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| Advanced Phylogenetics |  |
| Tentative Syllabus |
Advanced Phylogenetics PCB 6990 Fall, 2001, Monday 5:00 PM-8:00 PM
Instructors: Dr. Timothy Collins and Dr. Javier Francisco-Ortega;
WHERE? OE 167
Office hours: Tim Collins, Monday 1:00-4:00PM. Javier Francisco-Ortega: Monday 11:00-2:00 PM
Course Description: A survey of current issues and methods in phylogenetics for advanced students. There is no textbook. We will read reviews and papers from the primary literature. These will include both "classics", and as well as readings from the latest literature. We will typically read four or more papers per week. This is a very reading-intensive course. The emphasis will be on bringing students up to speed on current methodological and conceptual issues in the literature of phylogenetic analysis, as well as sampling the range of biological problems that can be addressed.
Prerequisites: Applied Phylogenetics PCB 5616 or equivalent, and permission of instructors.
Grading: P/F. There will be no exams. Your grade will be based on class participation and your review paper. We expect you to attend all classes, and to be on time. Come to class with a list of discussion points for each paper.
Review Paper: You will pick one of the topics below and critically review and synthesize the literature on that topic. This should include an exhaustive up-to-date bibliography of the literature. These will be circulated to the class and will form the basis of review/discussion during the last two class meetings of the course.
Following is a tentative schedule of topics and dates. If there are topics you feel are critical to your research that are not addressed in the schedule of topics, talk to us.
Date Topic
M August 27 organizational meeting
M September 3 the logical basis of phylogenetic inference
M September 10 evaluating competing phylogenetic methodologies
M September 17 integrating different data types/supertrees/consensus methods
M September 24 evaluating clade support: confidence and significance
M October 1 phylogenetic species concepts
M October 8 phylogenetic taxonomy
M October 15 biogeography/phylogeography
M October 22 phylogenies and conservation
M October 29 phylogenies and population genetics/ coalescent processes and population history
M November 5 reconstructing character evolution/ phylogenetic studies of adaptation
M November 12 comparative methods/ character correlations
M November 19 recognizing hybridization with genes
M November 26 phylogenies and epidemiology
M December 3 student review papers
M December 10 student review papers
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Reading list
The Logical Basis of Phylogenetic Inference
Farris, J. S. 1983. The logical basis of phylogenetic systematics, pp.7-36 in N.I. Platnick, and V. A. Funk (eds.) Advances in Cladistics. Columbia University Press, New York.
Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics 22:521-565.
Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. The MIT Press, Cambridge Massachusetts (Chapter 1).
Siddall, M. and Kluge, A. 1997. Probabilism and phylogenetic inference. Cladistics 13:313-336.
Evaluating Competing Phylogenetic Methodologies
Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. The MIT Press, Cambridge Massachusetts (Chapters 4 & 5)
Felsenstein,,J., 1978. Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zoology, 27:27-33.
Sanderson, M. J., and Kim, J. 2000. Parametric Phylogenetics, Systematic Biology 49: 817-829.
Lewis, P. O.2001. Phylogenetic systematics turns over a new leaf. TREE 16:30-37.
Hillis, D.M., Bull, J.J., White, M.E., Badgett, M.R. and Molineux, I.J., 1992. Experimental Phylogenetics: Generation of a known phylogeny, Science 255-589-592.
Sober, E. 1993.Experimental tests of phylogenetic inference methods. Systematic Biology 42: 85-89.
Hillis, D.M., Bull, J.J. , Whilt, M.E., Badgett, M.R. and Molineux, I.J. 1993. Experimental approaches to phylogenetic analysis. Systematic Biology 42:90-92.
Integrating Different Data Types/Supertrees/Consensus methods
Steel, M.A., Dress, A.W.M., and Böcker, S. 2000. Simple but fundamental limitations on Supertrees and Consensus tree methods. Systematic Biology 49: 363-369.
Evaluating Clade Support: Confidence and Significance
Felsenstein, J. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
Sanderson, M. J. 1995 Objections to bootstrapping: A critique. Systematic Biology 44:299-320.
Huelsenbeck, J. P. and Hillis, D.M. 1996. Parametric bootstrapping in molecular phylogenetics: Applications and performance pp. 19-45 in Molecular Zoology: Advances, Strategies, and Protocols (Ferraris, J. S. and S.R. Palumbi eds.) Wiley-Liss, New York.
Yee, M.S. 2000. Tree robustness and clade significance. Systematic Biology 49:829-836.
Bremer, K. 1988 The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803
Wilkinson, M., Thorley, J. H., and Upchurch, P. 2000. A chain is no stronger than its weakest link: Double decay analysis of phylogenetic hypotheses. Systematic Biology 49: 754-776
Phylogenetic Taxonomy
Phylocode article in Science by Elizabeth Pennisi end of March 2001 291:5512 2304 and later responses
DeQueiroz, K. and Gauthier, J. 1994. Toward a phylogenetic system of biological nomenclature. TREE 9:27-31.
Kron, K. A. 1997. Exploring alternative systems of classification. Aliso 15: 105-112.
Cantino, P.D., Olmstead, R. M. and Wagstaff, S. J. 1997. A comparison of phylogenetic nomenclature with the current system: A botanical case study. Systematic Biology 46: 313-331.
Phylogenetic Species Concepts
Wheeler, Q. D. and Meier, R. 2000. Species Concepts and Phylogenetic Taxonomy. Columbia University Press, New York.
Avise, J. C.2000 Cladists in Wonderland. Evolution 54:1828-1832.
Doyle, J. J. 1997. Trees within trees: Genes and species, molecules and morphology. Systematic Biology 46: 537-553.
Maddison, W.P. 1997. Gene trees and species trees. Systematic Biology 46: 523-536.
Biogeography/Phylogeography
Endler J. A. 1982. Problems in distinguishing historical from ecological factors in biogeography American Zoologist. 22: 441-452.
Templeton, A. R. 1998. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 7: 381-397.
Phylogenies and Conservation
Moritz, C. M.1996. Uses of molecular phylogenies for conservation.pp.203-214 in New Uses for New Phylogenies (Harvey, P.H., Brown, A.J.L., Smith, M.J. and Nee, S. eds) Oxford University Press, Oxford.
Harvey, P. H. and Steers, H. 1999. One use of phylogenies for conservation biologists: Inferring population history from gene sequences pp. 101-120. in Genetics and Extinction of Species (Landweber, L. F. and Dobson, A. P. eds.). Princeton University Press, Princeton, New Jersey.
Moritz, C., and Faith, D.P.1998 Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology 7:419-429.
Krajewsji, C. 1994. Phylogenetic measures of biodiversity: A comparison and critique. Biological Conservation 69:33-39
Phylogenies and Population Genetics/ Coalescent Processes and Population History
Hudson, R.R. 1990. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7:1-44.
Posada, D., and Crandall, K. A. 2001. Intraspecific gene genealogies: Trees grafting into networks. TREE 16:37-45.
Phylogenies and Epidemiology
Leitner, T., and Fitch, W. M. 1999. The phylogenetics of known transmission histories. pp. 315-345 in The Evolution of HIV (Crandall, K. A. ed.) Johns Hopkins University Press, Baltimore.
Gao, F. E. et al. 1999. Origin of HIV1 in the Chimpanzee Pan troglodytes troglodytes. Nature 397: 436-441.
Weiss, R. A. and Wrangham, R. W. 1999. From Pan to Pandemic, Nature 397: 385-386.
Bush, R. M., Bender, C.A., Subbarao K, Cox N., and Fitch, W.M. 1999. Predicting the evolution of human influenza A. Science 286:1921-1925.
Reconstructing Character Evolution/ Phylogenetic Studies of Adaptation
Omland, K.E. 1999. The assumptions and challenges of ancestral state reconstructions. Systematic Biology 48: 604-611.
Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48:612-622.
Bush, R. M. 2001. Predicting adaptive evolution. Nature Reviews/Genetics 2:387-392.
Pagel, M. 1999. Inferring the historical pattern of biological evolution. Nature 401:877-884.
Comparative Methods/ Character Correlations
Recognizing Hybridization with Genes
McDade, L. A. XXXX Hybridization and Phylogenetics pp. 305-331 in Hoch
Last Updated: 30 July 2001