• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

Course – 3rd Edition

Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies

February 8th-18th, 2021




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This course will be delivered live online

Online live sessions from Monday 8th to Thursday 11th and from Monday 15th to Thursday 18th; 16:00 to 19:30 (GMT+1, Madrid time zone).


Course Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies


Graduate or postgraduate degree in Biology (including palaeontologists no matter the degree).

Participants should bring their personal laptop (Windows, Mac, Linux) with R installed.

A good internet connection is required to follow the course.




February 8th-18th, 2021

Schedule and Course length

Online live sessions from Monday 8th to Thursday 11th and from Monday 15th to Thursday 18th; 16:00 to 19:30 (GMT+1, Madrid time zone).

28 hours live online.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.




Places are limited to 18 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Liam Revell instructor for Transmitting Science

Dr. Liam Revell
University of Massachusetts Boston / Universidad
Católica de la Santísima Concepción
USA / Chile

Luke J. Harmon instructor for Transmitting Science

Dr. Luke J. Harmon
University of Idaho
United States of America

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science


1. Introduction to phylogenies and the comparative method.

2. Introduction the basics of the R statistical computing environment.

3. Introduction to reading, writing, manipulating, and visualizing phylogenies and comparative data in R.

4. Models of phenotypic trait evolution on trees: Brownian motion.

5. Simulating Brownian motion on trees using R.

6. Introduction to the phylogenetic comparative method: Phylogenetic independent contrasts.

7. Phylogenetic independent contrasts and exploring the properties of contrasts regression using simulation in R.

8. Phylogenetic generalized least squares regression and phylogenetic generalized ANOVA.

9. Multivariate statistical methods with phylogenies: Phylogenetic principal components analysis, canonical correlation analysis, and other approaches.

10. Phylogenetic PCA and phylogenetic CCA in R.

11. Continuous character models of trait evolution on phylogenies.

12. Fitting continuous character models to univariate trait data in R.

13. Ancestral state reconstruction I: Continuous characters.

14. Reconstructing ancestral states for continuous traits on phylogenies using R.

15. Ancestral state reconstruction II: Discrete characters.

16. Reconstructing ancestral states for discrete traits on phylogenies using R.

17. Exploring the limitations of ancestral state reconstruction for continuous and discrete characters on phylogenies using R.

18. Testing for the influence of one discrete character on a second using Pagel’s (1994) method.

19. Exploring the promise and limitations of the Pagel (1994) method using R.

20. Analysing discrete character coevolution, and the evolution of discrete and continuous characters using the threshold model.

21. Fitting models of discrete and continuous character evolution on trees using the threshold model.

22. Multi-rate, multi-regime, and multivariate models of character evolution on phylogenies.

23. Fitting multi-regime and multivariate models for continuous character evolution in R.

24. Visualizing trees and phylogenetic comparative data.

25. Plotting phylogenies and comparative data using R.

26. Wrap-up and optional additional exercise or lecture.


  • Course Fee
  • Early bird (until December 31st, 2020):
  • 486 € *
    (388.8 € for Ambassador Institutions)
  • Regular (after December 31st, 2020):
  • 595 € *
    (476 € for Ambassador Institutions)
  • The price is VAT included.
    * Participants from companies/industry will have an extra charge of 100 €.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.