, Massachusetts.
   
QH83       Sneath, P. H. A. and R. R. Sokal.  1973.  Numerical taxonomy; the
.S58       principles and practice of numerical classification. W. H. Freeman,
           San Francisco.

QH325      Li, W.-H.  1997.  Molecular evolution.
.L655      Sinauer Associates, Sunderland, Mass.
1997       
   
QH366.2    Harvey, P. H. and M. D. Pagel.  1991.   The comparative method in
.H385      evolutionary biology. Oxford University Press, Oxford and New York.
1991    

QH371      Sober, E.  1988.   Reconstructing the past: parsimony, evolution,
.S63       and inference.  MIT Press, Cambridge, Massachusetts.
1988  

QH431.A1   Felsenstein, J. 1988. Phylogenies and quantitative characters.
A54 v.29   Annual Review of Ecology and Systematics  19: 445-471.
           (also available  on the web)

QL351      Hennig, W.  1979.  Phylogenetic systematics.  University of
.H413      Illinois Press Urbana.
1979

??         Forey, P. L. et. al.  1992.  Cladistics: A Practical Course in
           Systematics.  Clarendon Press, Oxford.

Some data sets you can download and use

These 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 ftp 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 Netscape that's in the Files menu).

A 15-species, 40-character discrete-characters (0/1) data set of fossil elephants by Pascal Tassy and Pierre Darlu. From a paper in Geobios 19: 587-600 1986. Click here to download.
A 14-species, 232-base set of DNA data assembled by Masami Hasegawa of the Institute for Statistical Mathematics, Tokyo. These are sites extracted by Hasegawa from primate sequences done by a number of Japanese researchers. They are not contiguous sequences but are only the third-position or noncoding sites. They are from the D-loop region of mitochondrial DNA. These sequences are in non-interleaved format: to run them on PHYLIP programs you may need to choose the I option in the program menu. Click here to download.
A 16-species, 1992-site DNA data set from the paper by Clint Turbeville and others:
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.
A 76-species protein sequence data set for Transcription Elongation Factor Alpha (EFTU-alpha), alignment by the Protein Information Resource of the National Biomedical Research Foundation. Click here to download. Some species are represented more than once, and some by fragments.

What are some other related courses?

Biology 454 (Evolutionary Mechanisms): The main evolution course at the University, taught yearly by Joel Kingsolver (Zoology Department) and Doug Schemske (Botany Department). Both are well-known researchers in evolutionary biology. Text in past has been Futuyma's "Evolutionary Biology" or Ridley's "Evolution". This year it is Freeman and Herron's "Evolutionary Analysis".
Zoology 414 (Molecular Evolution): Molecular evolution course by Scott Edwards, who is a very active researcher in that area. Texts are Li and Graur "Fundamentals of Molecular Evolution" and Avise "Molecular Markers". Winter quarter.
Botany 527 (Plant Molecular Systematics and Evolution): Taught by Richard Olmstead and Ben Hall. Olmstead is a well-known molecular systematist and currently editor of Systematic Biology, Hall is a molecular geneticist (the discoverer of large and small subunit ribosomal RNA!) who has become increasingly interested in molecular evolution. Was offered Winter 2000.
Genetics 453 (Evolutionary Genetics): This is an undergraduate-level course on evolution and genetics. Given every Winter, it overlaps somewhat with Biology 454 and with Zoology 414 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. It should be understood that this is basically an undergraduate course.
Genetics 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, 2001. Text: my own notes, sold inexpensively by ASUW Publications in the HUB.
Computational Molecular Biology: There is a forthcoming course sequence (two quarters) organized by Phil Green of the Department of Molecular Biotechnology. I will be one of the instructors. It will be Winter and Spring quarters of 2001. Exact course number is not yet announced.
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:

Newsgroups

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

sci.bio.systematics: Discussion of systematics, including phylogeny and classification. Most postings are serious discussions by researchers. However, lately it's been filled with an endless and incomprehensible argument among four people (two cladists and two evolutionary-systematists) about which way to classify.
bionet.molbio.evolution: Discussion among researchers about molecular evolution. Low volume, high quality.
sci.bio.paleontology: Tends to be filled with postings by fossil enthusiasts and tends to be dinosaur-centered. Some creation/evolution debating too.
bionet.population-biology: Supposed to be the forum for discussion by population biologists. But they don't post much there. Occasionally someone sees the "population" in the group title and starts a discussion of human overpopulation issues, which are best discussed elsewhere. This helps ensure that real population biologists will continue to avoid the group.
sci.bio.evolution: 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 others about whether humans are still evolving (answer: yes, but it's extremely slow compared to cultural change) and whether laughter is selectively advantageous. Not intended for evolution/creation debates: Josh screens these out.
talk.origins: The arena for endless debate between creationists and others, with frequent digressions into theology. Extremely high noise to signal ratio. When a decisive point is made, the opponent changes the subject or just refuses to respond.

World Wide Web Pages

The amazing Tree of Life, a phylogeny of all life, in the making. A professional data base system of systematics, in effect.
TREEBASE, a searchable data base of phylogenies from various papers. It's early days yet so it has almost entirely angiosperm phylogenies in it.
My own PHYLIP, a free package of computer programs for inferring phylogenies.
Our phylogeny software pages, the largest and most comprehensive list of phylogeny programs that are available.
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 Harvard Biolinks evolution page, with lots of links to other evolution resources.
The talk.origins Evolution FAQs (Frequently Asked Questions).

This page maintained fitfully by Joe Felsenstein