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.

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

All academic work must meet the standards contained in "A Culture of Honesty."  
Each student is responsible to inform themselves about those standards before
performing any academic work.