Figure: https://doi.org/10.1098/rspb.2024.1412

23-26 June 2026

This 4-day course provides a hands-on introduction to phylogenetic methods and comparative evolutionary analyses, bridging the gap between microevolutionary processes and macroevolutionary patterns. Participants will learn how to read, interpret, and construct phylogenetic trees from molecular data, map traits and gene families, and apply phylogenetic comparative methods to explore evolutionary questions. Through a combination of lectures, practical labs, and project work, you will gain the skills to critically analyse phylogenetic relationships, reconstruct ancestral traits and sequences, and explore the evolutionary dynamics underlying species diversification and trait evolution.

This course is designed for evolutionary biologists, bioinformaticians, and genomics researchers who wish to gain practical skills in phylogenetic analysis and comparative genomics. Prior experience with basic molecular biology and evolutionary concepts is expected. Familiarity with R and command-line UNIX is required; however, all necessary code will be shared and introduced.

By the end of the course, participants will be able to:

• Interpret and visualise phylogenetic trees, including assessing support and resolving incongruences.
• Build phylogenetic trees from molecular sequence data using alignment, model selection, and inference methods.
• Analyse trait evolution on phylogenies, including ancestral state reconstruction and mapping continuous and discrete traits.
• Apply phylogenetic comparative methods to investigate gene family evolution and evolutionary scenarios.
• Perform molecular species delimitation, infer phylogenetic networks, and understand the limitations of tree-based approaches in complex evolutionary contexts.
• Integrate phylogenetic and genomic analyses in a small-scale project, presenting results in a reproducible and interpretable way.

Day 1 – Foundations & Tree‑thinking - 2-7 PM Berlin time

Lecture 1: Introduction to macroevolution and deep-time processes; What is a phylogeny and what is not? Nodes, branches, topology, lengths. Types of phylogenies (molecular, morphological, fossil‑calibrated); tree formats, ultrametric vs non-ultrametric; dealing with phylogenetic uncertainty. Species tree vs gene tree.

Lab 1: reading and comparing trees (same species, different topologies). Identifying monophyly, paraphyly, polyphyly, sister groups, incongruences, etc.

Phylogenetic uncertainty. Support methods: Bootstrap vs posterior probability. Consensus trees. Visualising trees with support, comparing alternative trees, visualisation tools and FigTree or iTOL. Introduction to R (ape, ggtree).

Lecture 2: How to build a tree. How to get the molecular data. Phylogenomics. Orthology/paralogy. Alignment. Trimming. Inferring trees. Models. Different inference methods (ML and BI).

Lab 2: Introduction to UNIX-Linux. OrthoFinder. Output interpretation.

Day 2 – Trait Evolution on Trees - 2-7 PM Berlin time

Lecture 3: Models of trait evolution; phylogenetic signal; continuous vs discrete trait evolution; phylogenetic dependence. Coalescence. Controversies in phylogenies. Why is there no "right tree"?. Uncertainty.

Lab 3: MAFFT alignment, trimming. Alignment visualisation (JalView). Model choice. Tree inference. Topology test. Visualise phylogenetic patterns.

Lecture 4: Ancestral state reconstruction: what it means and what it doesn't. Dating.

Lab 4: Ultrametric trees inference. MCMCtree. Map traits on the tree. Ancestral trait reconstruction. Compare traits with and without phylogenetic structure.

Day 3 – Comparative Methods - 2-7 PM Berlin time

Lecture 5: Phylogenetic comparative methods (PCM). Comparative genomics. Gene gains and losses. Synteny.

Lab 5: Synteny. CAFE5.

Lecture 6: Ancestral Sequence Reconstruction (ASR). Gene content analysis. Gene duplications, transfers, Horizontal Gene Transfer.

Lab 6 : ALErax. ASR. Comparing evolutionary scenarios.

Day 4 – Advanced Topics -from microevolution to macroevolution - 2-7 PM Berlin time

Lecture 7: Micro vs macroevolution: time scales. Phylogeography: what it asks and what it doesn't.

Lab 7: Simple phylogeographic example. Interpreting geographic patterns in trees. When there are not enough trees. Hybridisation, introgression, and recombination. BAM. Medusa.

Lecture 8: Molecular Species Delimitation methods. Difference between species and populations. Intro to phylogenetic networks.

Lab 8: Species Delimitation (mPTP, bPTP, ASAP). Inferring and visualising networks. Compare tree vs network.

Lab 9: Prepare your project.

Seminar: Present your final project.

1- Bayesian Phylogenetics with RevBayes - ONLINE, 21-24 April

2 - Phylogenetic Comparative Methods in R - ONLINE, 15-19 June

3 - - Demographic modelling - ONLINE, 20-24 July