Introduction to Bayesian inference of phylogenies using molecular and fossil data in RevBayes
Upcoming Workshop
- October 23-27, 2017 – University of Gothenburg and ForBio workshop, Gothenburg, Sweden
Instructors
- Dr. Walker Pett, Iowa State University (http://willpett.github.io)
Funding
This workshop is supported by funds form the ForBio Research School in Biosystematics (Sweden) and by National Science Foundation (USA) grants DEB-1556615.
Workshop Description
Bayesian statistical methods enable analysis of macroevolutionary processes under complex phylogenetic models. This workshop will focus on the theory and practice of estimating time-calibrated phylogenies from neontological and paleontological data. We will teach these concepts by integrating theory-based lectures with hands-on practicals in the program RevBayes. RevBayes is a program that provides a flexible framework for Bayesian phylogenetic inference.
Topics
- Introduction to Bayesian inference and MCMC
- Probabilistic graphical models
- The Rev language
- Inferring phylogenies in RevBayes
- Estimating species divergence times
- Stochastic branching processes as tree priors, with particular emphasis on the fossilized birth-death model (FBD)
- Models of lineage-specific substitution rates (or rates of morphological change)
- Models of discrete morphological character change and accounting for acquisition biases
Install RevBayes & Accessory Programs
This workshop will use RevBayes v1.0.6. Please go to the link below to get executable versions for Windows and Mac OS X. For Linux systems, you can download the source code (also at the link provided) and follow the instructions for compiling using cmake.
The RevBayes workshops will also use additional for analysis of output and summarization of the MCMC. Please download and install the following:
- Tracer (http://tree.bio.ed.ac.uk/software/tracer/)
- FigTree (http://tree.bio.ed.ac.uk/software/figtree/)
- IcyTree (a web-based tree viewer; http://tgvaughan.github.io/icytree/)
- Text editors: Sublime Text or Atom
Workshop Schedule - Gothenburg
Day 1: 25 October 2017
Location: Gothenburg Botanical Garden, Carl Skottsbergs gata 22B, Room 10
| Time | Topic | Links & Files | |
|---|---|---|---|
| 09:00 - 10:00 | Theory: Introduction to MCMC in RevBayes | slides | |
| 10:00 - 12:00 | Practical: Introduction to MCMC in RevBayes | tutorial PDF | |
| 12:00 - 13:00 | Lunch | ||
| 13:00 - 16:00 | Practical: Phylogenetic Models in RevBayes | tutorial PDF, data file, mcmc_JC.Rev, mcmc_GTR.Rev |
Day 2: 26 October 2017
Location: Gothenburg Botanical Garden, Carl Skottsbergs gata 22B, Room 6
| Time | Topic | Links & Files | |
|---|---|---|---|
| 09:00 - 10:30 | Theory: Bayesian Divergence-Time Estimation | slides | |
| 10:30 - 12:00 | Practical: Total-Evidence Dating in RevBayes | tutorial PDF, Data files, Rev scripts | |
| 12:00 - 13:00 | Lunch | ||
| 13:00 - 16:00 | Practical: Total-Evidence Dating in RevBayes, continued |
Recommended Background Material
Tutorials
This workshop covers phylogenetic analysis under complex statistical models. Because of the challenging material, workshop participants will benefit from working through introductory material before taking the course. This is particularly true for anyone without a previous introduction to Bayesian phylogenetics.
- Basic Introduction to Rev and MCMC (tutorial PDF)
- Introduction to MCMC Simulation (tutorial PDF)
- Substitution Models for Time-Constrained Trees (tutorial pdf)
- Partitioned Data Analysis (tutorial pdf)
- Model Selection using Bayes Factors (tutorial pdf)
Reading
Höhna, Landis, Heath, Boussau, Lartillot, Moore, Huelsenbeck, Ronquist. 2016. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Systematic Biology, 65:726-736.
Heath, Huelsenbeck, Stadler. 2014. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences 111(29):E2957–E2966.
Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology 63:753–771.
Gavryushkina, Heath, Ksepka, Stadler, Welch, Drummond. 2017. Bayesian total evidence dating reveals the recent crown radiation of penguins. Systematic Biology, 66(1):57-73.
du Plessis, and Stadler. 2015. Getting to the root of epidemic spread with phylodynamic analysis of genomic data. Trends in Microbiology, 23:383-386.
Stadler, Kühnert, Bonhoeffer, and Drummond. 2013. Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proceedings of the National Academy of Sciences, 110:228-233.