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Advanced Courses in Life Sciences

3rd Edition

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

July 16th-19th, 2019, Crete (Greece)

Evolution

Evolution Logo

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

LOCATION

Arolithos

Servili Tilissos
715 00 Heraklion, 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 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.

Instructors

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

Coordinator

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

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

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 March 31st, 2019):
  • 620
  • Regular (after March 31st, 2019):
  • 760
  • This includes course material, coffee breaks and lunches (VAT included).
  • Course Fee + Accommodation Package
  • Early bird (until March 31st, 2019):
  • 620 + 300 = 920
  • Regular (after March 31st, 2019):
  • 760 + 300 = 1,060
  • This includes course material, coffee breaks, transportation from and to Heraklion city, accommodation from Monday to Friday, 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

If you take the Accommodation Package option you will be hosted in Arolithos (take a look at the venue), in shared en-suite twin or triple rooms, although you will only share rooms with other classmates. The possibility exists that rooms will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a room 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 single rooms is limited and if you prefer to have one please let us know as soon as possible. If you require more information on accommodation issues please contact the course coordinator.

If you do not want the Accommodation Package, there are several accommodation options in Heraklion. However please be aware that it takes about 25 minutes by car from Heraklion to Arolithos and there is no public transport between both. Therefore course participants will find that staying in Arolithos is more convenient.

How to get to Arolithos from Heraklion, Chania or Rethimnon.

Arolithos street

Arolithos street (Heraklion, Crete, Greece)

Arolithos twin room

Arolithos twin room (Heraklion, Crete, Greece)

Arolithos twin room

Arolithos twin room (Heraklion, Crete, Greece)

Schedule

Course Schedule
  • Tuesday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 19:00 Lessons.
Accommodation Package Schedule
  • Monday:
    • 19:00 Meeting point at Heraklion Archaeological Museum (Heraklion) to take the bus to Arolithos. If you are planning to arrive later, you can find more information on the Arolithos website.
    • 19:30 Registration in the Youth Hostel.
    • 20:00 Dinner.
  • Tuesday to Thursday:
    • 8:30 to 9:00 Breakfast.
    • 20:30 Dinner.
  • Friday:
    • 8:30 to 9:00 Breakfast.
    • 19:00 Meeting point in the Hotel to take the bus to The Archaeological Museum.
    • 19:45 Arrival at Heraklion.

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.

Funding

Discounts

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

2nd Edition: 2018 (Barcelona, Spain)

Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies - 2nd Edition 2018

1st Edition: 2016 (Barcelona, Spain)

Course Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies - 1st Edition, March 14th-17th, 2016

Testimonials

Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies – 2nd Edition

“The course was excellent. The professors Liam Revell and Luke Harmon have a great experience and it enabled us to discuss the subjects presented. Likewise, the location and ambience of the course were ideal for our studies. Congratulations to professors and organizers.”

José Ribeiro Universidade Federal do Pampa, Brazil

Organizers

Transmitting Science 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

Registration