• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

Online Course – 2nd Edition


October 19th-30th, 2020



This course will be delivered ONLINE: 35 hours of online live lessons. A good internet connection is required to follow the course.

Morphological phylogenetics principles applications and techniquesCourse Overview

An accurate reconstruction of evolutionary relationships among species is the cornerstone of evolutionary biology. Building phylogenetic trees thus provides the fundamental framework upon which systematic, biogeographic and evolutionary research operates. Morphological phylogenetics provides a unique toolkit for inferring relationships, considering that the vast majority of the species that have ever lived are now extinct and can only be assessed based on morphological data. Additionally, combining fossils and morphological data with molecular data from extant species is becoming the most comprehensive method of assessing phylogenetic relationships on deep time and the time of origin of major evolutionary lineages.

In this course, we will focus on the analysis of morphological data (and combining morphological data with molecular data) using multiple optimality criteria for phylogenetic inference. We will discuss the best available approaches to construct morphological data sets and their impact on phylogenies. We will follow with theory and hands-on practice of phylogenetic programs using maximum parsimony, maximum likelihood and Bayesian inference. Participants will learn how to combine morphological and molecular data for total evidence analyses, how to conduct time-calibrations using tip and node dating, different birth-death models, morphological clocks and combined evidence relaxed clock analyses.

Softwares: MesquiteTNTRAxMLIQTree, Mr. Bayes and BEAST.


Prior knowledge of basic systematic concepts is recommended but not imposed. All participants must have a personal laptop and a good internet connection.




This course will be delivered online.

Please check the schedule for the live online part, and be aware that it is GMT+1 (Madrid time zone).


October 19th-30th, 2020




35 hours on-site.

This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School and ForBio.

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.

Tiago Simoes instructor for Transmitting Science

Dr. Tiago Simões
Harvard University
United States of America

Oksana Vernygora instructor for Transmitting Science

Oksana Vernygora
University of Alberta


  • Theory of morphological character construction:
      • Homology: assessment and tests.
      • Avoiding logical and biological biases in morphological characters.
      • Challenges behind morphological data sets in the era of big data.
    • Working with data files:
      • File structure of main types of data matrices (NEXUS, PHYLIP, TNT).
      • Creating and editing data files.
    •  Practice:
      • Exercise 1.1: Morphological character construction.
    • Maximum Parsimony:
      • Principles and assumptions.
      • Fitch, Farris, and Goloboff algorithms.
      • Tree search using New Technology (T.N.T) – introduction to the T.N.T. software.
    • Practice: maximum parsimony analysis using T.N.T.:
      • Morphological data analysis using Traditional and New Technology search algorithms.
      • Implied weights parsimony analysis.
      • Working with trees – constructing consensus, calculating support values, mapping synapomorphies, etc.
    • Probabilistic methods in phylogenetics:
      • Concepts and assumptions.
      • Differences between probabilistic methods and parsimony (includes discussion on the performance comparison MP vs ML and BI for morphological data).
    • Maximum likelihood:
      • Theory of maximum likelihood.
      • Application in phylogenetics.
    • Exercise 1: Maximum likelihood analysis in IQ-tree using web-server.
    • Exercise 2: Maximum likelihood analysis using command line version of IQ-tree.
    • Bayesian inference:
      • Bayes theorem and its application in phylogenetics.
      • Introduction to Markov chain Monte Carlo (MCMC) method.
      • Metropolis coupling of MCMC chains.
      • Priors.
    • Introduction to Mr Bayes software.
    • Clock-based (time calibrated) Bayesian inference analysis:
      • Principle behind molecular clock.
      • Introduction to morphological clock.
      • Types of clocks (strict, autocorrelated, uncorrelated, local).
    • Tree priors:
      • Birth-Death model.
      • Fossilized Birth-Death model.
    • Exercise 1: Bayesian inference analysis using Mr Bayes:
      • Writing and adding Mr Bayes block to a data set.
      • Performing non-clock analysis and overview of each component.
      • Analysing output.
    • Exercise 2: Model-fit analysis using Bayes factor.
    • Exercise 3: Time-calibrated analysis in Mr Bayes.
    • Combined data sets:
      • Combining different types of data (molecular and morphological.
      • Divergence time estimation using combined evidence clocks.
      • Analysing output.
    • Clock analysis using BEAST:
      • Major differences to Mr Bayes
      • Overview of the modular configuration of BEAST 2.
    • Exercise 1: Data partitioning and running combined evidence analysis.
    • Exercise 2: Time-calibrated analysis using BEAST 2 (Morphology and combined evidence datasets).


  • Course Fee
  • Early bird (until August 31st, 2020):
  • 590 € *
    (472 € for Ambassador Institutions)
  • Regular (after August 31st, 2020):
  • 730 € *
    (584 € for Ambassador Institutions)
  • This includes course material (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

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


Course Schedule
  • Monday to Friday:
    • 15:00 to 18:30 online live lessons (GMT+1).

The rest of the time will be taught with recorded classes and assignments, to be done between the live sessions.


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

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

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country 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.


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