academic year 2024/25

Academic Coordinator: Giorgio Matassi

Period: Second semester

Duration: 28 hours

Program: 

The course will include a theoretical component as well as a significant practical component. In the practical part, students will analyze (on their own computers) all the steps involved in reconstructing a phylogenetic tree. All software used will be freeware. Broadly, the topics covered will include the following:

• Metaphors in Science: Trees and networks.
• Timeline of Evolutionary Thought.
• Phylogenetics: Basic definitions.
• Molecular Evolution (Overview): Modes and tempos of evolution (natural selection, neutral evolution, gradualism, punctuated equilibrium).
• Homology: Orthologs, paralogs, and gene families.
• Applications of Phylogenetic Trees: How to read a tree (best practices, dangers, misconceptions).
• Bioinformatics: Databases; finding and retrieving nucleotide and protein sequences.
• Pairwise Sequence Alignment.
• Building a Suitable Dataset for Phylogenetic Analysis: Taxon sampling, etc.
• Multiple Sequence Alignment (MSA): Assessing MSA quality.
• Evolutionary Models.
• Introduction to Information Theory in Biology: Shannon entropy.
• Phylogenetic Methods: Maximum parsimony, distance-based methods, maximum likelihood, Bayesian inference.
• Tree Reliability: Statistical tests for trees, statistical branch support, inconsistency.
• Hypothesis Testing.

This course aims to provide students with a comprehensive understanding of molecular phylogenetics, combining theoretic