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Advanced Courses in Life Sciences

2nd Edition

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

October 8th-11th, 2018, Barcelona (Spain)


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


Can Carol

C/ Font de la Reina, 5
08786 Capellades, Barcelona (Spain)

How to get there


October 8th-11th, 2018




32 hours on-site.

This course is equivalent to 2 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 24 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
United States of America

Luke J. Harmon instructor for Transmitting Science

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


Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science


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.


Monday, October 8th, 2018.

  • Morning:

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]

  • Afternoon:

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.

  • Morning:

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]

  • Afternoon:

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.

  • Morning:

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]

  • Afternoon:

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.

  • Morning:

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]

  • Afternoon:

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.


  • Course Fee
  • {{content-1}}
  • Early bird (until March 31st, 2018):
  • 565
  • Regular (after March 31st, 2018):
  • 705
  • This includes course material, coffee breaks and lunches (VAT included).
  • Course Fee + Accommodation Package
  • {{content-1}}
  • Early bird (until March 31st, 2018):
  • 565 + 270 = 835
  • Regular (after March 31st, 2018):
  • 705 + 270 = 975
  • This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Thursday, breakfasts, lunches and dinners (VAT included).

We offer the possibility of paying in two instalments (contact the course coordinator). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.


Accommodation Package

If you take the Accommodation Package you will be hosted in the Rural House Can Carol, in single-sex shared dormitories (2 – 4 people) with bathroom en-suite.

If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.

A supplemental charge will be added if you prefer to stay in a single room.

Accommodation is included from Sunday (check-in) to Thursday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Thursday (included).

Other accommodation options

If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)


Course Schedule
  • Monday to Thursday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 19:00 Lessons.
Accommodation Package Schedule
  • Sunday:
    • 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Capellades. If you are planning to arrive later, you can find more information on How to get there.
    • 20:00 Registration in the Hotel.
    • 20:30 Dinner.
  • Monday to Wednesday:
    • 8:30 to 9:00 Breakfast.
    • 20:30 Dinner.
  • Thursday:
    • 8:30 to 9:00 Breakfast.
    • 19:00 Meeting point in the Hotel to take the bus to Barcelona city.
    • 20:30 Arrival at Plaza Catalunya (Barcelona).

The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.



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

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

Spanish unemployed scientists, as well as Spanish PhD students 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.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Previous editions of this course


1st Edition, March 14th-17th, 2016

Course Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies - 1st Edition, March 14th-17th, 2016Twenty-two people belonging to the following countries and institutions participated in this edition:

  • United Kingdom: Royal Botanic Gardens – Kew, University of Bristol, University of Sussex.
  • India: Indian Institute of Science, National Centre for Biological Sciences.
  • South Africa: University of KwaZulu-Natal.
  • Hungary: Hungarian Academy of Sciences.
  • Spain: Universitat de Barcelona.
  • Belgium: Université Catholique de Louvain, Université de Liège, Vrije Universiteit Brussel.
  • Denmark: Natural History Museum of Denmark – University of Copenhagen.
  • Argentina: Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”.
  • United States of America: University of Utah.
  • Serbia: University of Belgrade.
  • Germany: Botanischer Garten und Botanisches Museum Berlin-Dahlem – Freie Universität Berlin.
  • Brazil: Universidade de São Paulo.


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