Assumes the material in Modules 1 and 10. Overview of methods for analysis of interspecific DNA and protein sequence data. Coverage will include parsimony, maximum likelihood, distance-based, and Bayesian methods for phylogenetic estimation. Probabilistic models for sequence change will be emphasized. Related topics that will be presented are the comparative method, divergence time estimation, phylogenetic hypothesis testing, and detection of positive selection. Statistical methodology will be a focus and some related computational algorithms will be outlined. Brief introductions will be made to software packages such as PAUP*, Beast, PHYLIP, and MrBayes.
Background reading: Felsenstein, J. (2004) “Inferring Phylogenies”, Sinauer Associates, or Yang, Z. (2006) “Computational Molecular Evolution (Oxford Series in Ecology and Evolution),” Oxford University Press.