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BI549: Molecular Phylogenetics and Evolution - Fall 2007

Course Description: Phylogenetic analyses are increasingly important in many different fields of biological research, particularly as advances in molecular genetic techniques have made large DNA sequence datasets readily available. This course covers the basic methods of phylogenetic analysis and their application in fields such as systematics, comparative biology, and molecular evolution. Lectures will emphasize the logical bases and computational details of various tree-building algorithms and associated methods of hypothesis testing, as well as novel applications of phylogenetic analysis in various fields of biology. Computer-based labs will give students the opportunity to implement these methods using a variety of phylogenetic software.

Syllabus

Download PDF file

Final Exam: TBA

Powerpoint Presentations

Lecture 1 (Introduction) Lecture 2 (Definitions, Intro to Parsimony) Lecture 3 (Parsimony) Lecture 4 (Branch lengths, consensus trees, support indices) Lecture 5 (Weighted parsimony) Lecture 6 (Parsimony problems, examples - ref#1, ref#2) Lecture 7 (Maximum Likelihood) Parsimony Analysis Results Lecture 8 (Bayesian Analysis) Lecture 9 (Mixed Models, Model Adequacy - ref#1, ref#2) Lecture 10 (Hypothesis Testing - ref#1, ref#2) Lecture 11 (Multilocus Phylogeny Methods) Lecture 12 (Molec-Morph Conflict) Lecture 13 (Rates and Dates)

Discussion Readings

Drummond, A. J., S. Y. W. Ho, M. J. Phillips, and A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. Plos Biology 4:699-710. [Pybus, O. G. 2006. Model selection and the molecular clock. Plos Biology 4:686-688.]

Donoghue, P. C. J., and M. J. Benton. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends in Ecology & Evolution 22 : 424-431.

Carstens, B. C., and L. L. Knowles. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from Melanoplus grasshoppers. Systematic Biology 56:400-411.

Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55:21-30.

Sennblad B, Bremer B 2000 Is there a justification for differential a priori weighting in coding sequences? A case study from rbcL and Apocynaceae s.l. Systematic Biology 49: 101-113.

Broughton RE, Stanley SE, Durrett RT 2000 Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis. Systematic Biology 49: 617-627.

Assignments

• First Day Quiz

Readings FYI

 

LINKS

GenBank

Web of Science

Journals

• Cladistics: The International Journal of the Willi Hennig Society
• Evolution
• Molecular Biology and Evolution
• Molecular Ecology
• Molecular Phylogenetics and Evolution
• Journal of Molecular Evolution
• Proceedings of the National Academy of Sciences
• Systematic Biology

Phylogenetic Software

• PAUP* Home Page
• MacClade Home Page
• Mesquite Home Page
• Joe Felsenstein's List of Phylogeny Programs
• Dept. of Biology, Oxford University (software)
• Hennig Society Software Page
• The Genetic Software Forum

Systematics Sites

• The Tree of Life
• UC Berkley Phylogeny Page
• Animal Diversity Web