• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

Live Online Course – 6th Edition


November 28th – December 9th, 2022

Live sessions will be recorded


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Course overview & Programme

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. Customized course materials will be provided.

Software: MesquiteTNTRAxMLIQTree, Mr. Bayes and BEAST.

  • 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).

Prior knowledge of concepts in systematics and phylogenetics is strongly recommended.

All participants must have a personal computer (Windows, Macintosh). Webcam and headphones are strongly recommended for the smooth running of the class, as well as a good internet connection.


Tiago Simoes instructor for Transmitting Science

Dr. Tiago Simões
Harvard University
United States of America

Nicolas Mongiardino Koch instructor for Transmitting Science

Dr. Nicolas Mongiardino Koch
University of California San Diego
United States of America

Testimonials for this course

Morphological phylogenetics: principles, applications, and techniques (online) – 2nd edition

“I really like the detailed handouts for some of the sessions. It would be great to have these for all of the sessions. Sometimes the course progressed so quickly it was hard to manipulate a dataset while at the same time to understand the process and change the input files. The instructors were exceptional in their knowledge and up-to-date firsthand knowledge of analyzing morphological data and provided some of the recent papers on the topic which was very good. They were also very open with their knowledge, often times I find that scientists are a bit guarded with giving out detailed information. “Knowledge is power” …. Hats down for an awesome course!!!”

Morphological phylogenetics: principles, applications, and techniques (online) – 2nd edition

“The lectures were well-delivered and course materials were very helpful. The online format certainly seemed to make it more difficult to ensure that everyone was up to speed during the practicals. Perhaps the practicals would be more streamlined with increased use of breakout rooms so that one of the instructors could work with students individually if necessary.”

Dates & Schedule

November 28th – December 9th, 2022

16:00-19:30 (Madrid time zone)

10 live online sessions, Monday to Friday, 16:00 to 19:30 (Madrid time zone).

Total course hours: 40

35 hours of live online lessons, and 5 hours of participants working on their own.

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.



This course will be delivered live online

This course will be taught using a combination of live (synchronous) sessions on Zoom 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 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.

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Fees & Discounts

  • Course Fee
  • Early bird (until October 31st, 2022):
  • 590 €
    (472 € for Ambassador Institutions)
  • Regular (after October 31st, 2022):
  • 730 €
    (584 € 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.