Bayesian Phylogenetics in RevBayes

Location: Workshop on Molecular Evolution at MBL, Woods Hole, MA
Dates: 7/20, 2018 to 7/29, 2018
Instructors: Michael Landis, Tracy Heath, John Huelsenbeck, Paul Lewis
Register: https://molevol.mbl.edu

Description

Instruction in Bayesian phylogenetic inference and divergence-time estimation will be taught at the Workshop on Molecular Evolution at the Marine Biological Laboratory (MBL). This course was founded in 1988 and is the longest-running workshop serving the field of evolutionary biology. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetics, development, behavior, physiology, and ecology. The workshop also welcomes participants from federal agencies and science journalists. A priority of this workshop is to foster an environment where students can learn from each other as well from the course faculty.

For the full workshop content, list of faculty, and schedule, please see the main course website.

Instructions for working with the RevBayes tutorials on MBL computing resources are provided in the section on Using RevBayes on the MBL Cluster below.

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 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
    Tuesday 09:00-09:30 Welcome to the Workshop Thomas Couvreur, Fabien Condamine
    Tuesday 09:30-10:15 RevBayes Introduction RevBayes Intro. Sebastian Höhna
    Tuesday 10:15-10:30 Coffee break
    Tuesday 10:30-11:00 Substitution Models in Phylogenetics Bayesian Statistics. Sebastian Höhna
    Tuesday 11:00-12:00 Substitution Models in Phylogenetics 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 Substitution Models in Phylogenetics Sebastian Höhna
    Wednesday 09:30-10:15 Introduction to divergence time estimation Molecular dating Rachel Warnock
    Wednesday 10:15-10:30 Coffee break
    Wednesday 10:30-12:00 Node dating Rachel Warnock
    Wednesday 12:00-13:00 Lunch break
    Wednesday 13:00-15:00 The fossilized birth-death process Rachel Warnock
    Wednesday 15:00-15:15 Coffee break
    Wednesday 15:15-17:30 Total-evidence dating Rachel Warnock
    Thursday 09:00-09:30 Recap Rachel Warnock
    Thursday 09:30-10:15 Diversification rate estimation (Part I) Simple Diversification Rate Estimation Sebastian Höhna
    Thursday 10:15-10:30 Coffee break
    Thursday 10:30-12:00 Diversification rate estimation (Part II) Episodic Diversification Rate Estimation Sebastian Höhna
    Thursday 12:00-13:00 Lunch break
    Thursday 13:00-15:00 Diversification rate estimation (Part III) Branch-Specific Diversification Rate Estimation Sebastian Höhna
    Thursday 15:00-15:15 Coffee break
    Thursday 15:15-17:30 Diversification rate estimation (Part IV)
  • Background on state-dependent diversification rate estimation
  • State-dependent diversification with BiSSE and MuSSE
  • Sebastian Höhna
    Tuesday 09:40-10:30 Lecture: Introduction to Bayesian Phylogenetics and RevBayes Lecture slides 1 and Lecture slides 2 👨‍🏫
    Tuesday 10:30-11:00 Morning Coffee
    Tuesday 11:00-12:20 Lecture & Practical: Molecular Clocks
  • Molecular dating
  • Molecular dating
  • Lecture slides 3 and Lecture slides 4
  • 👨‍🏫
    Tuesday 12:20-13:20 Lunch 🥪
    Tuesday 13:20-14:40 Divergence Time Estimation (Time Calibration)
  • Molecular dating
  • Molecular dating
  • Lecture slides 5
  • 👨‍🏫
    Tuesday 14:40-15:10 Afternoon Coffee
    Tuesday 15:10-16:30 Total-Evidence Analysis
  • Molecular dating
  • Lecture slides 6
  • 👩🏻‍🏫, 👨‍🏫
    Sunday 09:00-12:00 Lecture: An Introduction to Bayesian Phylogenetics Lecture slides and other materials Paul Lewis
    Sunday 12:00-14:00 Lunch
    Sunday 14:00-17:00 Lecture: Likelihood-based Phylogenetic Inference Lecture slides and other materials John Huelsenbeck
    Sunday 17:00-19:00 Dinner
    Sunday 19:00-20:30 Lecture: Phylogenetic Inference and Graphical Models Lecture slides Michael Landis
    Sunday 20:30-20:45 Break
    Sunday 20:45-22:00 Lecture: Bayesian Divergence-Time Estimation Lecture slides Tracy Heath
    Monday 09:00-22:00 See course schedule
    Tuesday 09:00-22:00 See course schedule
    Wednesday 09:00-22:00 Free Day
    Thursday 09:00-22:00 See course schedule
    Friday 09:00-22:00 See course schedule
    Saturday 09:00-09:30 Lab: Introduction to RevBayes and the Rev Language Lab slides Michael Landis
    Saturday 09:30-10:00 Lab: Introduction to RevBayes and the Rev Language Getting Started with RevBayes and Rev Language Syntax Michael Landis
    Saturday 10:00-12:00 Lab: Phylogenetic Inference in RevBayes Nucleotide substitution models Michael Landis
    Saturday 12:00-14:00 Lunch
    Saturday 14:00-14:20 Lecture: Bayesian Divergence-Time Estimation, continued Lecture slides Tracy Heath
    Saturday 14:20-17:00 Lab: Divergence-Time Estimation in RevBayes Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Fossil and Extant Specimens Tracy Heath

    Using RevBayes on the MBL Cluster

    Executing RevBayes

    For the tutorials used in this workshop, you may want to use the version of RevBayes on the MBL cluster.

    Once you log in, you can use RevBayes from any directory on the cluster by just typing rb.

    rb
    
    Build from master (94149b) on Mon Jul 23 15:55:28 EDT 2018
    
    Visit the website www.RevBayes.com for more information about RevBayes.
    
    RevBayes is free software released under the GPL license, version 3. Type 'license()' for details.
    
    To quit RevBayes type 'quit()' or 'q()'.
    
    
    >
    

    Downloading Data Files

    Some of the tutorials you will us have data files associated with them. You will find hyperlinks to all of the required files on the tutorial page. These should be listed in the “Data files and scripts” box at the top of the tutorial page below the table of contents.

    For this workshop, we recommend that you create a new folder for each tutorial that you work through. Follow the directions in the tutorial for creating your directory structure. Then download the individual files using wget.

    For example, in the tutorial on divergence times, you will need to download the sequence data file:

    wget https://revbayes.github.io/tutorials/fbd/data/bears_cytb.nex
    

    Writing Rev Scripts

    Some tutorials require that you write several modular Rev scripts to define your model and MCMC analysis. We reccomend that you compose these files on your own computer or using the text editor on the MBL cluster. If you create these files on your personal machine, you will have to upload them to the cluster using scp or cyberduck.