Bi0260 Taxonomy, phylogenetics and zoological nomenclature

Faculty of Science
Spring 2017
Extent and Intensity
2/1/0. 3 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Mgr. Igor Malenovský, Ph.D. (lecturer)
RNDr. Andrea Tóthová, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Stanislav Pekár, Ph.D.
Department of Botany and Zoology - Biology Section - Faculty of Science
Contact Person: Mgr. Igor Malenovský, Ph.D.
Supplier department: Department of Botany and Zoology - Biology Section - Faculty of Science
Mon 20. 2. to Mon 22. 5. Tue 8:00–10:50 D31/238
Bi1030 Inverteb. phylog. & divers. && Bi2090 Verteb. phylog. & divers.
Examples and the chapter on nomenclature are primarily aimed at students of systematic zoology, all interested students of other branches of biology are however welcome, as most topics included in the course are general.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course, students should be able to employ basic terms and methods of biological systematics and taxonomy, especially those related to species delimitation, phylogeny reconstruction, natural classification and rules of zoological nomenclature, and use them in praxis.
  • 1. Systematics, taxonomy and a brief review on their history.
  • 2. Taxon, category, species concept, character, intraspecific variation.
  • 3. Phenetics, review and use of statistics in contemporary taxonomy. Taxonomic character from the viewpoint of statistics, traditional and geometric morfometrics, cluster analyses, ordinations, discriminant analysis, artificial neural networks, automatic species identification.
  • 4. Introduction into cladistics: similarity and relationship, homology, syn)apomorphy, (sym)plesiomorphy, determination of character polarity, principle of maximum parsimony, hypothesis in systematics.
  • 5. Quantitative cladistics: character coding, cladogram construction, character optimization and weighting, tree statistics, consensus, cladistic software.
  • 6. Methods of molecular taxonomy and phylogenetics: proteins, nucleic acids and their extraction, PCR, DNA cloning and sequencing, DNA hybridisation, RAPD, restriction analyses, microsatelites, DNA barcoding.
  • 7. Reconstruction of phylogeny using molecular data: alignment, maximum parsimony, maximum likelihood, Bayesian analysis, distance methods.
  • 8. Practical use of molecular methods in taxonomy: visit of a laboratory.
  • 9. Advantages and limits of molecular and morphological data, sources of error and conflict, integration of different types of data into a phylogenetic analysis. Applications of phylogenetic analysis: classification, historical biogeography, tests of coevolution and evolutionary scenarios.
  • 10. International code of zoological nomeclature: basic principles, availability, validity and formation of names.
  • 11. International code of zoological nomeclature 2: homonymy and synonymy, principle of priority versus stability, type concept in nomenclature, summary and model examples.
  • 12. Work with taxonomic material and literature: collections, taxonomic revision, description of new taxa, identification keys, biodiversity databases, electronic taxonomy.
  • DROZD, Pavel. Principy systematiky a taxonomie. Vyd. 1. Ostrava: Ostravská univerzita, 2004. 89 s. ISBN 807042995X. info
  • FLEGR, Jaroslav. Evoluční biologie. Vyd. 1. Praha: Academia, 2005. 559 s. ISBN 8020012702. info
  • Mezinárodní pravidla zoologické nomenklatury : přijaté Mezinárodní unií biologických věd. Translated by Václav Houša - Pavel Štys. 4. vyd. Praha: Česká společnost entomologická, 2003. 8, xxxi. ISBN 8023915398. info
  • SCHUH, Randall T. Biological Systematics. Priciples and Applications. 1. vyd. Ithaca and London: Cornell University Press, 2000. 239 pp. ISBN 0-8014-3675-3. info
  • KITSCHING, Jan J. and Peter L. et al. FOREY. Cladistics. The theory and practice of parsimony analysis. 2. vyd. Oxford: Oxford University Press, 1998. 228 pp. ISBN 0 19 850138 2. info
  • Zima J., Macholán M., Munclinger P., Piálek J. Genetické metody v zoologii. Univerzita Karlova v Praze, Karolinum, Praha, 239s, 2004 ISBN 80-246-0795-6.
  • MARHOLD, Karol and Jan SUDA. Statistické zpracování mnohorozměrných dat v taxonomii : (fenetické metody). 1. vyd. Praha: Karolinum, 2002. 159 s. ISBN 8024604388. info
  • WINSTON, Judith E. Describing species : practical taxonomic procedure for biologists. New York, N.Y.: Columbia University Press, 1999. xx, 518. ISBN 0231068247. info
  • Wägele, Johann-Wolfgang: Foundations of phylogenetic systematics. Verlag Dr. Friedrich Pfeil, München, 2005. 365 s. ISBN 3-89937-056-2.
  • MACHOLÁN, Miloš. Základy fylogenetické analýzy (Essentials of Phylogenetic Analysis). 1. vyd. Brno: Masarykova univerzita, 2014. 290 pp. ISBN 978-80-210-6363-1. doi:10.5817/CZ.MUNI.M210-6363-2014. Munishop Flexibooks info
Teaching methods
Lectures, class discussion, visit of a laboratory of molecular taxonomy, visit of natural history museum collections.
Assessment methods
Written test, usually consisting of 25 questions from throughout the contents of the course, 50% of correct answers is needed to pass.
Language of instruction
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, spring 2018, Spring 2019, Spring 2020, Spring 2021.
  • Enrolment Statistics (Spring 2017, recent)
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