Rough Schedule

Course introduction and Parsimony 25.04
Introduction to statistical modelling 02.05
Likelihood and substitution models 09.05
No Class (Paul Lewis’s seminars) 16.05
Bayesian inference and MCMC 23.05
Bayesian inference and MCMC continued 31.05
Clock models 06.06
Morphological models 13.06
Tree models 20.06
Introduction to projects 27.06

Week 1 materials

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

Homework

Install the software RevBayes
Reading What a Phylogenetic Tree Represents

Week 2 materials

schedule	topics
Slides	Intro to statistical models, graphical models, statistical consistency
Exercise 2	Introduction to RevBayes and the Rev language

Homework

Read Maximum likelihood and Bayesian inference by Steve Wang (up to the end of Section Maximum Likelihood Estimation on pg. 5)

Week 3 materials

Note this class will take place in the Old Library

schedule	topics
Slides	maximum likelihood, substitution models
Exercise 3	tree building using maximum likelihood

Don’t forget next weeks exercises!!

Week 4 materials

No class

During this time we’d like you to watch the following 4 video lectures by Paul Lewis and answer a set of questions we have prepared. Paul Lewis has made numerous important contributions to the field of statistical phylogenetics, as well as producing excellent tools and materials for learning about phylogenetic theory. The videos we’ll use were developed as part of the phyloseminar series.

The videos will take about 3.5 hours to watch. Read the questions before you watch each video and write down your answers in the linked google form – we’ll go over these in week 5. Remember the goal is not to understand everything! Also make note of any questions you have after watching these and we’ll try to answer them.

videos	topics	questions	forms
Part 1	trees and likelihood	Questions 1	Form 1
Part 2	trees, likelihood and rate heterogeneity	Questions 2	Form 2
Part 3a	Intro to Bayesian phylogenetics	Questions 3	Form 3
Part 3b	Intro to Bayesian phylogenetics	Questions 4	Form 4

Week 5 materials

schedule	topics
Slides	Follow up on Paul Lewis lectures
Exercise 4	Bayesian tree inference

Week 6 materials

schedule	topics
Slides	Introduction to MCMC inference
Exercise 4	Bayesian tree inference

Week 7 materials

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

Week 8 materials

schedule	topics
Slides	Morphological evolution
Exercise 6	Morphologoical models in RevBayes

Week 9 materials

schedule	topics
Slides	The fossilised birth-death process
Exercise 7a	Exploring the FBD model assumptions
Exercise 7b	Dating under the FBD model in RevBayes

Week 10 materials

schedule	topics
Slides	Projects overview
Projects page

Extra material

schedule	topics
Slides	Phylogenetic comparative methods
Exercise	Tutorial by Laura Soul & David Wright
Slides	More about birth-death process models
Exercise	RevBayes BiSSE tutorial

Acknowledgements

This course draws on material and exercises produced by Paul Lewis, Tracy Heath, Joëlle Bardio-Sottani, April Wright, Walker Pett, Joshua Justison, Sebastian Höhna, and many other RevBayesian community contributors. Thanks to Joël Koelewijn for feedback on the course content.