Taxonomy and taxonomic systems Elements important for data management

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

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

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

Hierarchy: common descent

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

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…

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’

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

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

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

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

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

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

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.

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)

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

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’

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

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!!

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

Synonyms Objective synonyms Subjective 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

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…

Problems with names With names themselves With identification 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

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

Indexing literature Zoological record Some free resources Started 1864, now available electronically Originally Linnaean Society, now commercial Unfortunately ridiculously expensive Some free resources http://www.organismnames.com http://www.biologybrowser.com/

Nomenclators Index Kewensis Index animalium Nomenclator Zoologicus Included in the IPNI database, http://www.ipni.org/index.html Index animalium http://www.sil.si.edu/digitalcollections/indexanimalium/ Nomenclator Zoologicus http://www.ubio.org/NomenclatorZoologicus/

Taxonomic databases Global Regional Taxonomic Integrated Taxonomic Information System (ITIS) Species 2000 Regional Species 2000 Europe, European Register of Marine Species (ERMS) Marine Species Database for Eastern Africa (MASDEA) Taxonomic Fungi…

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

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

FishBase

Algaebase