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Lecturer(s)
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Dvořák Petr, doc. Mgr. Ph.D.
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Course content
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Theoretical lecture Mutation, the theory of neutral evolution. Homology, orthology, paralogy. DNA sequencing of first, second and third generation. Gene selection for phylogenetic analyses. Multiple sequence alignment. Optimality criteria - distance, maximum parsimony, maximum likelihood and Bayesian inference. Phylogenomics - supermatrix and supertree. Interpretation of phylogenetic trees. Tree topology testing. An application of phylogenetic reconstruction in different fields of science and practise. Molecular clocks. Practicals Own computer requered. Sequence analysis, the building of sequence databases using GenBank, multiple sequence alignment, phylogeny reconstruction using MEGA program, analyses in grid environment CIPRES portal, a comparison of different optimality criteria, interpretation of obtained data.
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Learning activities and teaching methods
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Monologic Lecture(Interpretation, Training), Demonstration
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Learning outcomes
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The course is focused on theoretical and practical aspects of reconstruction of the phylogeny of organisms. Model systems for practical lectures will be selected among plants and microorganisms. However, knowledge and skills are transferable to all other organisms and viruses.
The student will be able to reconstruct phylogeny using one or more genetic markers.
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Prerequisites
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unspecified
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Assessment methods and criteria
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Analysis of Activities ( Technical works)
- Attendance of all practicals. - Compute an exercise at the exam.
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Recommended literature
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Philippe Lemey, Marco Salemi, Anne-Mieke Vandamme. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing 2nd Edition.
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