BIOL 615 Systematic & Comparative Biology - Fall 2008
 
Lectures:
5 Sept . Fri Introductions, syllabus (note - class meeting time changes to T/TH 9:45 - 11:15)  
9 Sept. Tues Taxonomy, classification, The Modern Synthesis, basic nomenclature Mayr 1991 Ch. 1 pp. 1-18
11 Sept. Thurs Journal article discussion - TBA  
16 Sept. Tues Taxonomy and classification prior to 1859: Pre-Socratic philosophers to Darwin Mayr 1982 Ch. 4 pp. 147-208; 7 & 8 pp. 301-371
18 Sept. Thurs Evolutionary classification, phenetics, cladistics: 1859 - present Mayr 1982 Ch. 5 pp. 209-250; 8 pp. 371-393 & Mayr 1991 Ch. 8-10
23 Sept. Tues

Journal article discussion - TBA

  
25 Sept. Thurs Systematic collections, publication, rules of zoological nomenclature Mayr 1991 Ch. 12-14 pp. 325-406
30 Sept. Tues Journal article discussion - TBA  
2 Oct. Thurs Parsimony, rooted and unrooted phylogenetic trees Felsenstein Ch. 1 pp. 1-10
7 Oct. Tues Tree search algorithms: Exhaustive, heuristic, and branch and bound searches Felsenstein Ch. 2-5 pp. 11-66
9 Oct. Thurs PAUP* 4.0/MacClade demonstration  
14 Oct. Tues Journal article discussion - TBA
16 Oct. Thurs Ancestral character states, branch lengths, types of parsimony, character weighting, consenus trees, and Bremer support Felsenstein Ch. 6-7 pp. 67-86; Ch. 30 pp. 521-528, 535-538, Ch. 19 330-331
21 Oct. Tues Distance matrix methods: Least squares, UPGMA, neighbor-joining Felsenstein Ch. 10-11, pp. 123-155, 159-175
23 Oct. Thurs Journal article discussion - TBA  
28 Oct. Tues Models of DNA and protein evolution Felsenstein Ch. 11 pp. 156-159, Ch. 13-14 pp. 196-229
30 Oct. Thurs Journal article discussion - TBA  
4 Nov. Tues Statistical properties of parsimony,maximum likelihood Felsenstein Ch. 9 pp. 97-122, Ch. 16 pp. 248-256
6 Nov. Thurs Maximum likelihood cont. Felsenstein Ch. 16 pp. 256-274
11 Nov. Tues Journal article discussion - TBA  
13 Nov. Thurs Bayesian inference of phylogeny, MrBayes 3.0 demonstration Felsenstein Ch. 18 pp. 288-306
18 Nov. Tues Journal article discussion - TBA  
20 Nov. Thurs Likelihood ratio tests, testing molecular clocks, ModelTest 3.5 demonstration Felsenstein Ch. 19 pp. 307-334
25 Nov. Tues Journal article discussion - TBA  
27 Nov. Thurs Thanksgiving (no class)  
2 Dec. Tues Bootstrap, jacknife, permutation tests, paired-sites tests Felsenstein Ch. 20 pp. 335-363, Ch. 21 pp. 364-372
4 Dec. Thurs Journal article discussion - TBA  
9 Dec. Tues Sequence alignment; Clustal X and POY 3.0 demonstration/comparison Felsenstein Ch. 29 pp. 496-520
11 Dec. Thurs Class manuscript presentations  
 
Location and time:

Tues & Thurs 9:45 - 11:15 AM, 103 Irving 1

 
Required text:

Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts.

*See list of typos at http://evolution.gs.washington.edu/book/typos.html
 
Other useful texts:  
Mayr, E. 1969. Principles of Systematic Zoology. McGraw-Hill, New York.
Mayr, E. 1982. The Growth of Biological Thought. Harvard University Press, Cambridge, Massachusetts.
Hillis, D. M., C. Moritz, and B. K. Mable. 1996. Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts.
 
Course requirements:
  • Final exam.
  • Attend and participate in all lectures and discussions.
  • Write one 15-25 page scientific manuscript that is: (1) a review or re-analysis of published phylogenetic data, (2) analyzes new character data collected in your research, or (3) considers conceptual and theoretical issues in phylogenetic systematics. The manuscript should be based on work that is not already completed, and it should be prepared for publication in a peer-reviewed journal. The target journal should be identified, and the manuscript should be formatted to conform to journal guidelines. Manuscripts will be "peer-reviewed" by the class and submitted to your instructor for final "editorial" review and grading on the last day of class.
 
Grading:
  • 50% Final exam
  • 40% Manuscript
  • 10% Participation
 
Journals:
Cladistics
Evolution
Genetics
Journal of Molecular Evolution
Molecular Biology and Evolution
Molecular Ecology
Molecular Phylogentics and Evolution
Nature
Proceedings of the National Academy of Sciences
Science
Systematic Biology
Trends in Ecology and Evolution
 
Other useful links:
abebooks.com
Animal Diversity Web
GenBank
Joe Felsenstein's List of Phylogeny Programs
PAUP* 4.0
MacClade 4.0
MrBayes 3.1
Oxford Evolutionary Biology Group Software
Tree of Life Web Project
UAF Journals List
UC Berkeley Phylogeny Site
Web of Science
 
Contact information:

Kevin G. McCracken
Institute of Arctic Biology &
Department of Biology and Wildlife
University of Alaska Fairbanks
Fairbanks, Alaska 99775
office (907) 474-6419 Rm. 028 MUS
email: fnkgm@uaf.edu
 
Office hours:
Monday-Wednesday 3:30 to 4:30 pm or by appointment