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Lecturer(s)
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Course content
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Data used for molecular phylogenetic analysis - RFLP, AFLP, SSR genotyping and sequencing data. What is a phylogenetic tree - basic terms. Methods to generate and analyze sequencing data - multiple alignment algorithms. Evolutionary models, model selection procedure - ModelTest and jModelTest. Phylogeny inference based on distance methods - UPGMA, NJ, Fitch-Margoliash, minimum evolution. Phylogeny inference based on maximum-likelihood and parsimony methods - principles and differences. Bayesien methods - Mr Bayes, BEAST. Phylogenetic analysis using protein sequences; rRNA sequences, universal tree of life, secondaray structures and their application in phylogenetics. Analysis of coding DNA sequences - gene structure, orthologs, paralogs and xenologs and their influence on phylogenetic inference. Evaluating of reliability of infered trees - jackknifing, bootstrap analysis, Bremer support. Dating of phylogenetic trees. Other methods - network-based tools (principles and analysis of model data using Splits Tree). Alignmet-free methods - principles. SSR genotyping - fragment sizing and data analysis.
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Learning activities and teaching methods
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Monologic Lecture(Interpretation, Training), Dialogic Lecture (Discussion, Dialog, Brainstorming), Demonstration
- Homework for Teaching
- 20 hours per semester
- Preparation for the Course Credit
- 20 hours per semester
- Attendace
- 26 hours per semester
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Learning outcomes
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The course will introduce basic and advanced tools of molecular phylogenetics. Students will learn how to analyse moleceular diversity and phylogenetic relationships.
After the course, student should be able to: - analyze genetic diverzity - analyze sequencing data using multiple alignment methods - analyze phylogeny inference using different methods on DNA and protein level
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Prerequisites
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Successful completion of bachelor's level study requirements; successful completion of "Analysis of DNA sequences" course.
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Assessment methods and criteria
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Written exam, Student performance
Written test - 75% correctly answered questions; 80% attendance; completion of seminar project.
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Recommended literature
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Felsenstein, J. Inferring Phylogenies..
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Hall, B.G. (2017). Phylogenetic Trees Made Easy: A How To Manual. Oxford University Press.
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Nei, M., Kumar, S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press.
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Salemi, M. and Vandamme, A.M. (2003). The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. Cambridge University Press.
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