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Advanced Courses on Life Sciences

On-site Course – 4th Edition

Mapping Trait Evolution

August 3rd – 7th, 2020, Crete (Greece)




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Course overview

The course provides a comprehensive overview of the state-of-the-art methods in mapping phenotypic trait evolution and will provide participants with a springboard to using these methods to answering their own research questions.

We focus on analyses that use a phylogenetic tree and observed trait information from tip taxa (extant and/or extinct) to describe how traits have changed along the branches of a phylogeny. The course covers methods that estimate and test patterns related to changes in mean, covariation, and rate. Applications for continuous and categorical, and univariate and multivariate research designs are discussed.

At the end of this course, participants will have developed an understanding of:

(1) Brownian motion and Ornstein-Uhlenbeck models of evolution.

(2) How these models can be applied to estimate and test patterns of trait evolution.

(3) What the advantages and disadvantages are of different models/methods.

(4) How to recognize which model/method is most appropriate given a particular dataset and research question.

We provide several data sets that will be used to exemplify the application of these methods. We do, however, encourage participants to bring their own data so as to get direct experience with analysing precisely what they expect to analyse.

Methods from the following R packages will be discussed: ape, geiger, phytools, evomap, l1ou, bayou, surface, OUwie, mvMORPH, geomorph (this list may change as new packages become available).

Important note: Please bear in mind that this course is not about reconstructing (building) phylogenetic trees, the methods we cover in this course assume that a phylogeny is known.


Graduate or postgraduate degree in any Biosciences discipline. Knowledge of multivariate statistics.

A reminder of R-skills that are of particular relevance when applying phylogenetic comparative methods will be given the first day, though a medium level of R knowledge is needed for following the course (i.e. knowledge on how to load and save data, manipulate data frames, use basic plotting functions, and use functions to analyse data).

All participants must bring their own personal laptop (Windows, Macintosh, Linux).




Alexander Hotel

Gerakári, Municipality of Amari, 74 061
Crete, Greece

How to get there


August 3rd – 7th, 2020




35 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 18 participants and will be occupied by strict registration order. If the course fills up there will be an assistant instructor to help during the practise time.

Participants who have completed the course will receive a certificate at the end of it.

Jeroen B. Smaers instructor for Transmitting Science

Dr. Jeroen B. Smaers
Stony Brook University
United States of America


Monday. (R packages: ape, Geiger).

  • Morning: Phylogenetic data.
    • What is the basic structure of phylogenetic data?
    • How to visualize and manipulate phylogenetic data?
  • Afternoon: Models of evolution.
    • What are models of evolution?
    • What are the assumptions of the different models of evolution?
    • How are models of evolution utilized?

Tuesday. (R packages: ape, nlme, caper, evomap).

  • Morning: Phylogenetic regression.
    •  Assumptions, properties, and applications of the phylogenetic regression.
  • Afternoon: Phylogenetic ancova.
    • Testing for grade shifts using the phylogenetic regression.

Wednesday. (R packages: phytools, motmot, geiger, ape, evomap, BayesTraits)

  • Morning: Ancestral estimation.
    • Using models of evolution to estimate values of ancestral nodes.
  • Afternoon: Analysis of rates of evolution.
    • Estimation of rates of evolution.
    • Testing hypothesis about rates of evolution.

Thursday. (R packages: bayou, phylolm, surface, OUwie, mvMORPH).

  • Morning: Inferring the structure of a macroevolutionary landscape.
    • Using Ornstein-Uhlenbeck models to map macroevolutionary patterns.
  • Afternoon: Testing the structure of a macroevolutionary landscape.
    • Applications and assumptions of OU models.
    • Using OU models to test macroevolutionary hypotheses.

Friday. (R packages: geomorph).

  • Morning: Modularity and integration.
    • What is ‘phylogenetic’ modularity and integration?
    • Applications and assumptions.
  • Afternoon: Case study.


  • Course Fee
  • Early bird (until May 31st, 2020):
  • 490 € *
    (392 € for Ambassador Institutions)
  • Regular (after May 31st, 2020):
  • 615 € *
    (492 € 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 May 31st, 2020):
  • 870 €*

    (766 € for Ambassador Institutions)

  • Regular (after May 31st, 2020):
  • 990 €*
    (862 € for Ambassador Institutions)
  • This includes course material, coffee breaks, transportation between the Venue and Heraklion, 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


Course Schedule

Participants will make their own way

  • Monday to Thursday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 18:00 Lessons.
  • Friday:
    • 9:30 to 13:30 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:
    • 18:30 Meeting at Heraklion Archaeological Museum to take the bus to Gerakári.
    • 20:15 Check-in at Alexander Hotel.
    • 20:45 Dinner.
  • Tuesday to Thursday:
    • 08:00 to 09:00 Breakfast
    • 9:30 to 13:30 Lessons
    • 13:30 to 15:00 Lunch (included)
    • 15:00 to 18:00 Lessons
    • 20:30 Dinner
  • Friday:
    • 8:00 to 9:00 Breakfast.
    • 9:30 to 13:30 Lessons
    • 13:30 to 15:00 Lunch (included)
    • 15:00 to 18:00 Lessons
    • 18:30 Meeting at Alexander Hotel to take the bus to Heraklion.
    • 20:15 Arrival at Heraklion Archaeological Museum

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.


If you choose the Accommodation Package you will be hosted at Alexander Hotel  in Gerakári village, 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 Heraklion to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. If you require transportation from or to Chania (the other city of Crete with an airport), please contact the course coordinator who can arrange it at an additional cost.

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.


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.