Molecular phylogenetics and systematics - MB160P21

• Title: Molecular phylogenetics and systematics
• Czech title: Molekulární fylogenetika a taxonomie
• Guaranteed by: Department of Parasitology (31-161)
• Faculty: Faculty of Science
• Actual: from 2025
• Semester: winter
• E-Credits: 3
• Examination process: winter s.:
• Hours per week, examination: winter s.:2/0, Ex [HT]
• Capacity: unlimited
• Min. number of students: unlimited
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Explanation: Lectures will be held in the Parasitology lecture room on Mondays 9:00-10:30 am
• Additional information: http://www.natur.cuni.cz/~vlada/moltax/
• Note: enabled for web enrollment; priority enrollment if the course is part of the study plan
• Guarantor: doc. Mgr. Vladimír Hampl, Ph.D.
• Teacher(s): doc. Mgr. Vladimír Hampl, Ph.D.; Mgr. Marian Novotný, Ph.D.

Annotation

The aim of the course is to introduce the basic methods and techniques of molecular phylogenetics and the use of molecular
biological data in systematics and related biological disciplines. Content: Advantages and disadvantages of molecular data. Acquisition of molecular biological data for systematics purposes (sequencing, RFLP, RAPD, AFLP, microsatellites, protein fingerprinting). Processing molecular data - phenetic and cladistic approaches, distance and character data, methods for calculating distances based on different dendrogram construction, molecular clock, metabarcoding, forensic science.

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (30.08.2024)

Literature

Felsenstein J: Inferring phylogenies. Sinauer Associates, Inc., USA, 2004
Hillis DM, Moritz C a Mable BK: Molecular Systematics, second edition. Sinauer Associates, Inc., USA, 1996
Avise JC. Molecular Markers, Natural History and Evolution, second edition. Sinauer Associates, Inc., USA, 2004

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (07.10.2025)

Requirements to the exam

The exam will be composed of:

Written part (5 examples, compulsory) – 10 points
Oral part (theory) – 10 points

Additional points to earn during the semester:
Homeworks  – 10 points in total
Essay (2-3 pages) and presentation – 4 points

Evaluation:
15 - 19.5 points – dobře (C)
20 – 24.5 points – velmi dobře (B)
25 and above - výborně (A)

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (06.10.2025)

Syllabus

Plan of lectures:

1.  - Introduction to taxonomy, molecular characters, sequencing of DNA (Hampl)

2. – Other methods of obtaining molecular data – Multilocus methods (RAPD, RFPL etc.), microsatelites, minisatelites, SINE elements, protein mass fingerprint (Hampl)

3. – Alignment of sequences, Sequence databases and searches in them (Novotný)

4. – Calculation of genetic distances (Hampl)

5. – Phylogenetic trees I. – Introduction to trees, reconstruction of phylogenetic trees from the distance matrix (Hampl)

6. - Phylogenetic trees II. Rate heterogeneity, search through the tree space, maximum parsimony (Hampl)

7. - Phylogenetic trees III. - Maximum likelihood, Bayesian methods (Hampl)

8. - Phylogenetic trees IV. - Multigene analyses, robustness of branching, rooting of trees, topology tests (Hampl)

9. – Model tests, molecular clock (Hampl)

10. – Barcoding and forensic science (Hampl)

11. – Intraspecific relationships (Hampl)

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (07.10.2025)

Learning outcomes

After completing the course, students will be able to:

1. Summarize the principles and methodological approaches of molecular phylogenetics and their application in systematics and evolutionary biology.
   

2. Describe various types of molecular markers and evaluate their advantages and limitations for phylogenetic inference.
   

3. Process and align DNA sequence data and use molecular databases for data retrieval and comparison.
   

4. Calculate genetic distances and apply appropriate models for molecular evolution.
   

5. Construct and interpret phylogenetic trees using different analytical approaches, including distance-based, maximum parsimony, maximum likelihood, and Bayesian methods.
   

6. Assess the robustness, reliability, and rooting of phylogenetic trees using model testing and topology evaluation.
   

7. Apply molecular data to address intraspecific and interspecific relationships, including cases in barcoding, multigene analyses, and forensic applications.
   

8. Critically interpret molecular phylogenetic results in the context of taxonomy, systematics, and evolutionary hypotheses.

Last update: Gáliková Kristýna, Mgr. et Mgr., DiS. (21.10.2025)