An advanced introduction to theory and practice of phylogenetic analysis (evolutionary tree reconstruction), with a focus on molecular evolution. Basic concepts will be introduced in the context of a historical survey of phylogeny reconstruction. A comprehensive introduction to phylogenetic methods will be presented, including data selection, multiple sequence alignment, character state data versus distance matrices, sequence evolution models, and the four major approaches to phylogeny reconstruction: Parsimony, Distance matrix, Maximum likelihood, and Bayesian analysis. Sources of error and methods for assessing the reliability of phylogenetic inference will be discussed. We will cover additional topics as time allows, such as phylogenetic hypothesis testing, genome scale approaches, the interface between phylogenetics and population genetics, gene tree reconciliation, horizontal gene transfer, and phylogenetic networks. Course work will include readings from textbooks and seminal articles from the primary literature, problem sets, a final exam and possibly in class exams. Students in 03-727 will also carry out a major data analysis project, intended to familiarize the student with the practical application of principles taught in class. A short paper summarizing the results of this project will be required.
Fall: 6 units