taxonomy and taxonomic systems elements important for data management
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Taxonomy and taxonomic systems
Elements important for data management
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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
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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
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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
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Hierarchy: common descent
Animalia
Arthropoda Echinodermata Chordata
Crinoidea OphiuroideaAsteroideaHolothuroidea Echinoidea
…
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Hierarchy: sub-sets
Biota
Animalia
Arthropoda
Crustacea
…
Echinodermata
Fungi
…
…
Plantae
…
… ……
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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…
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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’
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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
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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
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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
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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
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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
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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
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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.
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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)
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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
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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’
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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
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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!!
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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
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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
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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…
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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
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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
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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/
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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/
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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…
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Biogeographical DBs
Global Biodiversity Information Facility (GBIF)
OBIS And its regional nodes
Taxonomic names are not always integrated
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Species databases
FishBase Hexacorallia CephBase, Brachnet, NeMys…
Tree of Life project http://tolweb.org/tree/phylogeny.html
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FishBase
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Algaebase