Course Description
Students will be introduced to a variety of comparative approaches for elucidating the evolution of species, populations, and molecules. Methods for phylogenetic, population genetic, and molecular evolutionary analyses will be covered with examples drawn from the primary literature. Computer labs will train students in the use of state-of-the- art analysis software.
Athena Title
Molecular Phylo and Evolution
Prerequisite
Permission of major or permission of department
Semester Course Offered
Offered spring
Grading System
A - F (Traditional)
Course Objectives
Since Darwin and Haeckel published their iconic tree figures some 150 years ago, phylogenetic analyses have provided a historical framework for interpreting the evolution of form and function. In recent years, phylogenetic inference has come to play a central role in Ecology, Genetics, Genomics and Molecular Biology. The primary aim of this course is to provide students with the training and experience necessary to frame, execute and correctly interpret phylogenetic, comparative and molecular evolutionary analyses relating to their own research. We will draw on review papers and the primary literature to learn how phylogenetically-based comparative studies can be used in retrospective investigations of a wide range of biological processes. Readings will be posted on the course website. The lab will provide students with hands-on training in state-of- the-art methods of phylogenetic inference. Throughout the course, students will have opportunities to analyze their own data or data compiled to address their specific research interests. This work will culminate in an original term project.
Topical Outline
Introduction to Phylogenetics Multiple sequence alignment Maximum parsimony Distance analysis Maximum likelihood Bayesian inference Coalescence-based species tree estimation Estimating divergence times and rates of sequence evolution Phylogeography Phylogenetically-based inference of character evolution Molecular evolution Phylogenomic analysis pipelines
Syllabus
Public CV