The second part of the course takes place in the summer semester Tuesdays 14:00-16:00 CET.
| date | topics | |
|---|---|---|
| 1 | 14.04 | Total-evidence dating |
| 2 | 21.04 | Diversification rate estimation I |
| 3 | 28.04 | Diversification rate estimation II |
| 4 | 05.05 | Introduction to PCMs |
| 5 | 12.05 | No class (Paul Lewis lectures) |
| 6 | 19.05 | No class (Paul Lewis lectures) |
| 7 | 26.05 | Ancestral state reconstruction (homework) |
| 8 | 02.06 | Intro to RevBayes |
| 9 | 09.06 | No class (Project work) |
| 10 | 16.06 | No class (Project work) |
| 11 | 23.06 | Model selection and model adequacy |
| 12 | 30.06 | Biogeography |
| 13 | 07.06 | Project work |
Course material will be updated here throughout the semester!
| schedule | topics |
|---|---|
| Slides | Recap |
| Exercise 6 | The FBD process (BEAST2) |
| Exercise 7 | Total-evidence dating (BEAST2) |
| schedule | topics |
|---|---|
| Slides | Intro to phylodynamics |
| Exercise 7 | Total-evidence dating (BEAST2) |
| Exercise 8 | The MSBD package (BEAST2) |
| schedule | topics |
|---|---|
| Slides | Phylodynamics continued |
| Exercise 9 | The BDMMPrime package (BEAST2) |
| schedule | topics |
|---|---|
| Slides | Intro to PCMs |
| Exercise 10 | Continuous trait models in R |
During this scheduled break 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 – we’ll go over these in week 6. The goal is not to understand everything but to strengthen your understanding of statistical phylogenetics.
Also make note of any questions you have after watching these and we’ll try to answer them.
| videos | topics | questions |
|---|---|---|
| Part 1 | trees and likelihood | Questions 1 |
| Part 2 | trees, likelihood and rate heterogeneity | Questions 2 |
| Part 3a | Intro to Bayesian phylogenetics | Questions 3 |
| Part 3b | Intro to Bayesian phylogenetics | Questions 4 |
There is no class this week because we have the Berg! 🍺🥳 In this time you should complete the following tasks on ancestral state reconstruction using R.
Start by reading Section 3.2 of Phylogenetic Comparative Methods: A Pracitcal Introduction by Natalie Cooper, including the sections on the Mk/ER, SYM, and ARD models. Next complete the accompanying exercise in R.
| schedule | topics |
|---|---|
| Reading | PCM Primer Section 3.2 |
| Exercise 11 | Ancestral state reconstruction in R |