Part 1

The first part of this course is a 3 day block course. The aim is to introduce you to the major approaches used to reconstruct trees in paleobiology. By the end of the block course you should be able to reconstruct undated and dated trees using a Bayesian phylogenetic approach.

Rough Schedule

• Day 1 - 12:00-16:00 (parsimony, likelihood, substitution models)
• Day 2 - 10:00-16:00 (Bayesian inference, MCMC, clock models, node dating)
• Day 3 - 10:00-16:00 (the fossilised birth-death process, total-evidence dating)

The course will take place in the Henke Str. Pal seminar room. You will need to bring your own laptop. Before course begins, make sure you have have R and RStudio installed.

Materials

Course material will be updated here throughout the week!

Day 1

schedule	topics
Slides	tree thinking, parsimony
Exercise 1	tree building using parsimony
Slides	maximum likelihood, substitution models
Exercise 2	tree building using maximum likelihood

Reading

• Re-familiarise yourself with how to read a phylogenetic tree (Part 1, Part 2) and rooting
• Watch A Brief History of Computational Phylogenetics

Homework

• Install the software MrBayes
• Install the software BEAST2
• Install the software FigTree and Tracer

Day 2

schedule	topics
Slides	Bayesian tree inference
Exercise 3	tree building using MrBayes
Slides	molecular dating, intro to BEAST
Exercise 4	tree building using BEAST

Reading

• Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
• Understanding the tripartite approach to Bayesian divergence time estimation

 

Day 3

schedule	topics
Slides	The fossilized birth-death process
Exercise 5	Simulations
Exercise 6	The FBD process using BEAST2

Reading

• Bayesian molecular dating: opening up the black box
• From fossils to phylogenies: exploring the integration of paleontological data into Bayesian phylogenetic inference