Day	Date	Lecture Topic	Readings	Lab Topic
W	Sept 3 S&T	Introduction to systematics	M&M: Ch.3 Simpson: Ch.1	Discussion: Systematics 2000; Define preliminary project
M	Sept. 8 S	Characters: definition, homology	Roth, 1988; Simpson: Ch.2: 7-12
W	Sept. 10 S	Character coding: states, ordering, weighting	Simpson: Ch.2: 7-12	Exercise: characters & states definition
M	Sept. 15 T	Tree building I: methods of phylogenetic inference, optimality criteria	M&M: Ch.4: 49-52 DO: Library journal Hillis et al: Ch. 11
W	Sept. 17 T	Tree building II: parsimony; maximum likelihood	M&M: Ch.5:86-110 Hillis et al: Ch. 11	Exercise: hyp. org. MacClade Usage: hyp. org., libr. data Ref: M&M: Ch.2, MacClade Usage Sheet
M	Sept. 22 T	Tree rooting and character polarity	M&M: Ch 4: 52-3
W	Sept. 24 T	Outgroup analysis	Maddison et al. (1984)	MacClade; PAUP handout; transfer files and analyze
M	Sept. 29 J. Wiens	Character analysis: polymorphic characters	Handouts
W	Oct. 1 S	Character analysis: qualitative vs. quantitative characters, gap coding; char. state ordering-step matrices	Handouts	Exercise: quantification of character states
M	Oct. 6 S	Consensus trees	M&M: Ch. 5: 120-123; Handouts
W	Oct. 8 S	Phylogenetic accuracy and tree evaluation	M&M: Ch.5:110-23	PAUP & MacClade: Consensus trees, bootstraps, decay indices, successive wt.
M	Oct. 13 T	Classification and systematics	Handouts
W	Oct. 15	Exam 1 (3 Sept. - 8 Oct.)		Internet resources: Collections servers; Tree of Life
M	Oct. 20 S	Character optimization	M&M: Ch. 5, Handouts
W	Oct. 22 S	Character evolution & correlations	M&M: Ch. 13, 17 Reading	PAUP & MacClade:
W	Oct. 29 T	Dealing with multiple data sets in phylogenetic analysis	Readings	Exercise: molecular data sets; step-matrices; combining data sets
M	Nov. 3 T	Species concepts	Frost and Hillis (1990)
W	Nov. 5 T	Types of data: distance data & methods	Hillis et al.: Ch. 11	Exercises, Handouts, Readings
M	Nov. 10 S	Phylogeny and Biogeography	Readings
W	Nov. 12 S	Phylogenetics and Biodiversity	Readings	Exercises and Discussion
M	Nov. 17	Open	Readings
W	Nov. 19	Open	Readings	Work on Projects
M	Nov. 24	Exam 2 (13 Oct. - 19 Nov.)
W	Nov. 26	Thanksgiving Holiday
M	Dec. 1 S	Open	Reading
W	Dec. 3	Open; Rough Draft due by 3 Dec.		Work on Projects
M	Dec. 8 1-3 pm	Oral Presentations		Oral Present.
W	Dec. 10 1-3 pm	Oral Presentations		Oral Present.
M	Dec. 15	Written Papers Due! 3 pm

Maddison, W. and D. Maddison. 1992. MacClade, version 3. Sinauer Associates, Sunderland, Massachusetts. [Available at bookstore.]

Two 3.5" double sided Mac disks (double or high density) for keeping MacClade & PAUP files. (Please also purchase a carrying case for these.)

A $5 - $10 fee may be charged at the end of the course for photocopying costs.

Brooks, D.R. and McLennan, D.A. 1991. Phylogeny, ecology, and Behavior: A Research Program in Comparative Biology. Univ. Chicago Press, Chicago.

Hennig, W. 1966. Phylogenetic systematics. University of Illinois Press, Urbana.

Hillis, D. M., Moritz, C., and Mable, B. K. 1996. Molecular Systematics, 2nd Ed. Sinauer.

Wiley, E. O. 1981. Phylogenetics, the Theory and Practice of Phylogenetic Systematics.. John Wiley and Sons, N. Y.