Analysing Macroevolutionary Processes using RevBayes

1st May – 3 May 2018 – University of Bristol

Course currently open to NERC GW4+ DTP students only: All years

Register here: https://nercdtp.onlinesurveys.ac.uk/analysing-macroevolutionary-processes-using-revbayes
Deadline for registration: 9 April 2018

Bayesian statistical methods enable analysis of macroevolutionary processes under complex phylogenetic models. This workshop will focus on the theory and practice of estimating key evolutionary parameters from neontological and paleontological data. These concepts will be taught by combining theory-based lectures with hands-on practicals in the program RevBayes. RevBayes is a program that provides a flexible framework for Bayesian phylogenetic inference.

RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. The primary strength of RevBayes is the simplicity to design, specify and implement new and complex (comparative) phylogenetic models. The graphical-model framework also provides pedagogical advantages: it removes the typical black box so that users can visualize the model they are specifying. This transparency will improve the understanding of phylogenetic models in our field, and will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny.

Features of RevBayes include unrooted and rooted phylogeny inference, divergence time estimation, diversification rate estimation, historical biogeography, and discrete and continuous trait evolution.

Our 3-day intensive workshop will provide you with hands-on training in the use of this invaluable software, taught by the software developers Sebastian Höhna (Ludwig Maximilian University) and Walker Pett (Iowa State University), together with other instructors who are experts in the use and development of phylogenetic models in paleobiology and macroevolution: Mark Puttick (University of Bath), Joseph O’Reilly and Rachel Warnock (University of Bristol). The workshop will have a limit to the numbers of participants to allow for plenty of time for interaction with these experts in the field.

Day 1

  • Introduction to Bayesian inference and MCMC
  • Probabilistic graphical models in phylogenetics & palaeontology
  • The Rev language
  • Inferring phylogenies in RevBayes
  • Models of discrete character change, with particular emphasis on models that can account for acquisition biases associated with fossil character data

 

Day 2

  • Estimating species divergence times
  • Stochastic branching processes as tree priors, with particular emphasis on the fossilized birth-death (FBD) and the FBD range model
  • Models of lineage-specific substitution rates (clock models)
  • Biogeographic dating using the dispersal-extinction-cladogenesis (DEC) model

 

Day 3

  • Estimating diversification (speciation and extinction) rates using temporal data
  • Models of non-uniform fossil recovery
  • Models of lineage-specific diversification and sampling rates

 

 

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