RevBayes for Botanists

Location: Botany 2018 Conference, Rochester, MN USA
Dates: 7/22, 2018
Instructors: Will Freyman, Rosana Zenil-Ferguson, Jordan Koch
Register: http://2018.botanyconference.org

Description

The study of plant systematics and phenotypic evolution has provided unparalleled statistical challenges when building phylogenetic trees and understanding trait evolution. In this workshop, we will introduce RevBayes, a powerful computing environment focused on Bayesian phylogenetic inference that enables users to set up custom and complex models. RevBayes uses a graphical modeling framework and a probabilistic programming language to specify models in a flexible, modular, and transparent manner. During the workshop, we will provide a lecture introducing the theoretical background necessary to understand the models and Bayesian inference jointly with a hands-on computer tutorial demonstrating how to explore phylogenetic inferences using RevBayes. Furthermore, we will show how to use RevBayes to build phylogenies and some comparative phylogenetic methods (i.e. discrete trait models, diversification). Participants are not assumed to have expertise in phylogenetic theory. However, we expect participants to be familiar with phylogenetic trees and their applications to evolutionary biology. We anticipate this workshop to be mostly suitable for PhD candidates, postdoctoral researchers, and faculty who want to learn these techniques. Participants need to bring their own laptop to connect to wired/wireless internet.

Software

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

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 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 🗣
Sunday 08:00-08:45 Intro to Bayesian inference Bayesian slides
MCMC slides
Rosana Zenil-Ferguson
Sunday 08:45-09:00 Break
Sunday 09:00-11:00 Intro to graphical models and RevBayes Introduction to Graphical Models Will Freyman
Sunday 11:00-11:15 Break
Sunday 11:15-12:00 Phylogenetic tree inference CTMC slides Rosana Zenil-Ferguson
Sunday 12:00-01:00 Lunch
Sunday 01:00-03:00 Phylogenetic tree inference in RevBayes Nucleotide substitution models Will Freyman
Sunday 03:00-03:10 Break
Sunday 03:10-03:40 Models linking trait evolution to diversification Diversification slides Rosana Zenil-Ferguson
Sunday 03:40-05:00 State-dependent speciation and extinction models State-dependent diversification with BiSSE and MuSSE Will Freyman