Instructor(s): Julia A. Palacios and Nicola F. Müller

General

This module covers the use of phylogenetic and bioinformatic tools to analyze pathogen genetic variation and to gain insight into the processes that shape their diversity. The module focuses on phylogenies and how these relate to population genetic processes in infectious diseases.

In particular, the module will cover Bayesian Evolutionary Analysis by Sampling Trees 2 (BEAST2). Class exercises will focus on estimating epidemic time scales, reconstructing changes in viral population sizes through time, and inferring spatial diffusion of viruses. Evolutionary processes including recombination and selection will also be considered.

Before the course

Please install the newest version (2.7.8) of BEAST2 on the computer you plan to use. BEAST2 requires Java. If you encounter installation issues, post in the SISMID Slack channel jul15-viral-evolution.

Also install:

• Tracer 1.7.2 to visualize MCMC traces.
• Figtree 1.4.4 to view phylogenies. If you get a Java error, try Figtree 1.4.5_pre.

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Schedule

Time	Wednesday, July 15	Thursday, July 16	Friday, July 17
9:00 am		Modeling the Evolution of Genomes through Time Nicola Slides • Tutorial	Recombination and Reassortment Nicola Slides • Tutorial
10:30 am		Coffee Break	Coffee Break
11:00 am		Coalescent and Birth–Death Tree Priors Julia Slides • Tutorial	Tree Distances, Summaries, and Convergence Julia Slides
11:45 am			Visualizing and Interpreting Trees Julia Tutorial
12:30 pm	Check-In	Catered Lunch	Catered Lunch
1:30 pm	Introduction to Bayesian Phylogenetics and BEAST Julia Slides	Structured Populations Nicola Slides • Tutorial	XML hacking Nicola Slides • Tutorial
3:00 pm	Coffee Break	Coffee Break	Coffee Break
3:30 pm	Getting BEAST2 to Run with SARS-CoV-2 Nicola Slides • Tutorial	Structured Birth–Death Models Nicola Tutorial	Dataset Preparation Slides
4:00 pm			alternative approaches Julia & Nicola Slides
4:30 pm	Understanding BEAST output and results Nicola	Priors, Convergence & Limitations Nicola Slides • Tutorial	Q&A and wrap-up Julia & Nicola
5:00 pm	Networking Mixer

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Some Reading Material (optional)

• Overview of BEAST2 packages: doi:10.1371/journal.pcbi.1006650
• Decoding Genomes: decodinggenomes.org
• Review of phylodynamics (coalescent focus): PLoS Comput Biol 100.2947, Statistical Challenges in Tracking the Evolution of SARS-CoV-2
• Review of phylodynamics in livestock: ScienceDirect S0169534721001300

Acknowledgements

These tutorials are, in part, from taming-the-beast.org and past SISMID workshops, based on work by Louis du Plessis, Veronika Boskova, David Rasmussen, Carsten Magnus, Sebastian Duchene, Timothy G. Vaughan, Denise Kühnert, Julia Pecerska, Marc Suchard, and Philippe Lemey.