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
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 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