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 2022 to 2023
• 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
• Additional information: http://www.natur.cuni.cz/~vlada/moltax/
• Note: enabled for web enrollment
• Guarantor: doc. Mgr. Vladimír Hampl, Ph.D.
• Teacher(s): doc. Mgr. Vladimír Hampl, Ph.D.; Mgr. Marian Novotný, Ph.D.

Annotation

English

The aim of the course is to introduce students into the basic methods and techniques of molecular phylogenetics and with the use of molecular
biological data in the systematics and related biological fields. Content: Specifics of molecular biological data, their
advantages and disadvantages. Acquisition of molecular biological data for the purposes of systematics (sequencing, RFLP, RAPD, AFLP,
allozymes, microsatellites, SSCP, reassociation analysis, immunological methods, protein fingerprinting). Processing
obtained data - phenetic and cladistic approaches, distance and character data, methods of calculation of distances based on various
types of character data, construction of dendrograms.

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

Czech

Cílem kurzu je seznámit posluchače se základními metodami a technikami molekulární fylogenetiky a s využitím molekulárně
biologických dat v systematice a navazujících biologických oborech. Obsah: Specifika molekulárně biologických dat, jejich
výhody a nevýhody. Získávání molekulárně biologických dat pro účely systematiky (sekvenování, RFLP, RAPD, AFLP,
alozymy, mikrosatelity, SSCP, reasociační analýza, imunologické metody, proteinový fingerprinting). Zpracovávání
získaných dat - fenetické a kladistické přístupy, distanční a znaková data, metody výpočtu distancí na základě různých
typů znakových dat, konstrukce dendrogramů.

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. (30.08.2024)

Requirements to the exam

The exam will be composed of:

Written test in which you will solve five simple computational examples using a paper and calculator - maximum of 10 points

Classical oral exam focused on theory - maximum of 8 points

During the semester, you can earn or lose points by solving or non-solving eight simple examples or questions (0,5 point each) from one lecture to the other.

You can also earn (but not loose) points by solving a few more difficult questions - maximum of 4 points

Yuu can earn (but not loose) points by writing and presenting an essay - 4 points.

The marking will be the following: 

11-13.5 points - dobře
14 - 17.5 points - velmi dobře
18 and more - výborně

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

Syllabus

English

Lectures will be held on Mondays 9:00-10:30 am

2. 10.  - Introduction, taxonomy, molecular characters, sekvencing of DNA (Hampl)

9. 10. - Alignment of sequences (Novotný)

16. 10. – Sequence databases and searches in them (Novotný)

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

30. 10. - SNP, sequence evolution, calculation of genetic distances (Hampl)

6. 11. – Phylogenetic trees I. - Protein distances, reconstruction of phylogenetic trees from the distance matrix, anatomy of trees (Hampl)

13. 11. (absent the lecture will be substituted) - Phylogenetic trees II. Rate heterogeneity, search through the tree space, maximum parsimony (Hampl)

20. 11. - Phylogenetic trees III. - Maximum likelihood, Bayesian metod (Hampl)

27. 11. - Phylogenetic trees IV. - Multigene analyses, robustness of branching, rooting of trees, topology tests, molecular dating (Hampl)

4. 12. – Forensic genetics, DNA barcoding (Hampl)

11. 12. – Intraspecific phylogeny, population structure and gene flow, phylogeography, examples (Hampl)

18. 12. – Metabarcoding – methods of diversity analyses from environmental sequencing data (Hampl)

8. 1. – Presentation of student essays

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (02.09.2024)