SSB 2023 Chamela Station Workshop on Phylogenetics and Comparative Method

Location: Chamela Biological Field Station, Institute of Biology, Universidad Nacional Autónoma de México (UNAM)
Dates: 1/16, 2023 to 1/22, 2023
Instructors: Ivalú Cacho González, Stacey Smith, Tracy Heath, Alejandro Gonzalez Voyer, Rosana Zenil-Ferguson, Joseph Uyeda, Isabel Sanmartin, Ricardo García-Sandoval

Description

The goal of this workshop is to offer a complete week-long immersion to the world of phylogenetic inference and the comparative method for students and postdocs. The instructors are international leaders in the field that will provide the theoretical foundation and practical tools to formulate and answer biological questions with a phylogenetic perspective. UNAM’s initiative to have this workshop in Mexico stems from the collective and deliberate effort of the Institute of Biology in collaboration with the Institute of Ecology, Faculty of Sciences, and Genomic Science Center.

This website will provide links to materials using RevBayes.

Software

Before the course starts, please install the following software on your own computer:

Bayesian Inference and Divergence-Time Estimation (Tracy Heath)

Lecture Slides:

• Introduction to Bayesian Inference
• Bayesian Divergence-Time Estimation

Workshop Tutorials (choose your own adventure):

• Nucleotide substitution models: Phylogenetic inference of nucleotide data using RevBayes
• Estimating a Time-Calibrated Phylogeny of Fossil and Extant Taxa using Morphological Data

Analysis of Biogeography (Isabel Sanmartín)

All materials: https://github.com/isabelsanmartin/Phylogenetics-Workshop-Chamela

Lecture Slides:

• Introduction to Biogeography in RevBayes

Workshop Tutorials:

• Introduction to RevBayes
• Introduction to the Dispersal-Extinction-Cladogenesis (DEC) Model in RevBayes
• Introduction to the Bayesian Island Biogeography (BIB) Model in RevBayes

Additional Materials

Helpful Video Lectures

• Paul Lewis’s Primer on Phylogenetics Part 1 - Trees & Likelihood
• Paul Lewis’s Primer on Phylogenetics Part 2 - Substitution Models
• Paul Lewis’s Primer on Phylogenetics Part 3a - Bayesian Statistics & MCMC
• Paul Lewis’s Primer on Phylogenetics Part 3b - Bayesian Phylogenetics

Video Tutorials

1. RevBayes Intro to MCMC
2. RevBayes Substitution Models
3. RevBayes Partitioned Data Analysis
4. RevBayes FBD Tutorial
5. RevBayes Convergence Assessment
6. RevBayes Intro to Posterior Prediction
7. History of Phylogenetic Comparative Methods
8. Introduction to RevGadgets
9. RevBayes BiSSE Tutorial