Please note that the lectures are given in Czech language. English version of the course can be requested in advance if there are at least 3 students. Lectures and practicals represent a continuation of the subject Multivariate methods in taxonomy (MB120P126). The aim of the lectures is to provide basic theoretical background of the cladistic approach as well as other methods of phylogeny reconstruction and to illustrate their practical applications. The aim of the practicals is to get students acquainted with the computer programs for the cladistic analyses and other methods of phylogeny reconstruction, especially with PAUP, MrBayes, Modeltest and TNT. Usage of the programs is illustrated by real data sets from botanical applications.
Last update: Mgr. Michal Štefánek (02.05.2022)
Prednášky a cvičenia nadväzujú na predmet Multivariační metody v taxonomii (MB120P126). Cieľom prednášok je oboznámenie s teoretickými základmi a praktickým uplatnením kladistických metód ako aj ďalších alternatívnych metód rekonštrukcie fylogenézy. Praktické cvičenia si kladú za cieľ oboznámiť študentov s počítačovými programami používanými v kladistike a iných metódach rekonštrukcie fylogenézy. Ide predovšetkým o programy PAUP, MrBayes, Modeltest a TNT.
Literature -
Last update: Mgr. Michal Štefánek (02.05.2022)
Wiley, E.O., Siegel-Causey, D., Brooks, D.R. & Funk, V.A., 1991: The compleat cladist. A primer of phylogenetic procedures. The University of Kansas Museum of Natural History. Special Publication no. 19. http://www.amnh.org/learn/pd/fish_2/pdf/compleat_cladist.pdf
Forey, P.L., Humphries, C.J., Kitching, I.J., Scotland, R.W., Siebert, D.J. & Williams, D., 1992: Cladistics. A practical course in systematics. Clarendon Press, Oxford.
Kitching, I.J., Forey, P.L., Humphries, C.J. & Williams, D.M., 1998: Cladistics. The theory and practice of parsimony analysis. Ed. 2. Oxford University Press, Oxford
Hall B.G. (2001): Phylogenetic trees made easy.
Felsenstein J. (2004): Inferring phylogenies.
Mount D.W. (2004): Bioinformatics. Sequence and genome analysis.
Salemi M. & Vandamme A.-M. (2003): The phylogenetic handbook. A practical approach to DNA and protein phylogeny.
Last update: Mgr. Michal Štefánek (02.05.2022)
Wiley, E.O., Siegel-Causey, D., Brooks, D.R. & Funk, V.A., 1991: The compleat cladist. A primer of phylogenetic procedures. The University of Kansas Museum of Natural History. Special Publication no. 19. http://www.amnh.org/learn/pd/fish_2/pdf/compleat_cladist.pdf
Forey, P.L., Humphries, C.J., Kitching, I.J., Scotland, R.W., Siebert, D.J. & Williams, D., 1992: Cladistics. A practical course in systematics. Clarendon Press, Oxford.
Kitching, I.J., Forey, P.L., Humphries, C.J. & Williams, D.M., 1998: Cladistics. The theory and practice of parsimony analysis. Ed. 2. Oxford University Press, Oxford
Hall B.G. (2001): Phylogenetic trees made easy.
Felsenstein J. (2004): Inferring phylogenies.
Mount D.W. (2004): Bioinformatics. Sequence and genome analysis.
Salemi M. & Vandamme A.-M. (2003): The phylogenetic handbook. A practical approach to DNA and protein phylogeny.
Requirements to the exam -
Last update: Mgr. Michal Štefánek (02.05.2022)
written test and oral examination
Last update: Mgr. Michal Štefánek (02.05.2022)
písemný test a ústní zkouška
Syllabus -
Last update: Mgr. Michal Štefánek (02.05.2022)
Cladistic approach (parsimony analysis):
Monophyletic, paraphyletic and polyphyletic groups; sister groups and outgroup comparison; polarisation of characters; optimisation of characters; cladistic rules; character coding.
Types of parsimony; Hennig's method; Wagner algorithm.
Comparison of trees; consistency and retention indices; tree length.
Methods of building trees; exhaustive search; heuristic analysis and other methods; consensus trees; bootstrap; conventions.
Techniques of parsimony analysis for large data sets.
Alternative methods of evolutionary reconstruction:
Methods based on distances, neighbour-joining method.
Maximum likelihood method, substitution models.
Bayesian inference of phylogeny.
Last update: Mgr. Michal Štefánek (02.05.2022)
Kladistika (parsimonická analýza):
Monofyletické, parafyletické a polyfyletické skupiny; sesterské skupiny a mimoskupinové porovnanie; polarizácia znakov; optimalizácia znakov; pravidlá kladistiky; kódovanie znakov.
Typy parsimónie; Hennigova metóda; Wagnerov algoritmus.
Porovnanie stromov; konsistenčný a retenčný index; dĺžka stromu.
Metódy tvorby stromov; vyčerpávajúce hľadanie, heuristická analýza a ďalšie metódy; konsenzuálne stromy; bootstrap; konvencie.
Techniky parsimonickej analýzy pre veľké dátové súbory.
Alternatívne metódy rekonštrukcie evolučných stromov:
Metódy založené na vzdialenostiach, metóda spájania susedných objektov (neighbor-joining method).
Metóda najväčšej vieryhodnosti (maximum likelihood method), modely zmeny (evolúcie) sekvencií DNA, substitučné modely.
