Bodega Applied Phylogenetics Workshop

Location: Bodega Bay, California, USA
Dates: 5/25, 2019 to 6/2, 2019
Instructors: Brian Moore, Cécile Ané, John Huelsenbeck, Sebastian Höhna, Michael Landis, Mike May, Bruce Rannala, Bob Thomson, Peter Wainwright


This workshop will introduce you to the theory and practice of statistical phylogenetics. You will be taught by faculty from world-class universities, all of whom are experts in the theory and practice that you will be taught.

Phylogenetic methods have revolutionized modern systematics and become indispensable tools in evolution, ecology and comparative biology, playing an increasingly important role in analyses of biological data at all levels of organization ranging from molecules to ecological communities. The estimation of phylogenetic trees is now a formalized statistical problem with general agreement on the central issues and questions. A nearly standard set of topics is now taught as part of the curriculum at many colleges and universities. On the other hand, application of phylogenetic methods to novel problems outside systematics is an area of special excitement, innovation, and controversy, and perspectives vary widely.

This Spring, for the eighteenth year, we will teach a workshop for graduate students interested in applying phylogenetic methods to diverse topics in biology. The 8-day course is an intensive exploration of problems to which modern phylogenetic approaches are being applied and the most current statistical tools and methods that are used to solve those problems. We cover a wide range of topics in comparative statistical phylogenetics. The course starts with recent advances in phylogenetic inference, and then focuses on methods for making inferences from phylogenies.

{"The course will be held at the Bodega Marine Laboratory on the beautiful Northern California coast, which has on-site housing. The course format will involve equal parts of lecture and hands-on software training with an emphasis on performing analyses using RevBayes"=>", with instruction in other inference software (MrBayes, BEAST, etc.) based on student interest. One afternoon during the week will be left free for field trips to local natural areas."}

Workshop Website
Date Time Topic Material Instructors
Tuesday 09:30-10:30 Lecture: Hierarchical Bayesian Modeling for Phylogenetic Inference using RevBayes Lecture slides 👩🏻‍🏫
Tuesday 10:30-11:00 Morning Tea
Tuesday 11:00-12:00 Lecture: Introduction to Bayesian Inference and MCMC in RevBayes Lecture slides 👩🏻‍🏫
Tuesday 12:00-13:30 Lunch 🥪
Tuesday 13:30-14:00 Resources for using RevBayes 👩🏻‍🏫
Tuesday 14:00-15:30 Lab: Phylogenetic Inference using RevBayes Nucleotide substitution models 💻
Tuesday 15:30-16:00 Afternoon Tea 🍵
Tuesday 16:00-17:30 Lab: Phylogenetic Inference using RevBayes, continued 💻
Wednesday 09:30-10:30 Lecture: Bayesian Divergence-Time Estimation Lecture slides 👩🏻‍🏫
Wednesday 10:30-11:00 Morning Tea
Wednesday 11:30-12:30 Lecture: Bayesian Divergence-Time Estimation, continued 👩🏻‍🏫
Wednesday 12:30-14:00 Lunch 🍜
Wednesday 14:00-15:30 Lab: Estimating Trees and Divergence Times Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Extant Taxa and Fossil Specimens 💻
Wednesday 15:30-16:00 Afternoon Tea 🍵
Wednesday 16:00-17:30 Lab: Estimating Trees and Divergence Times, continued 💻
Thursday 09:30-10:30 Lab: Historical Biogeography Simple Phylogenetic Analysis of Historical Biogeography 💻
Thursday 10:30-11:00 Morning Tea
Thursday 11:00-12:30 Lab: Modeling Branch-Heterogeneous Processes 💻
Thursday 12:30-14:00 Lunch 🍔
Thursday 14:00-15:30 Presentations by ANU Researchers 🇦🇺
Thursday 15:30-16:00 Afternoon Tea 🍵
Thursday 16:00-15:30 Discussion and Open Lab 🗣