Syllabus
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.
Annotation
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.