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Taxonomy and its Implications for Data Management Edward Vanden Berghe & Marc De Meyer 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 (but actually the study of the kinds and diversity of organisms) Taxonomy 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 Classification Any species should be named using the binominal nomenclature: Homo sapiens Musca domestica Basic scientific name: Genus species 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 Problems: ◦ Some unicellular organisms are neither plants nor animals ◦ Some organisms are unison of different organisms (like lichens) Basic scientific name: Genus species Published Spelled in Latin letters (Latin or latinized word) Written in italics Genus with capital letter Species without capital letter Many additional rules Note: in botany we speak of ‘validity’ of name! Availability of scientific name: Names have to be published to be available ◦ Rules for availability are part of the code ◦ Since 2012: web publication allowed! ◦ 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. Publication Zoology ◦ Allowed after 2011 ◦ Publication ISSN or ISBN ◦ Registration of publication in ZooBank (Official register of Zoological Nomenclature) ◦ Mention of Electronic archive intended to preserve the publication Botany ◦ Similar procedure but not equivalent of ZooBank required Electronic Publication 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 Reprint versus journal Online publication versus printed publication Differences in calendars (e.g. Russia in the beginning of the 20th century; French revolution) 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 Authority … but not absolutely so ◦ Botanical name can be same as zoological ◦ Registration of names not required, so this leaves a lot of scope for mistakes ◦ Replacement name Names are unique… 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 Specific epitheton DNA barcoding: providing an unique sequence as species recognition Problem: many new ‘unique sequences’ without linkage to available or valid names Molecular recognition Alternative: ‘BIN’ (Barcode Index Number) Algorithm to cluster sequences to produce operational taxonomic units that closely correspond to species. But BIN’s can change throughout time BIN should still be linked to scientific names Currently BIN’s are not recognized by the International codes Molecular recognition 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 for those adjectives based on Latin or latinized words Classification can change Higher classification: common descent Animalia Arthropoda Crinoidea Holothuroidea Echinodermata Chordata … Asteroidea Ophiuroidea Echinoidea Hierarchy: sub-sets Biota Animalia Arthropoda Echinodermata Crustacea … … … Plantae … Fungi … … … Regnum: Animalia, Plantae… Phylum (zoology)/Divisio (botany): Arthropoda, Echinodermata… Classis: Crustacea, Insecta… Ordo: Decapoda, Amphipoda, Isopoda… Familia: Xanthidae, Diogenidae… Genus: Xantho, Progeryon… Species: Xantho granulicarpus, Xantho hydrophilus… Hierarchy: ranks ‘Super-’, ‘Sub-’, ‘Infra-’ ◦ Subordo, infraordo, superfamilia… Tribus: between family and genus Extra ranks Subgeneric rank indicated with extra part interpolated between genus and species name Placed in parentheses (but not a trinomen) Begins with upper-case letter ◦ E.g. ‘Ceratitis (Pterandrus) rosa’ Names of rank of genus and above consist of a single part ◦ E.g. ‘Hominidae’ ‘Homo’, etc…. Subgenus Subspecific rank is lowest rank regulated by the Code. Indicated with extra part (trinomen) ◦ E.g. ‘Homo sapiens erectus’ Infrasubspecific names, not regulated (if published after 1960) in zoology ◦ E.g. variety, aberration, morph, etc…. But recognized in botany subspecies Rank Divisio Subdivisio Classis Subclassis Ordo Subordo Superfamilia Familia Subfamilia Tribus Subtribus Botany Bacteriology (-phyta/-mycota) (-phytina/-mycotina) (-phyceae/-mycetes/-opsida) (-phycidae/-mycetidae/-idae) -ales -ales -ineae -ineae -aceae -oideae -eae -inae -aceae -oideae -eae -inae Standard endings Zoology (-oidea) -idae -inae (-ini) 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 Nomenclature 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 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) But only if it concerns a Latin or latinized word! 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!! Name changes Not the same as available. Zoology: oldest available name is the valid name Note: in botany ‘valid’ is the same as ‘available’ in zoology. Here they speak of ‘accepted’ Validity of name Synomyms: two different names for the same species. Oldest takes priority. (objective and subjective synonyms) Homonyms: one name for two different species. Oldest takes priority. (primary and secondary homonyms) Validity of name 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 Typification Different kind of types: ◦ Primary types and secondary types ◦ Types fixed in original publication versus later designation Typification 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 Synonyms 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… Interpretation of the literature With names themselves ◦ Synonyms With identification ◦ =applying name to specimen ◦ Name will often depend on source of information used Need to document identification keys Problem integrating data from different sources ◦ Need for quality control Problems with names