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Advanced Courses in Life Sciences

6th Edition

Introduction to Macroevolutionary Analyses Using Phylogenies

January 13th-17th, 2020, Barcelona (Spain)


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Introduction to Macroevolutionary Analyses Using Phylogenies

Course Overview

Phylogenetic trees have changed the way we study and understand life on Earth. Taking phylogenetic information into account in our analyses is critical to account for the non-independence of biological data. Also, phylogenies allow us to get a deep-time perspective of the processes that have shaped the evolutionary history of groups, including diversification and trait evolution.

This course will introduce participants to the use, modification and representation of phylogenetic trees. Also, we will focus on the use of phylogenetic information to reconstruct ancestral characters and biogeographic histories, using different phylogenetic comparative methods.

This course will also tackle trait evolution modelling and the assessment of phylogenetic signal. Finally, we will learn about the shape of phylogenetic trees and its evolutionary causes, and how to estimate the rates of diversification throughout the history of groups. Participants are encouraged to bring their data sets to use in the practical classes.

The course includes an optional first introductory day to basic R.

Important note: Please bear in mind that this course is not about reconstructing (building) phylogenetic trees.

Software: Mesquite, FigTree, R (ape, TreeSim, TreePar, Geiger, OUwie, BioGeoBEARS).


Institut Català de Paleontologia Miquel Crusafont (ICP)

C/ de l’Escola Industrial, 23
08201 Sabadell, Barcelona (Spain)

How to get there


January 13th-17th, 2020




40 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.

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


Juan L. Cantalapiedra instructor for Transmitting Science

Dr. Juan L. Cantalapiedra
Universidad de Alcalá


Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science


Graduate or postgraduate degree in Biology (including palaeontologists no matter the degree).

Participants should bring their personal laptop (Windows, Mac, Linux) with this software installed:


Monday (Optional**). Introduction to R.

  • Environment.
  • Objects.
  • Scripts.
  • Functions.
  • Libraries.
  • Useful workflows and tips for phylogenetic analyses.


  • Morning: Introduction to phylogenies.
    • What is a phylogeny?
    • What can we do with phylogenies? (brief review).
    • Where do phylogenies come from?: Informal trees, maximum parsimony, maximum likelihood and Bayesian inference.
    • Dealing with phylogenies: Software outputs and formats.
  • Afternoon: Practice using Mesquite, R, FigTree.
    • Dealing with different formats.
    • Editing phylogenetic trees.
    • Plotting phylogenies.
    • Time-scaling phylogenies of fossil taxa can be easy.


  • Morning: Reconstructing character evolution on phylogenies.
    • Maximum parsimony.
      • Practice in Mesquite.
    • Maximum likelihood.
      • Practice in Mesquite and R.
    • Introduction to biogeographic reconstruction.
  • Afternoon:
    • Practice biogeographic reconstruction in R (BioGeoBEARS).


  • Morning: Trait model evolution and Phylogenetic signal.
    • Brownian Motion, macroevolutionary optima and early bursts.
    • Pagel’s Lambda & Blomberg et al.’s K. (and other tree transformations).
      • Practice using R (Geiger and OUwie).
  • Afternoon: Supervised practice with students’ data or review of methodologies.


  • Morning: Phylogenetic Comparative Methods.
    • Discrete characters:
      • Pagel’s Correlation Method.
        • Practice in Mesquite.
        • Mirror tree windows in Mesquite.
    • Continuous characters:
      • Phylogenetic Generalized Least Squares (PGLS).
        • Practice with caper in R.
  • Afternoon: Diversification.
    • Tree shape and diversification rates.
      • Lineage Through Time plots (LTT plots and Tree Simulation).
        • Practice in R (ape, TreeSim).
      • Models of diversification (temporal variation, among clade variation).
        • Practice using R (ape, laser, TreePar, Geiger).

** Participants that are familiar with R and have chosen the all-inclusive option could take this day off.


  • Course Fee
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  • Early bird (until October 31st, 2019):
  • 476 * (380.80 for Ambassador Institutions)
  • Regular (after October 31st, 2019):
  • 595 * (476 for Ambassador Institutions)
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

You can check the list of Ambassador Institutions HERE. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.org.

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 coordinators).


The course will take place in the city of Sabadell, Barcelona (Spain). Take a look at the venue.

You may stay in Barcelona city or Sabadell. You will find information about Hotels and Hostel in Sabadell here. It takes about 45 minutes by public transport to arrive to Sabadell from the centre of Barcelona city. The place of the course is about 15 minutes walking from the train stop.


Course Schedule
  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 19:00 Lessons.

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.



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 Spain, as well as PhD students based in Spain 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

4th Edition, September 19th-23rd, 2016

Course Introduction to Macroevolutionary Analyses Using Phylogenies - 4th Edition, September 19th-23rd, 2016Ten people belonging to the following countries and institutions participated in this edition:

  • United Kingdom: Royal Botanic Gardens – Kew, Birkbeck – University of London, University of Bristol.
  • Argentina: Universidad de Buenos Aires.
  • Turkey: Middle East Technical University.
  • Germany: Philipps-Universität Marburg.
  • Estonia: University of Tartu.
  • Italy: Università degli Studi di Milano, University of Turin.

3rd Edition, September 28th-October 2nd, 2015

Course Introduction to Macroevolutionary Analyses Using Phylogenies - 3rd Edition, September 28th-October 2nd, 2015Eighteen people belonging to the following countries and institutions participated in this edition:

  • South Africa: University of South Africa.
  • Mexico: National Autonomous University of Mexico.
  • Spain: Universidad Rey Juan Carlos, University of Alcalá.
  • Ireland: National University of Ireland – Galway.
  • Estonia: University of Tartu.
  • Denmark: Natural History Museum of Denmark – University of Copenhagen, University of Copenhagen.
  • Germany: Museum für Naturkunde – Berlin.
  • Italy: Second University of Naples.
  • United Kingdom: The James Hutton Institute, University of Nottingham, University of Bristol, National Museum of Scotland.
  • United States of America: University of California Santa Cruz.
  • Austria: University of Vienna.
  • Brazil: Universidad Estatal Paulista “Júlio de Mesquita Filho” – Río Claro.
  • Russia: Saint Petersburg State University.

2nd Edition, October 27th-31st, 2014

Course Introduction to Macroevolutionary Analyses Using Phylogenies - 2nd Edition, October 27th-31st, 2014Fourteen people belonging to the following countries and institutions participated in this edition:

  • Spain: Institut Català de Paleontologia Miquel Crusafont, Instituto Pirenaico de Ecología – CSIC.
  • Belgium: Katholieke Universiteit Leuven.
  • Sweden: Lund University.
  • Germany: Max Planck Institute for Demographic Research – Max Planck Society, Museum für Naturkunde – Berlin.
  • Portugal: University of Aveiro.
  • Argentina: University of Buenos Aires.
  • Denmark: University of Copenhagen.
  • United Kingdom: University of Leeds, University of Nottingham.
  • Switzerland: University of Zurich.

1st Edition, September 9th-13th, 2013

Course Introduction to Macroevolutionary Analyses Using Phylogenies - 1st Edition, September 9th-13th, 2013Eight people belonging to the following countries and institutions participated in this edition:

  • Spain: University of Cadiz.
  • United States of America: Smithsonian Institution, Michigan State University.
  • Colombia: Universidad Nacional de Colombia.
  • Denmark: Natural History Museum of Denmark – University of Copenhagen.
  • Australia: Australian National University, Australian Institute of Marine Science.
  • Japan: RIKEN BioResource Center.


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