Bayesian phylogenetics and macroevolution in RevBayes

Location: The Australian National University, Canberra, Australia
Dates: 3/26, 2019 to 3/28, 2019
Instructors: Tracy Heath

Description

This workshop will introduce participants to the theory and practice of phylogenetic inference methods for macroevolution using RevBayes. The three-day course is sponsored by the Centre for Biodivesity Analysis at the Australian National University.

The program for the three-day will entail: (Day 1) An introduction to RevBayes, MCMC, and basic tree inference; (Day 2) Combining data from fossil and ling taxa and Historical biogeography; (Day 3) Modeling complex processes on trees and discussion/open lab. A detailed schedule is given below.

It is recommended that you review the Pre-workshop Materials listed below if you do not already have a strong understanding of likelihood-based phylogenetics, probability, and Bayesian inference. These video lectures are by Paul Lewis and provide a clear overview of these topics. Additionally, a list of papers describing RevBayes and graphical models is provided as suggested background reading.

Venue

The Australian National University, Canberra, AUS

Workshop Website

http://cba.anu.edu.au/news-events/bayesian-phylogenetics-and-macroevolution-revbayes

Software

Before the course starts, please install the following software on your own computer:

Pre-workshop Materials

Please review the following materials before the workshop:

Papers

We recommend some selected papers for you to read prior to the workshop. These are not required and we will explain all the content throughout the workshop. However, some prior background knowledge will help to successfully work through the material.

Schedule

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 https://revbayes.com 👩🏻‍🏫
Tuesday 14:00-15:30 Lab: Phylogenetic Inference using RevBayes 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 Fossil and Extant 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 Historical Biogeographic Analysis using a Simple DEC Model 💻
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 🗣