Taxonomy and taxonomic systems Elements important for data management

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

Animalia

Arthropoda Echinodermata Chordata

Crinoidea OphiuroideaAsteroideaHolothuroidea Echinoidea

…

Hierarchy: sub-sets

Biota

Animalia

Arthropoda

Crustacea

…

Echinodermata

Fungi

…

…

Plantae

…

… ……

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 BacteriologyZoologyDivisio (-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

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 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

Synonyms With identification

=applying name to specimen Name will often depend on source of

information usedNeed 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 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 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 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