• Header of Evolution at Transmitting Science

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

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.

Instructors

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

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 April 30th, 2019):
  • 620 *
  • Regular (after April 30th, 2019):
  • 760 *
  • 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 April 30th, 2019):
  • 620 * + 300 = 920
  • Regular (after April 30th, 2019):
  • 760 * + 300 = 1,060
  • This includes course material, coffee breaks, transportation between the Venue and Heraklion or Chania city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

20 % discount will be applied to your fee If you belong to any of the Institutions listed HERE. Discounts (see Funding below) are not cumulative and apply only on the fee.

We offer the possibility of paying in two instalments (contact the course coordinator).

Accommodation

If you choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village (take a look at the venue), in shared en-suite twin rooms, although you will only share rooms with other course participants. There is a possibility that the rooms will be mixed. If this is an inconvenience for you, and you would prefer to stay in an all-female or all-male room, please indicate so in the “Comments” field of the Registration form (below).

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 both Heraklion and Chania (the two main cities of Crete with airports) to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. Once you have booked your flights, please let the course coordinator know which airport you are flying in and out of, in order to arrange your transportation.

If you do not wish to take the Accommodation Package, you can find a few other options in the surrounding area. However, please be aware that access to and travelling around the area requires a private vehicle as public transport is scarce. Therefore, course participants will find choosing the Accommodation Package more convenient.

Alexander Hotel, Gerakári

Alexander Hotel 1

Alexander Hotel twin room

Alexander Hotel, Gerakári

Alexander Hotel 2

Alexander Hotel, Gerakári

Alexander Hotel 3

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:
    • 18:30 Meeting in Heraklion (Archaeological Museum) or Chania (Coach Station) to take the bus to Gerakári.
    • 20:15 Check-in at Alexander Hotel.
    • 20:45 Dinner.
  • Tuesday to Thursday:
    • 8:30 to 9:00 Breakfast.
    • 20:30 Dinner.
  • Friday:
    • 8:30 to 9:00 Breakfast.
    • 18:30 Meeting at Alexander Hotel to take the bus to Heraklion or Chania.
    • 20:15 Arrival in Heraklion (Archaeological Museum) or Chania (Coach Station).

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).

Unemployed scientists living in Greece, as well as PhD students based in Greece 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