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Live Online Course – 8th Edition

MORPHOLOGICAL PHYLOGENETICS: PRINCIPLES, APPLICATIONS, AND TECHNIQUES

March 2nd-20th, 2026

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Contact: courses@transmittingscience.com

Course Morphological-Phylogenetics: Principles, Applications, Techniques

Course Testimonials

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Course 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. Customized course materials will be provided.

Places are limited to 18 participants.

Programme

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.
Exercise: 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.
- Practice:
  Maximum likelihood analysis in IQ-tree using web-server.
  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.
- Practice – 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.
- Practice – Model-fit analysis using Bayes factor.
- Practice: 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.
- Practice – Data partitioning and running combined evidence analysis.
Clock analysis using BEAST.
- Major differences to Mr Bayes.
- Overview of the modular configuration of BEAST2.
- Practice – Time-calibrated analysis using BEAST2 (morphology and combined evidence datasets).

Assumed Background

Graduate or postgraduate degree in Life Sciences.
Prior knowledge of concepts in systematics and phylogenetics is strongly recommended.

Software

During the course, participants will work with the following software, which will be provided: Mesquite, TNT, RAxML, IQTree, Mr. Bayes and BEAST.

Dates & Schedule

Online live sessions on March 2nd, 4th, 6th, 9th, 11th, 13th, 16th, 18th, and 20th, 2026.

From 16:00 to 19:30 (Madrid time zone).

Total course hours: 37 (31.5 hours of online live lessons, plus 5.5 hours of prerecorded classes and assignments.

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.

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. Nicolas Mongiardino Koch
Colorado State University
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!!!”

Anonymous comment on the post-course survey

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.”

Anonymous comment on the post-course survey

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Registration Fees

Course Fee
Early bird (until January 31st, 2026):
590 €
(472 € for Ambassador Institutions)
Regular (after January 31st, 2026):
690 €
(552 € 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?
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