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Advanced Courses in Life Sciences

4th Edition

The Use of Phylogenies in the Study of Macroevolution

September 19th-23rd, 2016, Barcelona (Spain)

The Use of Phylogenies in the Study of Macroevolution

Evolution leaves its footprint in the fossil record but also in and living taxa. This signal on the processes of origination of new organisms from ancestral lineages and their extinction can be recovered and depicted in phylogenetic trees.

First, this course will introduce participants to the use, modification and representation of phylogenetic trees. Then, we will focus on the use of phylogenetic information to reconstruct ancestral characters and biogeographic histories, learning how to apply 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 evolutionary history of groups. Participants are encouraged to bring their data sets to use in the practical class.

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

Software: Mesquite, FigTree, BayesTraits (using BayesTraits Wrapper in R), RASP and R (ape, TreeSim, TreePar, Geiger, OUwie, BioGeoBEARS).


Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, nº 1
08781 Els Hostalets de Pierola, Barcelona.

Spain – CRIP




40 hours on-site.

This course is equivalent to 4 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 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.


Juan L. Cantalapiedra instructor for Transmitting Science

Dr. Juan L. Cantalapiedra
Museum für Naturkunde – Leibniz Institute for Research on Evolution and Biodiversity


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).

Intermediate level of R is required (you are expected to install libraries, manipulate objects -vectors, tables, dataframes-, matching, and the basics of Graphics). If you are not familiar with R we recommend you to sign up for the previous course Introduction to R. Software’s other than R will be explained during the course.

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

  • R (http://www.r-project.org) with the following packages installed: ape, TreeSim, TreePar, Geiger, OUwie, BioGeoBEARS.


Monday, September 19th, 2016.

  • 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.

Tuesday, September 20th, 2016.

  • Morning: Reconstructing character evolution on phylogenies.
    • Maximum parsimony.
    • Maximum likelihood.

Practice using Mesquite and R.

  • Afternoon:
    • Bayesian Inference.

Practice using BayesTraits.

  • Introduction to biogeographic reconstruction.

Wednesday, September 21st, 2016.

  • Morning: Practice biogeographic reconstruction in RASP and R (BioGeoBEARS).
  • Morning / Afternoon: 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).

The rest of the day: Supervised practice with students’ data or review of methodologies.

Thursday, September 22nd, 2016.

  • Morning: Phylogenetic Comparative Methods.
    • Discrete characters:
      • Pagel’s Correlation Method.
    • Continuous characters:
      • Generalized Least Squares (GLS).
      • Generalized Estimated Equations (GEE).
  • Afternoon: Practice.
    • Visualization: Mirror tree windows in Mesquite.
    • Pagel’s Method in Mesquite and BayesTraits.
    • GLS and GEE in R.

Friday, September 23rd, 2016.

  • Morning: Tree shape and diversification rates.
    • Lineage Through Time plots (LTT plots, realized and reconstructed trees).
    • Models of diversification (temporal variation, among clade variation).
    • Character’s effects on diversification.
  • Afternoon:

Practice using R (ape, TreeSim, TreePar, Geiger).

  • Tree Simulation and LTT plots.
  • Testing diversification models (birth-death models, yule models…).


  • Course Fee
  • Early bird (until June 15th, 2016)
  • 470
  • Regular (after June 15th, 2016)
  • 660
  • This includes course material, coffee breaks and lunches.
  • Accommodation Package
  • Early bird (until June 15th, 2016)
  • 360
  • Regular (after June 15th, 2016)
  • 360
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
  • Course Fee + Accommodation Package
  • Early bird (until June 15th, 2016)
  • 830
  • Regular (after June 15th, 2016)
  • 1,020
  • This includes course material, coffee breaks and lunches.

We offer the possibility of paying in two instalments (contact the course coordinator). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.


If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinator.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)


Former participants will have a 5 % discount on the Course Fee.

Unfortunately there are no scholarships available for this course. However 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).

Spanish unemployed scientists, as well as Spanish PhD students 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.


Course ScheduleCourse + Accommodation Package Schedule
Sunday, September 18th, 201619:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to get there.
20:00 Registration in the Youth Hostel.
20:30 Dinner.
Monday, September 19th through Friday, September 23rd, 20169:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

8:00 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.
20:30 Dinner.

There will be two coffee breaks each day, halfway through each lesson session.

Saturday, September 24th, 20168:00 to 9:00 Breakfast.
9:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
10:00 Arrival at the wine cellar.
11:30 Bus to Barcelona city.
13:00 Arrival at Plaza Catalunya (Barcelona).

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.


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