Schedule

Course material will be updated here throughout the semester!

Rough Schedule

1. Course introduction and parsimony 16.04
2. Likelihood and substitution models 23.04
3. Bayesian inference and MCMC I 30.04
4. Bayesian inference and MCMC II 07.04
5. Bayesian inference and MCMC III 14.05
6. No class! (the Berg) 21.05
7. Molecular dating 28.05
8. Phylogenetic comparative methods 04.06
9. Morphological models and model adequacy 11.06
10. Diversification rates and intro to projects 18.06

Week 1 materials

schedule	topics
Slides	tree thinking, parsimony
Exercise 1	tree building using parsimony

Homework

• Re-familiarise yourself with how to read a phylogenetic tree and rooting
• Watch A Brief History of Computational Phylogenetics

Week 2 materials

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

Homework

• Install the software RevBayes
• Watch Phyloenetics primer part 1 by Paul Lewis and answer the associated questions

Week 3 materials

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

Homework

• Install the software FigTree and Tracer
• Watch Phyloenetics primer part 2 by Paul Lewis and answer the associated questions
• Reading Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology

Week 4-5 materials

schedule	topics
Slides	Bayesian inference II
Exercise 4	Bayesian tree inference

Homework

• Watch Phyloenetics primer part 3a by Paul Lewis and answer the associated questions

Week 6 - no class!

Week 7 materials

schedule	topics
Slides	Bayesian timetree inference
Exercise 5	Time tree inference in RevBayes

Homework

• Watch Phyloenetics primer part 3b by Paul Lewis and answer the associated questions

Week 8 materials

schedule	topics
Slides	Intro to PCMs
Exercise 6	PCMs using R

Week 9 materials

schedule	topics
Slides	Morphological models
Exercise 7a	Model selection using RevBayes
Exercise 7b	Model adequacy using RevBayes

Week 10 materials

schedule	topics
Slides	The fossilised birth-death process
Exercise	Exploring the FBD model assumptions
Exercise	Dating under the FBD model in RevBayes