SISMID_EvolutionaryDynamics

View the Project on GitHub JuliaPalacios/SISMID_EvolutionaryDynamics

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

Before the course

Please install the newest version (2.7.5) 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 mod04_evolutionary_dynamics_molecular_epidemiology_2023. Please also install Tracer 1.7.2 to visualize MCMC traces and Figtree 1.4.4.

Schedule (Times in Pacific Time)

Lecture room: Fishery Sciences Building (FSH) Room 107 located at 1122 NE Boat Street, Seattle, WA 98195.

Wednesday, July 12: Introduction
12:30-1:30: Registration at the Portage Bay Area located on the second floor of the South Campus Center (SCC), 1601 NE Columbia Rd, Seattle WA 98195 (Columbia Road entrance is on the third floor so head downstairs). </br>

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 13: Modeling evolution and tree priors

8:30am - 10:00am Lecturer: Nicola Modelling the evolution of genomes through time
Slides: here
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 - 5:00pm Lecturer: Nicola: Priors and convergence issues and how to solve them with SARS2
Slides: here
Tutorials: Prior-selection

Lecturer: Julia *Tree distances, summaries, and tree convergence
Slides1: here

Day 2 additional tutorial suggestions: Model adequacy, Coupled MCMC

Friday, July 14: Structured populations, networks, and XML

8:30am - 10:00am: Lecturer: Nicola Structured populations
Slides: here
Tutorial: MASCOT

10:3am - 11:15am: Lecturer: Nicola Multi-type birth-death models and visualizations </br> Tutorial: BDMM

11:15am - 12:00am: Lecturer: Julia: How to visualize and interpret trees and phylogenetic mapping
Slides: PhylogeneticMapping Post-processing of BEAST trees
Mini Tutorial ggtree

1:30pm - 3:00pm: Lecturer: Nicola: Recombination and Reassortment
Slides: here
Tutorials: Coalescent with Reassortment

3:30pm - 4:30pm: Lecturer: Nicola XML hacking
Slides: here
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, Bacter, SCoRe, Coalescent with Recombination

Some Reading Material

Acknowledgements

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: