Bayesian Phylogenetics in RevBayes

Location: The Field Museum, Chicago, IL USA
Dates: 10/5, 2018
Instructors: Tracy Heath

Description

This workshop will cover basic phylogenetic inference in RevBayes for researchers affiliated with the Field Museum.

Location: Bill Stanley Classroom, 9:00 AM to 12:00 PM.

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:

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 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 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
Tuesday 09:00-09:30 Welcome to the Workshop Sebastian Höhna
Tuesday 09:30-10:15 RevBayes Introduction Sebastian Höhna
Tuesday 10:15-10:30 Coffee break
Tuesday 10:30-12:00 Substitution Models in Phylogenetics Sebastian Höhna
Tuesday 12:00-13:00 Lunch break
Tuesday 13:00-15:00 Practical on inferring phylogenies (Part I) Nucleotide substitution models Sebastian Höhna
Tuesday 15:00-15:15 Coffee break
Tuesday 15:15-17:30 Practical on inferring phylogenies (Part II) Nucleotide substitution models Sebastian Höhna
Wednesday 09:00-09:30 Recap MCMC and Substitution Models Sebastian Höhna
Wednesday 09:30-10:15 Morphological models Joe O'Reilley, Mark Puttick
Wednesday 10:15-10:30 Coffee break
Wednesday 10:30-12:00 Divergence time estimation using the fossilized birth-death model Walker Pett
Wednesday 12:00-13:00 Lunch break
Wednesday 13:00-15:00 Practical on divergence time estimation using the fossilized birth-death model (Part I) Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data Walker Pett
Wednesday 15:00-15:15 Coffee break
Wednesday 15:15-17:30 Practical on divergence time estimation using the fossilized birth-death model (Part II) Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data Walker Pett
Thursday 09:00-09:30 Recap Walker Pett
Thursday 09:30-10:15 Diversification rate estimation (Part I) Sebastian Höhna
Thursday 10:15-10:30 Coffee break
Thursday 10:30-12:00 Diversification rate estimation (Part II) Rachel Warnock
Thursday 12:00-13:00 Lunch break
Thursday 13:00-15:00 Choice of practical on diversification rate estimation (Part I)
  • Simple Diversification Rate Estimation
  • Rachel Warnock, Sebastian Höhna
    Thursday 15:00-15:15 Coffee break
    Thursday 15:15-17:30 Choice of practical on diversification rate estimation (Part II)
  • Macroevolutionary Analysis of Stratigraphic Range Data
  • Episodic Diversification Rate Estimation
  • Environmental-dependent Speciation & Extinction Rates
  • Branch-Specific Diversification Rate Estimation
  • Background on state-dependent diversification rate estimation
  • State-dependent diversification with BiSSE and MuSSE
  • Rachel Warnock, Sebastian Höhna
    Friday 09:00-10:00 Lecture: An introduction to Bayesian phylogenetics using morphology Mark Puttick
    Friday 10:10-11:00 Lecture: An introduction to graphical models and Bayesian phylogenetics using RevBayes Rachel Warnock
    Friday 11:10-12:30 Lab: Phylogenetic inference using discrete morphology using RevBayes Discrete morphology - Tree Inference Joseph O'Reilly
    Monday 09:00-09:30 Welcome to the Workshop Luis Palazzesi
    Monday 09:30-10:15 RevBayes Introduction Sebastian Höhna
    Monday 10:15-10:30 Coffee break
    Monday 10:30-12:00 Substitution Models in Phylogenetics Sebastian Höhna
    Monday 12:00-13:00 Lunch break
    Monday 13:00-15:00 Practical on inferring phylogenies (Part I) Nucleotide substitution models Sebastian Höhna, Luis Palazzesi
    Monday 15:00-15:15 Coffee break
    Monday 15:15-17:30 Practical on inferring phylogenies (Part II) Nucleotide substitution models Sebastian Höhna, Luis Palazzesi
    Tuesday 09:00-09:30 Recap MCMC and Substitution Models Sebastian Höhna
    Tuesday 09:30-10:15 Divergence time estimation Sebastian Höhna
    Tuesday 10:15-10:30 Coffee break
    Tuesday 10:30-12:00 Tip-dating and the fossilized-birth-death model Sebastian Höhna
    Tuesday 12:00-13:00 Lunch break
    Tuesday 13:00-15:00 Divergence time estimation Relaxed Clocks & Time Trees Femke Thon, Sebastian Höhna
    Tuesday 15:00-15:15 Coffee break
    Tuesday 15:15-17:30 Practical on tip-dating and the fossilized-birth-death model Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data Femke Thon, Sebastian Höhna
    Wednesday 09:00-09:30 Recap Sebastian Höhna
    Wednesday 09:30-10:15 Diversification rate estimation (Part I) Sebastian Höhna
    Wednesday 10:15-10:30 Coffee break
    Wednesday 10:30-12:00 Diversification rate estimation (Part II) Sebastian Höhna
    Wednesday 12:00-13:00 Lunch break
    Wednesday 13:00-15:00 Practical on diversification rate estimation (Part I) Simple Diversification Rate Estimation Luis Palazzesi, Femke Thon, Sebastian Höhna
    Wednesday 15:00-15:15 Coffee break
    Wednesday 15:15-17:30 Practical on diversification rate estimation (Part II) Branch-Specific Diversification Rate Estimation Luis Palazzesi, Femke Thon, Sebastian Höhna
    Friday 09:00-10:00 Lecture: An Introduction to Bayesian Phylogenetics using RevBayes Tracy Heath
    Friday 10:00-11:00 Lab: Basic MCMC Introduction to MCMC using RevBayes Tracy Heath
    Friday 11:00-12:00 Lab: Phylogenetic Inference in RevBayes Nucleotide substitution models Tracy Heath