Genetics 570

Phylogenetic Inference

News about the course

There is a course newsgroup, which is called uwash.class.genet570. It can be read and posted to from within the U.W.
If you heard the course was closed, that is incorrect. There was a limit of 30 students. If that fills we will get it raised. It should be 70, the limit of the room's seating.
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.

Course syllabus

Genetics 570                                             Phylogenetic Inference
Spring, 1998                                                    Joe Felsenstein


                          Syllabus of lectures

 Date                   Topic                                           Reading

  3/30  What is a phylogeny? Parsimony - a small example             Chapter 1
  4/1   Parsimony algorithms - small parsimony problem               Chapter 2
   3    Exact enumeration - the number of trees                      Chapter 3

  4/6   Searching tree space heuristically                           Chapter 4
   8    Branch and bound                                             Chapter 5
   10   Reconstruction of ancestral character states. Branch lengths Chapter 6

  4/13  Variants of parsimony                                        Chapter 7
   15   Compatibility                                                Chapter 8
   17   Inconsistency and parsimony                                  Chapter 9

  4/20  A brief discussion of philosophy, parsimony, history etc.    Chapter 10
   22   Distance matrix methods: UPGMA, Fitch-Margoliash             Chapter 11
   24      "      "      : Neighbor-joining, Minimum evolution, etc. Chapter 11

  4/27  DNA distances incl. rate variation among sites,              Chapter 12
   30   Protein distances and models, Restriction sites and RAPD
  5/1   Microsatellite distances and models. Gene freq. distances and models

  5/4   Likelihood methods                                           Chapter 15
   /6       "      "                                                 Chapter 15
   /8   Testing trees, clocks, etc. by likelihood ratio tests        Chapter 16

  5/11  The bootstrap                                                Chapter 17
   13   The KHT test(s)
   15   Invariants ("evolutionary parsimony")

 5/18   Trees from continuous characters and gene frequencies        Chapter 20
   20   Comparative methods
   22   Comparative methods for discrete characters

 5/25   HOLIDAY (Memorial Day; last day of Folk Life Festival)
   27   Other kinds of trees: Coalescents                            Chapter 23
   29   Likelihoods on coalescents                                   Chapter 24

  6/1   Gene trees (of loci). Gene families
   /3   Tree distances. Consensus trees
   /5   Tests based on tree shape. Drawing rooted and unrooted trees


Final Exam:   2:30-4:30 Wednesday, June 10 in J280 HSB


Textbook:

Felsenstein, J. 1998. Inferring Phylogenies. ASUW Publishing, Seattle.
 (available at their office in HUB 113).

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. (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       
   
QH83       Wiley, E. O. 1981.  Phylogenetics : the theory and practice of
.W52       phylogenetic systematics. Wiley, New York.
   
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    

QH367.5    Eldredge, N. and J. Cracraft.  1980.   Phylogenetic patterns and
.E38       the evolutionary process : method and theory in comparative
           biology.  Columbia University Press, New York.

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.

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

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 an active researcher in that area. Texts are Li and Graur "Fundamentals of Molecular Evolution" and Avise "Molecular Markers". Winter quarter.
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. Note -- This is 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, 1999. Text: my own notes, sold inexpensively by ASUW Publications in the HUB.
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 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 Biopages 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