Principles and methods of taxonomy 1400-215MTAKS
The lecture presents both the principles of biological systematics (including nomenclature issues) and taxonomic (phylogenetic) methods, based mainly on molecular data, as well as their applications in various fields of biology, from molecular to environmental, including practical applications, e.g. in species conservation. The following topics are covered:
• The definition of taxonomy, its predictive value. Taxa and taxonomic ranks, biological nomenclature.
• Species in taxonomy – the concepts of morphological, biological, phylogenetic, and historical species, problems with definition (species in organisms with uniparental reproduction, polymorphic species, etc.).
• Biological systematics and evolution – phenetic trees (phenograms) and phylogenetic trees (cladograms) vs. ‘true’ phylogenies. Basic sources of information for reconstructing phylogenetic relationships: palaeontological and neontological data on the diversity of organisms.
• Phenetic taxonomy (phenetics) - the concept of overall similarity and ‘neo-Addansonian taxonomy’. Data matrix, distance measures and clustering methods. Phenetic trees and phylogeny of organisms.
• Phylogenetic taxonomy (cladistics) - basic terms and assumptions (apo- and plesiomorphy, homoplasy, mono-, para- and polyphyly). The principle of maximum parsimony. Felsenstein zone.
• Maximum likelihood and Bayesian methods in molecular phylogenetics. Nucleotide substitution models.
• Methods of assessing the stability of phylogenetic trees and their branches; taxonomic reasoning.
• Selected issues from the taxonomy of archaea, bacteria, protists, fungi, plants and animals.
• Molecular taxonomy in nature conservation: biodiversity estimation and species protection.
Main fields of studies for MISMaP
biotechnology
biology
Type of course
Mode
Course coordinators
Learning outcomes
Knowledge: student
1) presents the role of systematics in biology and the importance of taxonomic (phylogenetic) methods in evolutionary biology (K_W07 Bi2, K_W08 Bi2);
2) knows and compares methods of phylogeny estimation, describes their assumptions and indicates possible inconsistencies (K_W09 Bi2).
Skills: student
3) justifies the choice of a molecular marker and method appropriate to solve a specific research problem (K_U01 Bi2);
4) reads with understanding works in English in the field of taxonomy and evolutionary biology that use phylogenetic methods (K_U03 Bi2);
5) analyses phylogenetic trees and reads information from them (K_U04 Bi2);
6) presents the use of phylogenetic methods in solving selected research problems in evolutionary biology, systematics and biogeography and defines the practical aspects of such research, especially in the conservation of endangered species (K_U08 Bi2);
7) presents a selected taxonomic topic in the form of an oral presentation in English (K_U11 Bi2).
Assessment criteria
The exam will take the form of a seminar in which students present a topic related to taxonomy methodology, which must be developed in consultation with the lecturer. If there are more than 12 students in the class, an alternative written exam consisting of multiple-choice questions may be administered. To pass the written exam, students must achieve a minimum grade of 60%.
Bibliography
W. Hennig. 1965. Phylogenetic systematics. Annual Review of Entomology 10(1): 97–116.
J. Felsenstein. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zoology 27: 401–410.
E. Mayr. 1982. The growth of biological thought. Diversity, evolution, and inheritance. Harvard University Press, Cambridge, Mass. xiv, 974 pp.
E. Mayr & W. Bock. 2002. Classifications and other ordering systems. Journal of Zoological Systematics and Evolutionary Research 40 (4): 169–194.
Avise J.C. 2004. Molecular markers, natural history, and evolution. Sinauer, Sunderland (MA), USA. 2nd edition.
B.G. Hall. 2017. Phylogenetic trees made easy. A how-to manual. 5th edition. Oxford University Press, Oxford, 368 pp.
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: