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README.md

Introduction to Bayesian inference of phylogenies using molecular and fossil data in RevBayes

Upcoming Workshop

Instructors

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.

Download RevBayes v1.0.6

The RevBayes workshops will also use additional for analysis of output and summarization of the MCMC. Please download and install the following:

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.

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.