(Special Topics in Quantitative Biology)
Purpose
The purpose of the seminar will be to explore the underlying assumptions and rationales of analytic methods currently being used in phylogenetic studies. Although we will deal with phylogenetic methods in general, we are likely to concentrate on methods used in molecular phylogenetics because they present the most difficult problems.
Format
After several weeks of introductory lectures, each participant will be responsible for a discussion of a topic of interest, and a research paper on the same topic will be required at the end of the semester. A partial list of possible topics (in no particular order) includes the following:
Parsimony inference
Maximum-likelihood inference
Distance-based methods, such as neighbor-joining
Bayesian phylogenetic inference
Bootstrapping and permutation tests
Continuous vs. discrete characters
Correlated characters
Combining data sets
Tree-comparison and congruence indices
Consensus indices
Mapping ancestral character states
Phylogenetically independent contrasts
Testing prior hypotheses of relationship
Estimating rates of evolution
Analysis of tree shape
Molecular clocks
Sequence alignment
Coalescence
Readings
There is no textbook for the seminar. Prior to each weekly discussion, one or more papers will be available for downloading from this site. These papers should be read in preparation for the class.
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