Genetics 554                                            Phylogenetic Inference
Spring, 1996                                                   Joe Felsenstein

                         Syllabus of lectures

 Date                  Topic

3/25	  What is a phylogeny? Parsimony -- a small example
  27	  Parsimony algorithms -- small parsimony problem
  29	  Exact enumeration -- the number of trees
	  
4/1	  Searching tree space heuristically
  3	  Branch and bound
  5	  Reconstruction of ancestral character states. Branch lengths
	  
4/8	  Variants of parsimony
 10	  Compatibility
 12	  Inconsistency and parsimony
	  
4/15	  A brief discussion of philosophy, parsimony, history etc.
  17	  Distance matrix methods: UPGMA, Fitch-Margoliash
  19	      "         "        : Neighbor-joining, Minimum evolution, Generalized least squares
	  
4/22	  DNA distances incl. rate variation among sites, 
  24	  Protein distances and models, Restriction sites and RAPDs
  26	  Microsatellite distances and models.  Gene frequency distances and models
	  
4/29	  Likelihood methods
5/1	       "         "
  3	  Testing trees, clocks, etc. by likelihood ratio tests
	  
5/6	  The bootstrap
  8	  The KHT test(s)
 10	  Invariants ("evolutionary parsimony")
          
5/13	  Trees from continuous characters and gene frequencies
  15	  Comparative methods
  17	  Comparative methods for discrete characters
 	  
5/20	  Other kinds of trees: Coalescents
  22	  Likelihoods on coalescents
  24	  Gene trees (of loci).  Gene families
	  
5/27	  HOLIDAY (Memorial Day; last day of Folk Life Festival)
 29	  Tree distances. Consensus trees
 31	  Tests based on tree shape. Drawing rooted and unrooted trees

The course text is a series of handouts by the instructor. These are available free to the class. They are skeleton chapters from a proposed book, Inferring Phylogenies. They are copyright to the instructor, 1996. You can download copies of these chapters, as Postscript files. They can then be printed on any Postscript printer. On Macintoshes you may have to use the Laserwriter Font Utility to send them to the printer.

Click here to download the individual chapters (files of about 200k bytes in size) and the references. These materials are all copyright 1996 by Joe Felsenstein. They may be downloaded and copies printed for individual use, but may not be reproduced or disseminated to others. They are Postscript files. On Unix, DOS, or Windows systems, they can be printed by sending them to a Postscript printer. On Macintoshes this can be done using the Laserwriter Font Utility (I am told). u

Call number                         Book

612.0151   Doolittle, R. F. (ed.).  1990.   Molecular evolution: computer
M566       analysis of protein and nucleic acid sequences. Methods in
v.183      enzymology, vol. 183.  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. and G. J. Olsen.  1990.  Phylogeny reconstruction.
.M665      Chapter 11, Pp. 411-501 in D. M. Hillis and C. Moritz, eds.
1990       Molecular Systematics.  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.
   
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

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).

Botany 113

Systematic Botany. Taught by Richard Olmstead, who is active in molecular systematic research. Some coverage of methodology but mostly much detail on characters of individual groups of plants.

Zoology 414

Molecular evolution course by Scott Edwards, who is an active researcher in that area. New course. Texts are Li and Graur "Fundamentals of Molecular Evolution" and Avise "Molecular Markers". Winter quarter.

Others

There are more courses and I'll gradually try to put descriptions of them here.

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. Some percentage of them are semantic issues or legalistic discussions of taxon names.

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.

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