Molecular Phylogenetics 1400-226FGMOL
1. Windows environment for microcomputers on a local network. Clustal - a program for alignment and simple analyses of protein and DNA sequences. TreeView - a program for viewing and editing phylogenetic trees. Protein sequences of hemoglobin serving as molecular clocks.
2. GenBank - a database of nucleic acid sequences on the Internet. Searching for homologous sequences with the computer program Blast.
3. Aligning homologous sequences with the Clustal program. BioEdit - a sequence alignment editor and analysis program. Methods for building phylogenetic trees of macromolecules.
4. MEGA - a program for molecular evolutionary analysis. Phylogeny of hominids derived on the basis of their mitochondrial genes.
5. Maximum Parsimony in phylogenetics. Building phylogenetic trees on the basis rDNA sequences. Estimation of their robustness by the "bootstrap" method.
6."The Tree of Life" and why dividing it into five kingdoms is not adequate.
7. Models of DNA and protein sequence evolution. Calculating distances between DNA and protein sequences.
8. Isolation of green algae DNA and amplification of their 18S rRNA gene by PCR. Automatic cycle sequencing of 18S rRNA genes from algae.
9. The polyphyletic nature of photosynthesizing eukaryotes. Editing and combining the obtained sequences with the program Lasergene.
10. Paup - a program for phylogenetic analyses of protein and DNA sequences. Maximum likelihood method in phylogenetics. ModelTest - a program for choosing a model of DNA sequence evolution.
11. PHYML - a program for estimation trees by Maximum likelihood method and their robustness by approximate likelihood ratio test.
12.MrBayes program and Bayesian approach to phylogenetic inference.
13.Phylogenetic trees from RNA genes of a small ribosomal subunit used to illustrate the endosymbiotic theory of the origin of the eukaryotic cell.
Type of course
Mode
Prerequisites
Prerequisites (description)
Learning outcomes
After completing the course the student:
KNOWLEDGE AND ABILITIES
- Has knowledge of evolutionary origin of main groups of organisms, such as Bacteria, Protists, Fungi, Plants and Animals, including humans;
- Is able read and analyze scientific literature with respect to usage phylogenetic methods and interpretation of results;
- Is able to choose properly phylogenetic methods and programs for a given scientific question, perform calculations and interpret results;
- Is able to identify and present scientific problems of contemporary biology suitable for resolution by phylogenetic methodology;
- Is able to use phylogenetic methods in for solving issues of evolutionary biology, including endosymbiosis, lateral gene transfer, fossil DNA, anthropogenesis;
- Is able to present, in graphical form, relationships between genes and organisms;
- Is able to analyze phylogenetic trees and infer information contained within them;
- Knows how to use Internet databases of macromolecules, such as GenBank;
- Is able to compare phylogenetic methods (Bayesian, distance, based on criteria of maximum likelihood and parsimony);
- Knows how to use computer programs for reconstruction of phylogenetic relationships, such as MEGA, MrBayes, PhyML and Paup;
- Is able to use models of nucleotide substitutions and understands their parameters;
- Is able to use methods for checking tree robustness (bootstrap, posterior probability, aLRT test);
SOCIAL AWARENESS
- Appreciates the significance of phylogenetic methods in rationalization of biological diversity;
- Is able to distinguish scientific from pseudoscientific arguments about similarity between species and organisms;
- Understands the need for informing the public about the scientific theories concerning the origin of species, including humans.
Assessment criteria
Written finals and oral examination
Practical placement
none
Bibliography
Basics:
Phylogenetic Trees Made Easy: A How-To Manual, Third Edition Barry G. Hall.
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition Andreas D. Baxevanis, B. F. Francis Ouellette.
For enthusiasts:
Molecular Evolution and Phylogenetics Masatoshi Nei, Sudhir Kumar
Inferring Phylogenies Joseph Felsenstein
Molecular Systematics David M. Hillis (Editor), et al
Additional information
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