• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

Online Course – 1st Edition

Understanding Macroevolutionary Dynamics using RPANDA and jPANDA

January 31st-February 11th, 2022


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This course will be delivered live online

This course will be taught using a combination of live (synchronous) sessions on Zoom and tasks to be completed in between live sessions on the Slack platform.

RPandaCourse Overview

Phylogenetic analyses are central for understanding the ecological and evolutionary processes shaping present-day biodiversity patterns.

In this course participants will learn phylogenetic analyses with the RPANDA R package. They will also have a quick introduction to Julia and to the jPANDA Julia package.

The RPANDA package contains tools for macroevolutionary analyses on phylogenetic trees, in particular for the analysis of diversification and trait evolution from comparative data.

The instructors will introduce the theory behind these analyses, run practicals with illustrative examples, and guide the interpretation of the output of these analyses.

This workshop is primarily intended for (but is not exclusive to) graduate students and postdocs. Participants are encouraged to bring their own phylogenetic datasets (with potentially matching trait, biogeographic and paleoenvironmental datasets).

See the full program here


Graduate or postgraduate degree in Life or Earth Sciences. Basic knowledge of phylogenetics and R at user level is need it to follow the course.

Participants must have a personal computer (Windows, Mac, Linux). The use of a webcam and headphones is strongly recommended, and a good internet connection.




January 31st-February 11th, 2022

Schedule and Course length

Online live sessions on 31st of January, and 2nd, 4th, 7th, 9th, and 11th of February, 2022, from 14:00 to 17:00 (Madrid time zone). The rest of the time will be taught with assignments, to be completed between live sessions.

25 hours

18 hours of online live lessons, plus 7 hours of  participants working on their own.

This course is equivalent to 1 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.

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

Helene Morton instrutor for Transmitting Science

Dr. Hélène Morlon
Institut de Biologie de l’ENS (IBENS)

Sophia Lambert instructor for Transmitting Science

Sophia Lambert

Fabien Condamine instructor for Transmitting Science

Dr. Fabien Condamine
Institut des Sciences de l’Evolution de Montpellier

Ignacio Quintero instructor for Transmitting Science

Dr. Ignacio Quintero
Institut de Biologie de l’ENS (IBENS)

Julien Clavel instructor for Transmitting Science

Dr. Julien Clavel

Dr. Jonathan Drury

Durham University

Benoit Perez-Lamarque instructor for Transmitting science

Dr. Benoit Perez-Lamarque

Institut de Biologie de l’ENS (IBENS)

Nathan Mazet instructor for Transmitting Science

Nathan Mazet

Institut des Sciences de l’Évolution de Montpellier

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno

Transmitting Science


Session 1 (Sophia Lambert & Hélène Morlon):

  • Introduction to birth-death models and their use for estimating speciation and extinction dynamics from extant phylogenies
  • Running and interpreting constant & time-dependent diversification models
  • Optional: estimating diversity-through-time

Session 2 (Fabien Condamine & Hélène Morlon):

  • Introduction to environment-dependent diversification models for testing if and how past environmental changes influenced diversification rates
  • Running and interpreting environment-dependent diversification models
  • Testing for diversification rate shifts using RPANDA

Session 3 (Ignacio Quintero & Hélène Morlon):

  • Introduction to the Cladogenetic Diversification rate Shift (ClaDS) model for estimating branch-specific diversification rates
  • Introduction to Julia
  • Running and interpreting ClaDS using jPANDA

Session 4 (Julien Clavel & Hélène Morlon):

  • Introduction to trait evolution models and their use for testing hypotheses on the mode and tempo of trait evolution
  • Introduction to environment-dependent trait evolution models for testing if and how past environmental changes influenced rates of trait evolution
  • Running and interpreting environment-dependent trait evolution models

Session 5 (Jonathan Drury & Hélène Morlon):

  • Introduction to the trait matching competition model and its use for testing hypotheses on the role of competition in shaping trait evolution
  • Running and interpreting the matching competition model
  • Introduction to the matching competition birth-death model

Session 6 (Benoit Perez-Lamarque & Hélène Morlon):

  • Introduction to the BipartiteEvol model for modeling the eco-evolutionary emergence of bipartite interaction networks.
  • Running simulations with BipartiteEvol
  • Testing for phylogenetic signal in species interactions
  • Introduction to non-parametric analyses of phylogenetric trees (spectral density profiles) and their utility
  • Running and interpreting spectral density analyses


  • Course Fee
  • Early bird (until October 31st, 2021):
  • 536 €
    (428.8 € for Ambassador Institutions)
  • Regular (after October 31st, 2021):
  • 638 €
    (510.4 € for Ambassador Institutions)
  • The price is VAT included.
    After registration you will receive confirmation of your acceptance in the course. Payment is not required during registration.

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


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 Spain may benefit from a 40 % discount on the Course Fee. If you would like to enquire about this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict registration order.