Syllabus
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
Annotation
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.