Taxonomy and its Taxonomy and its Implications for Data Implications for Data

ManagementManagement

Edward Vanden Berghe &

Marc De Meyer

TaxonomyTaxonomy

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)

ClassificationClassification

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

Basic scientific name: Basic scientific name: Genus speciesGenus species

Any species should be named using the binominal nomenclature:

Homo sapiensMusca domestica

Basic scientific name: Basic scientific name: Genus speciesGenus 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 disputesProblems:

◦Some unicellular organisms are neither plants nor animals

◦Some organisms are unison of different organisms (like lichens)

Availability of scientific name: Availability of scientific name:

PublishedSpelled in Latin letters (Latin or latinized

word) Written in italicsGenus with capital letterSpecies without capital letterMany additional rules

Note: in botany we speak of ‘validity’ of name!

PublicationPublication

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.

Electronic PublicationElectronic 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 publicationBotany

◦Similar procedure but not equivalent of ZooBank required

AuthorityAuthority

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)

AuthorityAuthority

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…Names are unique…

… 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

Specific epithetonSpecific epitheton

Second part of species nameIs 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

Molecular recognitionMolecular recognition

DNA barcoding: providing an unique sequence as species recognition

Problem: many new ‘unique sequences’ without linkage to available or valid names

Molecular recognitionMolecular 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 timeBIN should still be linked to scientific

namesCurrently BIN’s are not recognized by the

International codes

Classification can changeClassification can change

Phylogeny = scientific study, ◦Research results can alter understanding◦Interpretation of facts can be different

between scientistsDifficult to construct a complete and

consistent classificationCan 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

Higher classification: common Higher classification: common descentdescent

Animalia

Arthropoda Echinodermata Chordata

Crinoidea OphiuroideaAsteroideaHolothuroidea Echinoidea

…

Hierarchy: sub-setsHierarchy: sub-sets

Biota

Animalia

Arthropoda

Crustacea

…

Echinodermata

Fungi

…

…

Plantae

…

… ……

Hierarchy: ranksHierarchy: ranks

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…

Extra ranksExtra ranks

‘Super-’, ‘Sub-’, ‘Infra-’◦Subordo, infraordo, superfamilia…

Tribus: between family and genus

SubgenusSubgenus

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….

subspeciessubspecies

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

Standard endingsStandard endings

Rank Botany Bacteriology ZoologyDivisio (-phyta/-mycota)Subdivisio (-phytina/-mycotina)Classis (-phyceae/-mycetes/-opsida)Subclassis (-phycidae/-mycetidae/-idae)Ordo -ales -alesSubordo -ineae -ineaeSuperfamilia (-oidea)Familia -aceae -aceae -idaeSubfamilia -oideae -oideae -inaeTribus -eae -eae (-ini)Subtribus -inae -inae

NomenclatureNomenclature

Publication◦To be valid, name has to be published in a

publication acceptable to the codeName 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

Name changesName 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 changesName 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!!

Validity of nameValidity of name

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 nameValidity 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)

TypificationTypification

Type serves as an anchor, to stabilise taxonomy

Type of a species: specimenZoology

◦Type of a genus: species◦Type of a family: genus

Botany: type is always a specimen

TypificationTypification

Different kind of types:◦Primary types and secondary types◦Types fixed in original publication versus later

designation

SynonymsSynonyms

Objective synonyms◦Preoccupied name…

Objective synonyms have the same typeSubjective 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 literatureInterpretation 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

classificationsImportance of having an intelligent

database, that aids in interpreting names◦Has to have information on synonyms, spelling

variations…

Problems with namesProblems with names

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