• Advanced Courses in Life Sciences

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Course – 3rd Edition

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

July 16th-19th, 2019, Barcelona (Spain)

Evolution

Evolution

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

REQUIREMENTS

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

Participants should bring their personal laptop (Windows, Mac, Linux) with this software installed:

Contact

courses@transmittingscience.com

LOCATION

Alexander Hotel

Gerakári, Municipality of Amari, 74 061
Rethymno
Crete, Greece

DATE

July 16th-19th, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

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

Places are limited to 20 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
Greece

Program

Tuesday, July 16th, 2019.

  • 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]


Wednesday, July 17th, 2019.

  • 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]

Thursday, July 18th, 2019.

  • 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]


Friday, July 19th, 2019.

  • 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.

Fees

  • Course Fee
  • Early bird (until October 31st, 2019):
  • 476 € *
    (380.80 € for Ambassador Institutions)
  • Regular (after October 31st, 2019):
  • 595 € *
    (476 € for Ambassador Institutions)
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
  • Early bird (until October 31st, 2019):
  • 826 € * (660.80 € for Ambassador Institutions)
  • Regular (after October 31st, 2019):
  • 945 € * (756 € for Ambassador Institutions)
  • This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (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

Schedule

Course Schedule

Participants will make their own way

  • Monday to Friday:
    • 9:00 to 13:30 Lessons.
    • 13:30 to 14:30 Lunch (included).
    • 14:30 to 18:30 Lessons.

The class 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.

Course + 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 Hostel.
    • 20:30 Dinner.
  • Tuesday to Thursday:
    • 08:00 to 09:00 Breakfast
    • 9:00 to 13:30 Lessons
    • 13:30 to 14:30 Lunch (included)
    • 14:30 to 18:30 Lessons
    • 20:00 Dinner
  • Friday:
    • 8:00 to 9:00 Breakfast.
    • 9:30 to 13:30 Lessons
    • 13:30 to 14:30 Lunch (included)
    • 14:30 to 18:30 Lessons
    • 18:00 Meeting in Hotel to take the bus to Barcelona city.
    • 19:30 Arrival at Plaça Catalunya (Barcelona)

The class 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.

Accommodation

If you choose the Accommodation Package you will be hosted at Rural House Can Carol, in shared en-suite rooms, although you will only share rooms with other course participants (male or female only).

If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.

The Accommodation Package includes transportation from the centre of Barcelona city to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour each way. 

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.

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

Funding

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.

Funding

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.