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Live Online Course – 16th Edition

Introduction to Macroevolutionary Analyses Using Phylogenies

January 11th, 13th, 14th, 18th, and 20th, 2027

Contact: courses@transmittingscience.com

Course 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 modeling and the assessment of phylogenetic signals. Finally, we will learn about the shape of phylogenetic trees, their 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).

Places are limited to 16 participants.

Programme

Introduction to R (pre-course module, taught with pre-recorded classes).
- Environment.
- Objects.
- Scripts.
- Functions.
- Libraries.
- Useful workflows and tips for phylogenetic analyses.
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.
Practice using Mesquite, R, FigTree.
- Dealing with different formats.
- Editing phylogenetic trees.
- Plotting phylogenies.
- Time-scaling phylogenies of fossil taxa can be easy.

Reconstructing character evolution on phylogenies.
- Maximum parsimony.
  - Practice in Mesquite.
- Maximum likelihood.
  - Practice in Mesquite and R.
- Introduction to biogeographic reconstruction.
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).
Supervised practice with students’ data or review of methodologies.

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.
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).

Assumed Background

Graduate or postgraduate degree in Biology (including palaeontologists regardless of degree).

Software

Participants must have a personal computer (Windows, Mac, Linux) with this software installed:

Mesquite: http://mesquiteproject.org/mesquite/mesquite.html
R: www.r-project.org
FigTree: http://tree.bio.ed.ac.uk/software/figtree/

Dates & Schedule

Online live sessions on January 11th, 13th, 14th, 18th, and 20th, 2027.

From 10:00 to 14:00 (Madrid time zone).

Total course hours: 40 (20 hours of online live lessons, plus 20 hours of prerecorded classes and assignments. A recorded short introduction to R by the instructor will be delivered some days before the course for those students not familiar with R).

This course is equivalent to 2 ECTS (European Credit Transfer System). The recognition of ECTS by other institutions depends on each university or school.

Format

In the live sessions we will combine online lectures with hands-on computational exercises, in R.

Live sessions will be recorded. However, attendance to the live sessions is required to obtain the course certificate.

This course will be delivered in English.

Instructor

Dr. Juan L. Cantalapiedra

Museo Nacional de Ciencias Naturales – CSIC
Spain

Registration Fees

Course Fee
Early bird (until October 31st, 2026):
470 €
(376 € for Ambassador Institutions)
Regular (after October 31st, 2026):
584 €
(467.2 € for Ambassador Institutions)
Prices include VAT.
After registration you will receive confirmation of your acceptance on the course.
Payment is not required during registration. Check discounts here.
How do I get the Ambassador Institution discount?
Registration