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Live Online Course – 2nd Edition

Understanding Macroevolutionary Dynamics using RPANDA and jPANDA

April 11th-21st, 2023

Live sessions will be recorded

Registration

Contact

courses@transmittingscience.com

RPanda

Course overview & Programme

Instructors

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).

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

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), with access to a good internet connection. The use of a webcam and headphones is strongly recommended.

Helene Morton instrutor for Transmitting Science

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

Julien Clavel instructor for Transmitting Science

Dr. Julien Clavel
CNRS
France

Benoit Perez-Lamarque instructor for Transmitting science

Dr. Benoit Perez-Lamarque

Institut de Biologie de l’ENS (IBENS)
France

Sophia Lambert instructor for Transmitting Science

Sophia Lambert
IBENS / MNHN
France

Joëlle Barido-Sottani instructor for Transmitting Science

Joëlle Barido-Sottani

Ecole Normale Supérieure de Paris
France

Nathan Mazet instructor for Transmitting Science

Nathan Mazet

Institut des Sciences de l’Évolution de Montpellier
France

Dates & Schedule

April 11th-21st, 2023

15:00-18:00 (Madrid time zone)

Online live sessions on April 11th, 12th, 14th, 17th, 19th, and 21st; 15:00 to 18:00 (Madrid time zone).

The rest of the time will be taught with assignments, to be completed between live sessions.

Total course hours: 25 

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.

Language

English

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.

Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.

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.

Coordinators

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Fees & Discounts

  • Course Fee
  • Early bird (until February 28th, 2023):
  • 556 €
    (444.80 € for Ambassador Institutions)
  • Regular (after February 28th, 2023):
  • 650 €
    (520 € for Ambassador Institutions)
  • Prices include VAT.
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.
  • How do I get the Ambassador Institution discount?
  • Registration

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.

Organiser

Logo Transmitting Science

Collaborators

Logo COBCYL
Logo COBCV
Logo COBEUSKADI
Logo COBGA

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