Bayesian phylogenetics: clock models

This exercise is part of the course Computational Molecular Evolution (22115).

Overview

In this exercise we will explore how to use the software tool BEAST2 to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When there is temporal information (e.g., fossils that can be used to date an internal node, or information about sampling-time for rapidly evolving sequences) we can instead use clock-based models. These models assume that sequences are evolving at a more or less constant rate, branch lengths are expressed in terms of time, and we can estimate times for internal nodes. Apart from being useful when the focus is on dating evolutionary events, time trees are also useful in that the clock model itself can lead to better inference of the phylogeny (essentially because it adds prior information to the problem, such that we dont have to infer all branch lengths only from limited amounts of sequence variation).

The main purpose with this exercise is to make you acquainted with BEAST2 and to learn how to fit clock-models using either fossil data (by setting a prior on the date for internal nodes) or using so-called heterochronous data, i.e., sequences where the individual leaves have been sampled at different, known times, and where evolution is sufficiently rapid that we can estimate the parameters in a clock-model by seeing how much change has happened over time.

For these tutorials you only need to report minimally: make a small report with a handful of uncommented screendumps showing your progress through the exercise. The important thing is that you get to be a bit familiar with the use of the program, such that you can use it in the mini project later.

• In the exercises below, you should simply follow the instructions on the tutorial pages.
• In the virtual box you should start programs from the command line, by simply writing the name of the executable. The names of the executables that you will need for this exercise are:
  • beauti
  • beast
  • tracer
  • treeannotator
  • figtree

Introduction to BEAST2

• Create a new directory for storing the results of this exercise:

cd /path/to/molevol
mkdir bayes2
cd bayes2

• Open this link in a new tab: Introduction to BEAST2
• Follow instructions down to the optional part.
• Note: If you are running the BEAST2 programs from the command line (not starting them by double clicking an app), then to get the graphical interface for BEAST2 shown in figure 11 in the tutorial, you should start the program as follows:

beast -options

Prior selection and clock calibration using Influenza A data

• Open this link in a new tab: Prior selection and clock calibration using Influenza A data
• NOTE: Only do the part about heterochronous data (not the homochronous part, although you can if you want to)