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, mikrosatelity, proteinový fingerprinting). Zpracovávání získaných dat - fenetické a kladistické přístupy, distanční a znaková data, metody výpočtu distancí na základě různých typů znakových dat, konstrukce dendrogramů, molekulární hodiny, metabarcoding, forenzní věda.
Poslední úprava: Hampl Vladimír, doc. Mgr., Ph.D. (30.08.2024)
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.
Poslední úprava: Hampl Vladimír, doc. Mgr., Ph.D. (30.08.2024)
Literatura
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
Materiály na webu.
Poslední úprava: Hampl Vladimír, doc. Mgr., Ph.D. (30.08.2024)
Požadavky ke zkoušce
The exam will be composed of:
Written test in which you will solve five simple computational examples using a paper and calculator - a maximum of 10 points
Classical oral exam focused on theory - maximum of 5 points (you can skip it if you do not need points)
You can earn points by writing and presenting an essay - 4 points
During the semester, you can earn or lose points by solving or non-solving ten simple compulsory assignments (0,5 points each) from one lecture to the other (maximum gain or loss of 5 points)
You can also earn points by solving ten more difficult brain exercises - a maximum of 10 points
The marking is the following:
15 - 17.5 points – dobře (C) 18 - 21.5 points – velmi dobře (B) 22 and above - výborně (A)
Poslední úprava: Hampl Vladimír, doc. Mgr., Ph.D. (02.09.2024)
Sylabus -
Lectures will be held in the Parasitology lecture room on Mondays 9:00-10:30 am
30. 9. - Alignment of sequences (Novotný)
7. 10. – Sequence databases and searches in them (Novotný)
14.10. Introduction to taxonomy, molecular characters, sequencing of DNA (Hampl)
21. 10. – Other methods of obtaining molecular data – multilocus methods (RAPD, RFPL etc.), microsatelites, minisatelites, SINE elements, protein mass fingerprint (Hampl)
28.10. – State holiday
4. 11. - Calculation of genetic distances (Hampl)
11. 11. – Phylogenetic trees I. – introduction to trees, reconstruction of phylogenetic trees from the distance matrix (Hampl)
18. 11. - Phylogenetic trees II. Rate heterogeneity, search through the tree space, maximum parsimony (Hampl)
25. 11. - Phylogenetic trees III. - Maximum likelihood, Bayesian methods (Hampl)
2. 12. - Phylogenetic trees IV. - Multigene analyses, robustness of branching, rooting of trees, topology tests (Hampl)
9. 12. – Model tests, molecular clock (Hampl)
16. 12. – Barcoding and forensic science (Hampl)
6. 1. – Intraspecific relationships (Hampl)
13. 1.– Presentation of student essays
Poslední úprava: Hampl Vladimír, doc. Mgr., Ph.D. (02.09.2024)
Lectures will be held in the Parasitology lecture room on Mondays 9:00-10:30 am
30. 9. - Alignment of sequences (Novotný)
7. 10. – Sequence databases and searches in them (Novotný)
14.10. Introduction to taxonomy, molecular characters, sequencing of DNA (Hampl)
21. 10. – Other methods of obtaining molecular data – multilocus methods (RAPD, RFPL etc.), microsatelites, minisatelites, SINE elements, protein mass fingerprint (Hampl)
28.10. – State holiday
4. 11. - Calculation of genetic distances (Hampl)
11. 11. – Phylogenetic trees I. – introduction to trees, reconstruction of phylogenetic trees from the distance matrix (Hampl)
18. 11. - Phylogenetic trees II. Rate heterogeneity, search through the tree space, maximum parsimony (Hampl)
25. 11. - Phylogenetic trees III. - Maximum likelihood, Bayesian methods (Hampl)
2. 12. - Phylogenetic trees IV. - Multigene analyses, robustness of branching, rooting of trees, topology tests (Hampl)
9. 12. – Model tests, molecular clock (Hampl)
16. 12. – Barcoding and forensic science (Hampl)
6. 1. – Intraspecific relationships (Hampl)
13. 1.– Presentation of student essays
Poslední úprava: Hampl Vladimír, doc. Mgr., Ph.D. (02.09.2024)
