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Taxonomy

Taxonomy. MarBEF/IODE training workshop Oostende, March 2007. Taxonomy. Science concerned with Nomenclature: give ‘scientific’ names to species Strictly regulated, different ‘codes’ for botany, zoology, bacteria Classification: create and name groups, ‘taxa’

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Taxonomy

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  1. Taxonomy MarBEF/IODE training workshop Oostende, March 2007

  2. Taxonomy • Science concerned with • Nomenclature: give ‘scientific’ names to species • Strictly regulated, different ‘codes’ for botany, zoology, bacteria • Classification: create and name groups, ‘taxa’ • ‘Systematics’ is often used as an equivalent

  3. Scientific names • In principle, Latin or Latinised names • Regulated by the codes: • Codes are drafted and maintained by Commissions • International Code for Zoological Nomenclature • International Code for Botanical Nomenclature • International Code for Bacterial Nomenclature • Commissions are arbiter in case of disputes • Problem: many unicellular organisms are neither plants nor animals, have two names

  4. Classification • 1,700,000 names! We need a system to organise this information • Hierarchical classification • Classification is based on phylogeny (common descent) • Hypothesis: life only originated once; all organisms descend from a single ancestor • Basis of objectivity in classification

  5. Hierarchy: common descent

  6. Hierarchy: sub-sets Biota Animalia Plantae Echinodermata … Arthropoda Crustacea … Fungi … … … … …

  7. Hierarchy: ranks Regnum: Animalia, Plantae… Phylum: Arthropoda, Echinodermata… Classis: Crustacea, Insecta… Ordo: Decapoda, Amphipoda, Isopoda… Familia: Xanthidae, Diogenidae… Genus: Xantho, Progeryon… Species: Xantho granulicarpus, Xantho hydrophilus…

  8. Extra ranks • ‘Super-’, ‘Sub-’, ‘Infra-’ • Subordo, infraordo, superfamilia… • Not for genus and species (except subspecies) • Tribus: between family and genus • Infraspecific • Subspecies only rank recognised in zoology • Botany: varietas, forma • Botany: ‘Divisio’ instead of ‘Phylum’

  9. Standard endings Rank Botany Bacteriology Zoology Divisio (-phyta/-mycota) Subdivisio (-phytina/-mycotina) Classis (-phyceae/-mycetes/-opsida) Subclassis (-phycidae/-mycetidae/-idae) Ordo -ales -ales Subordo -ineae -ineae Superfamilia (-oidea) Familia -aceae -aceae -idae Subfamilia -oideae -oideae -inae Tribus -eae -eae (-ini) Subtribus -inae -inae

  10. Uni-, bi- et multinomens • Names of rank of genus and above consist of a single part • E.g. ‘Hominidae’, ‘Homo’ • Names of rank species and below consist of several parts • E.g. ‘Homo sapiens’ • Subspecies… indicated with extra parts • E.g. ‘Homo sapiens erectus’ • Several name parts, one name

  11. Format of taxonomic names • Names of genera and lower are often written in italics • E.g. ‘Homo’ and ‘Homo sapiens’ • Subgenus is written between brackets between genus and specific epitheton • Holothuria (Thymiosicya) impatiens • Subgenus and above are written with initial capital • Genus name often abbreviated to first character at subsequent mentions • E.g. H. sapiens

  12. Specific epitheton • Second part of species name • Is often an adjective • Takes gender from the genus name (which is always a noun) • Can be other than adjective • Noun in apposition • Locality • Named after a person • genitive

  13. Classification can change • Phylogeny = scientific study, • Research results can alter understanding • Interpretation of facts can be different between scientists • Difficult to construct a complete and consistent classification • Can result in name changes • Species moves from one genus to another… • Epitheton changes when genus has other gender

  14. Nomenclature • Publication • To be valid, name has to be published in a publication acceptable to the code • Name has to be unique within the domain of the code • Zoological name can be same as botanical • Typification • Name has to be supported by a type

  15. Publication • Names have to be published to be valid • Rules for validity are part of the code • No thesis, nor WWW! • Date of publication determines seniority of the name • Important in case of dispute • Start of the nomenclature: • Zoology: Linnaeus (1758). Systema naturae… 10th ed. • Botany: Linnaeus (1753). Species plantarum. 1st ed.

  16. Authority • Author of the publication that contains the description becomes ‘author’ of the taxon name • Date of description is the date that the publication became publicly available • Not necessarily the same as the date on the cover of the publication • Journals have a tendency to be published late • Differences in calendars (e.g. Russia in the beginning of the 20th century)

  17. Authority • Authority is very important in taxonomy, often added to the name • For many journals mandatory for taxa of rank genus and below • E.g. Homo sapiens Linnaeus, 1758 • Zoology: with year of publication • E.g. Zostera noltii Hornemann • Botany: without year

  18. Names are unique… • … but not absolutely so • Botanical name can be same as zoological • There is no central register (yet), so this leaves a lot of scope for mistakes • ‘Preoccupied name’ • Has to be replaced with another name – ‘replacement name’

  19. Name changes • If a species is transferred from one genus to another, the species’ name changes • Zoology: the original author’s name is placed between brackets • Spongia aurea Montagu, 1818 • Hymeniacidon aurea (Montagu, 1818) • Botany: parentheses + author of the new ‘combination’ • Halophila stipulacea (Forsskål) Ascherson

  20. Name changes • Specific epitheton is often adjective, has to be declined according to rules of latin grammar • Turbo littoreus Linnaeus, 1758 • Littorina littorea (Linnaeus, 1758) • Specific epitheton can be noun, which has its own gender • Tellina (Moerella) pygmaeus Lovén, 1846 • Taxonomists, but especially other users of taxonomic names, are often mistaken! • Tellina pygmaea: wrong!!

  21. Typification • Type serves as an anchor, to stabilise taxonomy • Type of a species: specimen • Zoology • Type of a genus: species • Type of a family: genus • Botany: type is always a specimen

  22. Synonyms • Objective synonyms • Preoccupied name… • Objective synonyms have the same type • Subjective synonyms • An author has described a taxon, but a subsequent author has stated that the specimens of that species actually belong to a taxon that has been described before

  23. Interpretation of the literature • Difference between misidentifications and synonyms not always clear • List of names below a taxonomic name in a taxonomic revision often contain both! • Different authors use different classifications • Importance of having an intelligent database, that aids in interpreting names • Has to have information on synonyms, spelling variations…

  24. Types of tax info systems • ‘Nomenclators’: list of names • Taxonomic • List of names, plus taxonomic information (author, reference for description publication…) • Who’s valid?? • Species database • Information on biology, identification… • Distribution • For a group of species or for a region

  25. Nomenclators • Index Fungorum • Animals • Nomenclator Zoologicus (genus level) • Index Animalium • Plants • International Plant Names Index

  26. Taxonomic databases • Global • Integrated Taxonomic Information System (ITIS) • Species 2000 • Systema Naturae 2000 • UNESCO Register of Marine Organisms • Regional • Species 2000 Europe, European Register of Marine Species (ERMS) • Marine Species Database for Eastern Africa (MASDEA) • Taxonomic • Fungi…

  27. Biogeographical DBs • Global Biodiversity Information Facility (GBIF) • OBIS • And its regional nodes • Taxonomic names are not always integrated

  28. Species databases • FishBase • Hexacorallia, Algaebase, CephBase, Brachnet, NeMys… • www.marinespecies.org • Tree of Life project • http://tolweb.org/tree/phylogeny.html

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