Taming the BEAST-A Community Teaching Material Resource for BEAST 2

Abstract

Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the "Taming the Beast" (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.

Keywords: Bayesian inference; MCMC; phylodynamics; phylogenetics.

Figure 1.

Boxplot showing the feedback received from 35 respondents (out of 36 workshop participants) on 5 feedback questions. Of the 35 respondents, all but 3 indicated that they would definitely recommend the workshop to a colleague.

Figure 2.

Structure of the Taming the BEAST web resource as hosted on GitHub. The diagram on the left shows three possibilities for tutorials available on the website. On the diagram solid lines indicate ownership and dashed lines access. Tutorial 1 is owned by the taming-the-beast organization on GitHub, and does not have any external contributors. Tutorial 2 was created by contributor a, but ownership has been transferred to taming-the-beast. Tutorial 3 was created by contributor b, who has retained ownership. In all three cases, it is essential that at least one of the website administrators has access to the tutorial. The website itself is also hosted on GitHub as a project. When a user visits the website tutorials appear as on the right of the figure. The left panel contains links to a printable PDF version of the tutorial, the data file (or files) used in the tutorial, example BEAST 2 XML files, examples output files and a link to the GitHub repository of the tutorial. Recent changes to the tutorial are also listed.