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

Mon 14 - 12:15-17:00 (parsimony, likelihood, and substitution models)
Tue 15 - 11:00-17:00 (Bayesian inference, MCMC, clock models, node dating)
Wed 16 - 11:00-17:00 (the fossilised birth-death process)

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 and rooting
Watch A Brief History of Computational Phylogenetics

Homework

Install the software RevBayes
Install the software FigTree and Tracer
Windows users should also install Git Bash

Day 2

schedule	topics
Slides	Intro to RevBayes
Exercise 3	Intro to RevBayes and the Rev language
Exercise 4	Bayesian tree inference

Reading

Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology

Day 3

schedule	topics
Slides	Bayesian timetree inference
Exercise 5	Time tree inference in RevBayes (demo only)
Slides	The fossilized birth-death process
Exercise 6	Simulations
Exercise 7	The FBD process using RevBayes

Reading