Conor Meehan

Introduction to Bayesian phylodynamics

  • This tutorial outlines the basics concepts in Bayesian phylogenetics, and how it applies to molecular epidemiology (i.e. phylodynamics)
    Please note this is not an exhaustive tutorial on how to use Bayesian phylogenetics to build trees (as this would take too long). Following a course such as Taming the BEAST is suggested if you wish to learn this.

Learning outcomes

  • Recognise the Monte Carlo Markov Chain process
  • Describe some common Bayesian epidemiology priors
  • State the molecular clock hypothesis
  • Describe the coalescent and its use for estimating population dynamics
  • Identify the origins of a new pathogen using phylogenetics
  • Recognise the approaches used to determine transmission dynamics of pathogens

Prerequisites

Approximate time to finish tutorial

  • Lecture: 1 hour
  • Tutorials: 45 mins
  • Pre/post surveys: 10 minutes

Order of tutorial

Please do the pre-learning quiz, then watch the presentation.
During the presentation there are points to stop and do exercises, which are linked below. The answers to the questions in the exercises are linked within each one.
Once finished the tutorial, take the post-learing quiz.

Introduction to Phylodynamics Pre-tutorial Survey

Presentation

Tasks from slides with sample answers

What can Bayesian analyses estimate that other methods such as ML cannot?

Click here for answer Can give estimate of tree phylogeny and other parameters * Divergence date/location * Rate of speciation/extinction


What does the posterior probability represent?

Click here for answer * Probability that the hypothesised tree is true, given the observed data and priors


Give an example of a prior you may input for molecular epidemiology analyses.

Click here for answer * Divergence date/location * Rate of speciation/extinction * Many examples of metadata acceptable


What are the two main types of molecular clock?

Click here for answer * Strict * Relaxed


What is a coalescent event?

Click here for answer When two alleles/individuals come together to form an ancestor (i.e. two branches meet)


What molecular evidence should be gathered to prove zoonitic transmission?

Click here for answer * Closely related sequences from likely sources


List 3 assumptions that need to be fulfilled to undertake population dynamic analysis

Click here for answer * Suitable for coalescent analysis because: * Geographically diverse * Random sampling * No obvious population subdivisions * Ample phylogenetic information * Independent estimate of model of evolution


What kind of phylogenetic tree building approach is needed to incorporate location data into the process?

Click here for answer Phylogeographic (e.g.BSSVS model)


Worksheets

Assessing the quality of a Bayesian phylogenetic run

Building a Bayesian phylogenetic tree




Introduction to Phylodynamics Post-tutorial Survey

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