Introduction to Phylogenetics

3 Credits · Level: Graduate, Undergraduate

The history of life is profoundly shaped by ancestor-descendant relationships found across a wide range of time and spatial scales. This course will help you understand ancestor-descendant relationships by learning how phylogenies are used as a powerful hypothesis testing tool, and by constructing and interpreting trees. We will start by introducing tree thinking - concepts in phylogenetic analysis, the patterns trees represent, and how to interpret trees. We will consider a range of data types, including DNA and protein sequence and the multiple sequence alignment process, as well as discrete and continuous phenotypes. The course will cover the range of methods for phylogenetic inference, including maximum likelihood and Bayesian approaches, and how to assess confidence in tree topologies. The course will include comparative methods including phylogenetic regression, and predictive models of character evolution over time. The course will combine lecture with hands-on exercises using R scripting and software packages. Each student will carry out an independent project developed over the course of the semester. Interest in coding and prior completion of BIOL 1850 or BIOL 4650 recommended.