• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

Live Online Course – 11th Edition

Introduction to Macroevolutionary Analyses Using Phylogenies

January 16th-20th, 2023

Live sessions will be recorded

Introduction to Macroevolutionary Analyses Using Phylogenies

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).

  • 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).

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

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

A good internet connection is required. The use of webcam and headphones is strongly recommended.

Juan L. Cantalapiedra instructor for Transmitting Science

Dr. Juan L. Cantalapiedra
Universidad de Alcalá
Spain

Dates & Schedule

January 16th-20th, 2023

15:00-19:00 (Madrid time zone)

Online live sessions from Monday to Friday, from 15:00 to 19:00 (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) 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, prerecorded lessons, 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 15 participants and will be occupied by strict registration order.

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

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

Fees & Discounts

  • Course Fee
  • Early bird (until November 30th, 2022):
  • 476 €
    (380.8 € for Ambassador Institutions)
  • Regular (after November 30th, 2022):
  • 556 €
    (444.8 € for Ambassador Institutions)
  • Prices include VAT
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during 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.

Registration

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