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1st Edition

Using Phytools (and other R packages) to Study Macroevolution on Phylogenies

March 14th-17th, 2016, Barcelona (Spain)

Using Phytools (and other R packages) to Study Macroevolution on Phylogenies

LOCATION

Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, 1
08781 Els Hostalets de Pierola, Barcelona.

How to get there

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.

Instructor

Liam Revell instructor for Transmitting Science

Dr. Liam Revell
University of Massachusetts Boston
United States of America

Coordinators

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Sergio Almécija coordinator at Transmitting Science

Dr. Sergio Almécija
The George Washington University
United States of America

Requirements

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.

Program

Monday, March 14th, 2016.

  • 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, March 15th, 2016.

  • 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, March 16th, 2016.

  • 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. Analyzing discrete character coevolution, and the evolution of discrete and continuous characters using the threshold model. [Lecture]


Thursday, March 17th, 2016.

  • 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.

Previous editions of this course

 

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

Course Using Phytools (and other R packages) 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.

Fees

  • Course Fee
  • Early bird (until November 15th, 2015):
  • 495
  • Regular (after November 15th, 2015):
  • 695
  • This includes course material, coffee breaks and lunches.
    (VAT included)
  • Accommodation Package
  • Early bird (until November 15th, 2015):
  • 300
  • Regular (after November 15th, 2015):
  • 300
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
    (VAT included)
  • Course Fee + Accommodation Package
  • Early bird (until November 15th, 2015):
  • 795
  • Regular (after November 15th, 2015):
  • 995
  • This includes course material, coffee breaks, local transportation, lodging, breakfasts, lunches, dinners and social (tourist) activities.
    (VAT included)

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

Accommodation

If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinators.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)

Funding

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

Unfortunately there are no scholarships available for this course. However 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 coordinators. 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.

Schedule

Course ScheduleCourse + Accommodation Package Schedule
Sunday, March 13th, 201619:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to get there.
20:00 Registration in the Youth Hostel.
20:30 Dinner.
Monday, March 14th through Thursday, March 17th, 20169:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

8:30 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.
20:30 Dinner.

There will be two coffee breaks each day, halfway through each lesson session.

Friday, March 18th, 20168:30 to 9:00 Breakfast.
9:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
10:00 Arrival at the wine cellar.
11:30 Bus to Barcelona city.
13:00 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.

Organizers

Transmitting Science Logo
Centre de Restauració i Interpretació Paleontològica (CRIP) Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
Distributed European School of Taxonomy (DEST) Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo
Registration closed

PLEASE NOTE:
Registration for this course is not yet available.
If you want to receive information once the registration is open, please subscribe without any obligation by selecting the topic Evolution.