- Course title
- Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies
- University / Organization
- Transmitting Science
- Course website (further registration info)
- Els Hostalets de Pierola, Barcelona
- Academic level
- Both Msc and PhD
- Transmitting Science
- Course director
- Course lecturer(s)
- Dr Liam Revell (University of Massachusetts Boston, United States of America)
Dr Luke J. Harmon (University of Idaho, United States of America)
- Course aim
- 2nd Edition
*USING GEIGER, PHYTOOLS, AND OTHER COMPUTATIONAL TOOLS TO STUDY MACROEVOLUTION ON PHYLOGENIES*
October 8th-11th, 2018, Barcelona (Spain)
This is a course on phylogenetic comparative methods.
Graduate or postgraduate degree in Life or Earth Sciences. Basic knowledge of R and statistics. All participants must bring their own personal laptop. We would like to encourage participants to bring along their own data.
- Course contents / programme
Monday, October 8th, 2018.
1. Introduction to phylogenies and the comparative method. [Lecture]
2. Introduction the basics of the R statistical computing environment. [Exercise]
3. Introduction to reading, writing, manipulating, and visualizing phylogenies and comparative data in R. [Exercise]
4. Models of phenotypic trait evolution on trees: Brownian motion. [Lecture]
5. Simulating Brownian motion on trees using R. [Exercise]
6. Introduction to the phylogenetic comparative method: Phylogenetic independent contrasts. [Lecture]
7. Phylogenetic independent contrasts and exploring the properties of contrasts regression using simulation in R. [Exercise]
8. Phylogenetic generalized least squares regression and phylogenetic generalized ANOVA. [Exercise]
Tuesday, October 9th, 2018.
9. Multivariate statistical methods with phylogenies: Phylogenetic principal components analysis, canonical correlation analysis, and other approaches. [Lecture]
10. Phylogenetic PCA and phylogenetic CCA in R. [Exercise]
11. Continuous character models of trait evolution on phylogenies. [Lecture]
12. Fitting continuous character models to univariate trait data in R. [Exercise]
13. Ancestral state reconstruction I: Continuous characters. [Lecture]
14. Reconstructing ancestral states for continuous traits on phylogenies using R. [Exercise]
Wednesday, October 10th, 2018.
15. Ancestral state reconstruction II: Discrete characters. [Lecture]
16. Reconstructing ancestral states for discrete traits on phylogenies using R. [Exercise]
17. Exploring the limitations of ancestral state reconstruction for continuous and discrete characters on phylogenies using R. [Exercise]
18. Testing for the influence of one discrete character on a second using Pagel’s (1994) method. [Lecture]
19. Exploring the promise and limitations of the Pagel (1994) method using R. [Exercise]
20. Analysing discrete character coevolution, and the evolution of discrete and continuous characters using the threshold model. [Lecture]
Thursday, October 11th, 2018.
21. Fitting models of discrete and continuous character evolution on trees using the threshold model. [Exercise]
22. Multi-rate, multi-regime, and multivariate models of character evolution on phylogenies. [Lecture]
23. Fitting multi-regime and multivariate models for continuous character evolution in R. [Exercise]
24. Visualizing trees and phylogenetic comparative data. [Lecture]
25. Plotting phylogenies and comparative data using R. [Exercise]
26. Wrap-up and optional additional exercise or lecture.
- Required Knowledge and preparation
- Teaching methods
- Starting month
- Course type
- Consecutive days
- Online course
- Duration (net days)
- October 8th-11th, 2018
- Course fee
- Direct e-mail to register
- Paper submission required?
- Logo of institution
- front approval
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