This course was a part of IRL IFUMI project.
Teachers
- Paul Bastide (PB ‐ IMAG, Montpellier, France)
- Gonzalo Bello (GB – Instituto Oswaldo Fiocruz, RJ, Brazil)
- Miraine Davila Felipe (MDF – UTC, Compiègne, France)
- Olivier Gascuel (OG – CNRS & MNHN, Paris, France)
- Martin Grana (MG – Instituto Pasteur, Montevideo, Uruguay)
- Enrique Lessa (EL – Universidad de Montevideo, Uruguay)
- Daiana Mir (DM – Universidad de Salto, Uruguay)
- Gonzalo Moratorio (GM – Institut Pasteur Montevideo, Uruguay)
- Hugo Naya (HN – Instituto Pasteur, Montevideo, Uruguay)
- Hector Romero (HR – Universidad de Montevideo, Uruguay)
- Anna Zhukova (AZ – Institut Pasteur, France)
Program
Friday 12/3: Introduction to evolution for mathematicians (EL)
Monday 12/6: Phylogenetic tree inference in a likelihood framework
- Molecular evolution, speciation, selection, pathogen evolution (EL)
- Continuous time Markov models, model selection (LRT, AIC, BIC) (MDF)
- Models for DNA and proteins, likelihood calculation (OG)
- The 10h gene of HIV (OG)
- Hands‐on, ML tree inference using Seaview/IQ‐TREE (OG, AZ, MG, HR)
Tuesday 12/7: Ancestral character reconstruction, dating, phylogeography
- The spread of pathogens (GB)
- Unrooted, rooted and dated trees, molecular clock models (OG)
- Methods and algorithms for ancestral character reconstructions (ACR) (AZ)
- HIV‐1 CRF19 epidemics in Cuba (AZ)
- Hands‐on, dating using LSD2, ACR with PastML (AZ, OG, HR)Wednesday 12/8: The comparative approach
Wednesday 12/8: The comparative approach
- Heritability of traits (HN)
- Stochastic processes on trees: Brownian motion and beyond (MDF)
- Phylogenetic regression (mixed models, ANOVA) (PB)
- Heritability of viral load in HIV (PB)
Thursday 12/9: Modeling and reconstructing the evolution of traits
- Pathogen spread, continuous phylogeography (HR)
- Heterogeneous and multidimensional models (PB)
- Bayesian analysis of continuous traits (MCMC, HMC, Beast) (PB)
- Hands‐on using Beast: Yellow fever virus (Beast tutorial) (PB, GB, HR)
Friday 12/10: Molecular epidemiology, phylodynamics
- Mathematical epidemiology, virus evolution, variant tracking (HR)
- Tree models (MDF)
- Phylodynamics inference and applications (AZ)
- HIV spread and phylodynamics (DM)
- Math‐oriented seminars (pedigree, differential equations in phylodynamics…)