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Research Index
Syllabus
COA 690/790 Special Topics: Introduction to Cladistics
Spring Semester
Instructor: Dr. Jinx Campbell, Asst. Professor of Marine Mycology
Course Description:
A lecture and lab course on the theory of phylogenetics, and its uses in classification, taxonomy and speciation. Emphasis is placed on using current software to analyze data.
Course Objectives:
- Understand the principles of cladistic theory and systematics
- Understand the theory of maximum parsimony and maximum likelihood
- Be able to construct a morphological and molecular data set
- Be able to align sequence data using ClustalX and Se-Al
- Be able to produce cladistic trees using maximum parsimony and maximum likelihood algorithms using the programs PAUP and MrBayes
- Be able to compare trees and determine the “best” tree for the dataset
- Understand the difference between gene trees and species trees
- Understand the theory of biogeography
Lectures:
- Basic cladistic theory, terminology, classification
- Phylogenetic data
- Finding an alignment
- Tree building methods: Maximum parsimony
- Tree building methods: Maximum likelihood
- Tree building methods: Bayesian analysis
- Tree comparison and consensus
- Tree support
- Combining datasets and incongruence
- Character tracing and analysis
- Turning results into a Figure
Labs:
- Classification and relationship: The Caminacules
- Finding data on the internet
- BLAST searches, aligning data with ClustalX and Se-Al
MacClade
- Maximum parsimony using PAUP*
- Maximum likelihood using PAUP*
- Bayesian analysis using MrBayes
- Tree length, tree scores, parametric tests (K-H, S-H), consensus trees, agreement subtrees
- Bootstrap, Jack-knife, decay index, Bayesian posterior probabilities
- Incongruence Length Difference, partition homogeneity test, percent clades correct measure
Grading:
Final exam at end of course.
The final exam consists of a written question and answer paper (25%) and a practical (75%) covering all aspects of the labs in the course.
A = 90–100%
B = 80–89%
C = 70–79%
D = 60–69%
F = below 59%
Software used:
- AutoDecay: See Bremer (Evolution 42:795-803. 1988; Cladistics 10(3):295-304. 1994). Available free from: http://www.bergianska.se/index_forskning_soft.html
- ClustalX: Available free from: http://www-igbmc.ustrasbg.fr/BioInfo/ClustalX/Top.html
- MacClade: Available from: http://www.sinauer.com/detail.php?id=4707, priced at $125. Dr Campbell has a lab license for this software.
- ModelTest: Available free from: http://darwin.uvigo.es/software/modeltest.html
- MrBayes: Available free from: http://morphbank.ebc.uu.se/mrbayes/
- PAUP: Available from http://www.sinauer.com/detail.php?id=8060, priced at $100. Dr Campbell has a lab license for this software.
- Se-Al: Available free from: http://evolve.zoo.ox.ac.uk/software.html?id=seal
- TreeView: Available free from: http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
Recommended Reading:
No course textbook but the following are recommended.
- Felsenstein, J. 2002. Inferring Phylogenies. Sinauer Associates. Sunderland, Massachusetts.
- Forey PL, Humphries CJ, Kitching IL, Scotland RW, Siebert DJ and Williams DM. 1997. Cladistics: a practical course in systematics. Clarendon Press, Oxford, UK.
- Hillis, D. M., Moritz, C., and Mable, B. Molecular Systematics (2nd ed.) Sinauer Associates. Sunderland, Massachusetts.
- Li, W. 1997. Molecular Evolution. Sinauer Associates. Sunderland, Massachusetts.
- Lipscomb D. 1998. Basics of Cladistic Analysis. George Washington University, Washington, DC.
- Nei, M. and Kumar, S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York, New York.
- Page, R. D. and Holmes, E. C. 1998. Molecular Evolution: A Phylogenetic Approach. Blackwell Science, Oxford.
- Wiley EO, Siegel-Causey D, Brooks DR and Funk VA. 1991. The compleat cladist. A primer of phylogenetic procedures. The University of Kansas Museum of Natural History Special Publication No. 19.
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