Bi0260 Taxonomy, phylogenetics and zoological nomenclature

Faculty of Science
Spring 2024
Extent and Intensity
2/1/0. 3 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
Mgr. Igor Malenovský, Ph.D. (lecturer)
RNDr. Andrea Špalek Tóthová, Ph.D. (lecturer)
prof. Mgr. Stanislav Pekár, 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
Timetable
Mon 19. 2. to Sun 26. 5. Wed 14:00–16:50 D31/238
Prerequisites
Bi1030 Inverteb. phylog. & divers. && Bi2090 Verteb. phylog. & divers.
Examples and the chapter on nomenclature are primarily aimed at students of zoology, however, all interested students of other branches of biology are 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
The course provides information on basic principles and methods of biological systematics, with a special reference to zoology. Namely, it deals with the problems of delimitation and description of new/revision of extant animal taxa at all levels of systematic hierarchy (species, infra- and supraspecific taxa), phylogenetic analyses (including their applications), and main rules of zoological nomenclature.
Learning outcomes
At the end of the course, students should be able to:
- understand basic terms and methods of biological systematics and taxonomy;
- know how to delimit and formally correctly describe new animal taxa at every level of systematic hierarchy, or how to synonymize it;
- carry out a simple phylogenetic analysis using the cladistic method;
- critically read and use taxonomic literature, electronic databases and results of phylogenetic studies;
- know how to contact a curator in a natural history museum collection with a request to study material.
Syllabus
  • 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.
Literature
  • DROZD, Pavel. Principy systematiky a taxonomie. Vyd. 1. Ostrava: Ostravská univerzita, 2004, 89 s. ISBN 807042995X. 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
  • WINSTON, Judith E. Describing species : practical taxonomic procedure for biologists. New York, N.Y.: Columbia University Press, 1999, xx, 518. ISBN 0231068247. info
  • MACHOLÁN, Miloš. Základy fylogenetické analýzy (Essentials of Phylogenetic Analysis). 1. vyd. Brno: Masarykova univerzita, 2014, 290 pp. ISBN 978-80-210-6363-1. Available from: https://dx.doi.org/10.5817/CZ.MUNI.M210-6363-2014. Munishop Flexibooks info
  • BAUM, David A. and Stacey D. SMITH. Tree thinking : an introduction to phylogenetic biology. Greenwood Village: Roberts and Company Publishers, 2012, xx, 476. ISBN 9781936221165. info
  • SCHUH, Randall T. Biological Systematics. Priciples and Applications. 1st ed. 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. 2nd ed. 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
  • Wägele, Johann-Wolfgang: Foundations of phylogenetic systematics. Verlag Dr. Friedrich Pfeil, München, 2005. 365 s. ISBN 3-89937-056-2.
  • FLEGR, Jaroslav. Evoluční biologie. Vyd. 1. Praha: Academia, 2005, 559 s. ISBN 8020012702. info
Teaching methods
Theoretical lectures, class discussion on case studies published in scientific literature, practical excercises (e.g. compilation of character matrix, construction of a cladogram using cladistic methodology, derivation of classification based on phylogeny), demonstration of specialized software, a visit of a laboratory of molecular taxonomy, a visit of a natural history museum collection.
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
Czech
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 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2023, Spring 2025.
  • Enrolment Statistics (Spring 2024, recent)
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