Evolution and phylogeny reconstruction KZ-JO-06-01-000004
Preliminary conditions: Computer skills and elementary knowledge of computer science, a basic knowledge on the principles of organisms systematics and classification, genetics and evolution, an ability to find and process biological information into knowledge, an ability to use the relevant published biological scientific literature and to know its practical application.
Lecture: Evolution, systematics and classification. Typological, morphological, biological, evolutionary and molecular species concepts in the light of phylogeny reconstruction. Classic, fenetic, evolutionary, phylogenetic and molecular taxonomy. Characters in classification; homology and homoplasy and their importance for phylogeny reconstruction. Technics of phylogenetic analyses – algorithms, criteria, a consensus tree construction. Computer methods in phylogeny reconstruction.
Laboratory: Computer programs and bioinformatic databases in phylogenetic reconstruction. Phylogenetic analyses based on morphology and molecular characters. Using DNA sequences obtained from GenBank for phylogenetic analyses. Sequence alignments and analyses. Analysis of the phylogenetic signal and DNA saturation. Substitution model selection (Akaike information criterion, Bayesian information criterion, reversible jump Markov Chain Monte Carlo criterion). Tree construction using different algorithms and computer programs ( MEGA, MrBAYES); tree topology and reliability of clades. Tree editing. Oral presentation of the results of computer analyses and simulations (accompanied by the electronic presentation).
Didactic methods
Multimedial lecture (e-learning on the platform Moodle).
Laboratory: exercises involving computer programs and internet data, computer simulations, discussion, work in focus groups.
Supplementary literature
Course coordinators
Assessment criteria
Basic criteria:
Lecture: positive rating over 50% of points scored (in the final test)
Laboratory: evaluation of results obtained during computer analyses
Form of testing:
Lecture: final written test (including open and closed questions)
Laboratory oral presentation of results of computer analyses and simulations (accompanied by the electronic presentation).
Bibliography
Wägele J.-W. Foundations of Phylogenetic Systematics. Verlag Dr. Friedrich Pfeil, München, 2005.
Xiong J. Essential bioinformatics. Cambridge University Press, 2006.
Hall B.G. Phylogenetic trees made easy: A how-to manual. Third edition. Sinauer Associates Inc., 2008.
Salemi M., Vandamme A. M. The phylogenetic handbook. Cambridge University Press, 2003.
Wheeler Q.D. (ed.). The New Taxonomy. CRC Press, Boca Raton – London – New York, 2008.
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: