1. komponenta

Lecture type	Total
Lectures	30
Practicum	30
Seminar	15

* Load is given in academic hour (1 academic hour = 45 minutes)

The course integrates content from lectures, practical exercises, seminar papers and independent assignments.

LECTURES:
(1) Theory vs. hypothesis: Introduction to the theory of evolution
(2) Cosmic evolution, chemical evolution, geochemistry
(3, 4) History of evolutionary biology and misconceptions
(5, 6) Origin of life and evolution of prokaryotes
(7, 8) Eukaryogenesis and evolution of eukaryotes
(9, 10) Phylogenetic systematics and molecular phylogenetics
(11, 12) Biogeography and phylogeography
(13, 14) Human evolution
(15) Discussion, debate and consultation

PRACTICAL EXERCISES:
First topic: History of Evolutionary Thought and Misconceptions (LUCA, Prokaryotes, Eukaryotes)
- The "Great Chain of Being" (Scala Naturae) as an incorrect concept
- Lamarckism and Lamarckian expressions still present in scientific language
- Introduction to the basic mechanisms of biological evolution
- Writing an essay describing the fundamental mechanisms of evolution
- Correcting texts containing inaccurate statements

Second topic: Interpretation of Dendrograms (Evidence for Evolution)
- Tree structure: leaf, branch, node
- Rooted and unrooted trees
- Selection of an outgroup
- Definition of basal and crown groups
- Types of trees: cladogram, phylogram, chronogram
- Fossil calibration and the molecular clock
- Interpretation of groups with respect to ancestors (polyphyly, monophyly)
- Interpretation of groups with respect to descendants (holophyly, paraphyly)
- Interpretation of characters (apomorphies: synapomorphies, plesiomorphies; homoplasies)

Third topic: Data Organization and Preparation of Matrices for Bioinformatic Analyses
- Searching scientific literature in databases such as Google Scholar, PubMed, Web of Science, and Scopus
- Correct citation of references and identification of the first published record of data
- Creating metadata tables in Excel
- Searching for taxonomic groups (example: Vertebrata)
- Using species databases (e.g., Catalogue of Life)
- Numerical coding of characters suitable for computational analysis
- Reference tree and recording dendrograms in Newick format
- Recording branch lengths and statistical support values in Newick format
- Recording chronograms in Newick format

Fourth topic: Cladistic Analysis, Introduction to Bioinformatics, and Basics of Phylogenetic Systematics
- Numerical coding of character matrices and character states
- Coding characters that are not applicable (N/A)
- Selection and coding of the outgroup traits
- Construction of cladograms using simple methods (UPGMA, Single Linkage, Neighbor Joining)
- Rooting cladograms with a priori defined outgroups
- Importing a reference tree (or many reference trees) in Newick format
- Reconstruction of ancestral character states for each character on the reference tree(s)
- Mapping reconstructed characters onto the reference cladogram

Fifth topic: Molecular Phylogenetics and Fundamentals of Bioinformatics
- Browsing sequence databases (NCBI, BOLD Systems)
- Identification of nucleotide and protein sequences (BLAST)
- Organization of a dataset of molecular sequences for a selected taxonomic group (in FASTA format)
- Selection of an outgroup and retrieval of outgroup sequences
- Sequence alignment (MUSCLE, Clustal, MAFFT)
- Trimming sequence ends prior to analysis
- Identification of variable and invariant regions of sequences
- Identification of parsimony-informative sites within the sequences
- Selection of the best model for Maximum Likelihood analysis
- Reconstruction of dendrograms using Maximum Parsimony and Maximum Likelihood analyses
- Interpretation of the resulting phylogram, its branch lengths and statistic support of the nodes
- Identification of the position of a mitochondrial gene within the mitogenome
- Construction of a chronogram in MEGA-11 and calibration of the tree using fossils and molecular clock

Sixth topic: Problem-based tasks
- Problem-solving exercises based on all practical sessions

Seventh topic: Practical assignment
- The student must conduct their own phylogenetic analysis
- The student must demonstrate knowledge of evolutionary mechanisms and terminology
- The student must demonstrate basic knowledge of bioinformatics and phylogenetics

SEMINARS:
(1, 2) Cosmic evolution, geochemistry, the origin of life (LUCA)
(3, 4) Prokaryotes: bacteria and archaea (molecular evolution)
(5, 6, 7) The origin of eukaryotes and their supergroups (classical examples of selection)
(8, 9, 10) Macroevolutionary and microevolutionary patterns and trees
(11, 12, 13) Phylogenetics: from ancient DNA fragments to phylogenomics
(14, 15) Primate evolution, including humans

1. Phylogenetic Trees Made Easy: A How-To Manual - 5th Edition, Hall, Oxford University Press, 2017.
2. Human Evolution: An Illustrated Introduction - 5th Edition, Lewin, Wiley-Blackwell, 2004.
3. Fundamentals of Molecular Evolution - 2nd Edition, Graur & Li, Oxford University Press, 2000.
4. Eukaryotes are a holophyletic group of polyphyletic origin, Skejo & Franjević, Frontiers in microbiology, 2020.
5. Evolution: An Introduction - 2nd Edition, Stearns & Hoekstra, Oxford University Press, 2005.
6. The Organic Codes, Barbieri, Cambridge University Press, 2003.
7. Evolution - 5th Edition, Futuyma & Kirkpatrick, Oxford University Press, 2023.

Enrollment :
Passed : Genetics

Mandatory course - Regular study - Biology