Instructor(s): Julia A. Palacios and Nicola F. Müller.
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). This software will be used in class exercises that are mainly focused on estimating epidemic time scales, reconstruction changes in viral population sizes through time, and inference of spatial diffusion of viruses. Evolutionary processes including recombination and selection will also be considered.
Please install the newest version (2.7.7) of BEAST2 on the computer that you will be using before the workshop starts. BEAST2 is coded in java and does require java to be installed to work. The tutorials covered here work with the newest version of BEAST2 (which is developed largely independent from BEAST1). If there are any issues with the installation, please post the error in the SISMID slack channel module-evolution-and-molecular-epi-of-viruses. Please also install Tracer 1.7.2 to visualize MCMC traces and Figtree 1.4.4. If you get a java error when trying to open Figtree 1.4.4, try Figtree 1.4.5_pre instead.
The workshop will take place in the Randall Rollins Building (RR 201)
Wednesday, July 24: Introduction
1:30pm - 3:00pm: Lecturer: Julia. Introduction to Bayesian Phylogenetics and BEAST
Slides: here
3:30pm - 5:00pm: Lecturer: Nicola. Getting BEAST2 to run with SARS2
Slides: here
Tutorial: Intro to BEAST2 tutorial
Thursday, July 25: Modeling evolution and tree priors
8:30am - 10:00am Lecturer: Nicola Modelling the evolution of genomes through time
Slides: here
pdf
Tutorial: BModelTest
10:30am - 12:00am: Lecturer: Julia Coalescent and Birth death tree priors
Slides: here
1:30pm - 3:00pm Lecturer: Julia
Tutorial: Ne inference
3:30pm - 4:40pm Lecturer: Nicola: Priors and convergence issues and how to solve them with SARS2
Slides: here
pdf
Tutorials: Prior-selection
4:40pm - 5:00pm: Lecturer: Nicola and Julia How does phylodynamics relate to transmission dynamics?
Slides: here
pdf
Day 2 additional tutorial suggestions: Model adequacy, Coupled MCMC
Friday, July 26: Structured populations, networks, and XML
8:30am - 10:00am: Lecturer: Nicola Structured populations
Slides: here
pdf
Tutorial: MASCOT
10:30am - 11:00am: Lecturer: Nicola Multi-type birth-death models
Tutorial: BDMM
11:00am - 11:40am: Lecturer: Julia: How to visualize and interpret trees and phylogenetic mapping
Slides: PhylogeneticMapping
Mini Tutorial ggtree
11:40am - 12:00am Lecturer: Julia Tree distances, summaries, and tree convergence
Slides1: here
1:30pm - 3:00pm: Lecturer: Nicola: Recombination and Reassortment
Slides: here
pdf
Tutorials: Coalescent with Reassortment
3:30pm - 4:30pm: Lecturer: Nicola XML hacking
Slides: here
pdf
Tutorials: XML-hacking
4:30pm - 5:00pm: Q&A and wrap up
Additional tutorial suggestions: Discrete trait analysis (using BEAST1), Continous diffusion model (in BEAST1),MultiType tree, Mascot-GLM, Masoct-Skyline, Bacter, SCoRe, Coalescent with Recombination
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Overview of a lot of BEAST2 packages: https://doi.org/10.1371/journal.pcbi.1006650
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Decoding Genomes: https://decodinggenomes.org/
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Review of phylodynamics (with a focus on the coalescent): https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002947
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Review of phylodynamics in livestock: https://www.sciencedirect.com/science/article/pii/S0169534721001300
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Review for phylodynamics for cell biologists: https://science.sciencemag.org/content/371/6526/eaah6266.abstract
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Review on combining phylogenetics with other data sources: https://doi.org/10.1093/sysbio/syw054
The tutorials we covered in this module were adapated tutorials from https://taming-the-beast.org/ (publication here) and from past SISMID tutorials. Other than us, these tutorials and the lectures used here are partly based on work by:
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Louis du Plessis
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Veronika Boskova
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David Rasmussen
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Carsten Magnus
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Sebastian Duchene
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Timothy G. Vaughan
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Denise Kühnert
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Julia Pecerska
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Marc Suchard
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Philippe Lemey