Taxonomy (Biology)

Taxonomy is the classification of organisms in an ordered system that indicates natural relationships. It is a subdiscipline of Systematics which is the study of those relationships. The word taxonomy is also used in non-biological contexts in to describe any system of classification. Nomenclature is the study of names of organisms (not the organisms themselves) and is a subdiscipline of taxonomy. Often you'll see a reference to "taxonomy and nomenclature" or "systematics and taxonomy".

The nomenclature of biological taxonomy is based on Latin, though since the beginning, errors and inconsistencies have crept in, so it is not completely compliant with the grammar or usage of Latin.

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Carl Linne (1707-1778), who wrote as Carolus Linnaeus, was a Swedish botanist who developed the taxonomic system, called binomial nomenclature, that is used throughout Biology. His original system was first published in 1735 under the title Systema Naturae. The system has evolved over time, but remains essentially the same.

At the top, the Linnaean system designates six Kingdoms: Plantae (plants), Animalia (animals), Fungi (mushrooms and other fungi), Chromista (brown algae and others), and Bacteria (prokaryotes). The arrangement, naming and scope of each of those Kingdoms (or any grouping within them) can vary depending on the person studying and reviewing the taxonomy, especially with regards to ongoing research in the many fields of study. However, those groups are generally recognized even by those in disagreement with them.

Definitions:
- Kingdom The highest formal taxonomic classification into which organisms are grouped.
- Phylum A primary division of the kingdom ranking above a class. Botanists use the term Division.
- Class A primary taxonomic category of organisms ranking below a phylum and ranking above an order.
- Order A primary taxonomic category of organisms ranking below a class and above a family.
- Family A primary taxonomic category of organisms ranking below an order and above a genus.
- Genus A primary taxonomic category of organisms ranking below a family and above a species. It is comprised of species displaying similar characteristics. In taxonomic nomenclature, the genus is used, either alone or followed by a Latin adjective or epithet, to form the species name.
- Specific epithet The term for the uncapitalized second word used in binomial nomenclature to designate a species. In the species name Anolis carolinensis the specific epithet is the word carolinensis.
- Species A primary taxonomic category of organisms, ranking below a genus and comprised of related organisms capable of interbreeding. In writing, organisms in this category are represented in binomial nomenclature by an uncapitalized Latin adjective or noun following a capitalized genus name, as seen in Anolis carolinensis. The genus is often shorthanded, as found in A. carolinensis.
- Trinomial nomenclature A three-part taxonomic designation indicating genus, species, and subspecies, such as Anolis sagrei sagrei.
- Taxon (pl. Taxa) any grouping within the taxonomic system. Plantae is a taxon, and Anolis and Homo sapiens taken together are taxa.

Within each rank (kingdom, genus, etc.) other ranks may be recognized. The primary lesser ranks used include groups using prefixes such as "sub", "super" and "infra", such as suborder and superfamily. These are useful in grouping taxa below or above a certain major rank without changing their more formal (and usually more familiar) taxonomy. In addition to those prefixes, Tribe is another commonly used grouping above the genus level. Usually understanding the meaning of a taxonomic grouping is apparent from its use.

Examples of Linnaean Taxonomy

The usual taxonomic classifications of five species follow: the fruit fly, so familiar in genetics laboratories (Drosophila melanogaster), humans (Homo sapiens), the peas used by Gregor Mendel in his discovery of genetics (Pisum sativum), the "fly agaric" mushroom Amanita muscaria, and the bacterium Escherichia coli. The eight major ranks are given in bold; a selection of minor ranks are given as well.

Rank	Fruit Fly	Human	Pea	Fly Agaric	E. coli
Domain	Eukarya	Eukarya	Eukarya	Eukarya	Bacteria
Kingdom	Animalia	Animalia	Plantae	Fungi
Phylum or Division	Arthropoda	Chordata	Magnoliophyta	Basidiomycota	Proteobacteria
Subphylum or subdivision	Hexapoda	Vertebrata	Magnoliophytina	Hymenomycotina
Class	Insecta	Mammalia	Magnoliopsida	Homobasidiomycetae	Gammaproteobacteria
Subclass	Pterygota	Theria	Magnoliidae	Hymenomycetes
Order	Diptera	Primates	Fabales	Agaricales	Enterobacterales
Suborder	Brachycera	Haplorrhini	Fabineae	Agaricineae
Family	Drosophilidae	Hominidae	Fabaceae	Amanitaceae	Enterobacteriaceae
Subfamily	Drosophilinae	Homininae	Faboideae	Amanitoideae
Genus	Drosophila	Homo	Pisum	Amanita	Escherichia
Species	Drosophila melanogaster	Homo sapiens	Pisum sativum	Amanita muscaria	Escherichia coli

Table Notes:

The ranks of higher taxa, especially intermediate ranks, are prone to revision as new information about relationships is discovered. For example, the traditional classification of primates (class Mammalia — subclass Theria — infraclass Eutheria — order Primates) has been modified by new classifications such as McKenna and Bell ^[1] (class Mammalia — subclass Theriformes — infraclass Holotheria) with Theria and Eutheria assigned lower ranks between infraclass and the order Primates. See mammal classification ^[2] for a discussion. These differences arise mainly because there are only a small number of ranks available and a large number of branching points in the fossil record.

Within species further units may be recognised. Animals may be classified into subspecies (for example, Homo sapiens sapiens, modern humans) or morphs (for example Corvus corax varius morpha leucophaeus, the Pied Raven). Plants may be classified into subspecies (for example, Pisum sativum subsp. sativum, the garden pea) or varieties (for example, Pisum sativum var. macrocarpon, snow pea), with cultivated plants getting a cultivar name (for example, Pisum sativum var. macrocarpon 'Snowbird'). Bacteria may be classified by strains (for example Escherichia coli, a strain that can cause food poisoning).

A mnemonic for remembering the order of the taxa is:Keep Pot Clean Otherwise Family Gets Sick. Other mnemonics are available at mnemonic-device.eu Mnemonic Device and thefreedictionary.com Acronyms.

Terminations of names (suffixes)

Taxon above the genus level are often given names based on the type genus, with a standard termination. The terminations used in forming these names depend on the kingdom, and sometimes the phylum and class, as set out in the table below.

Rank	Plants	Algae	Fungi	Animals	Bacteria^[3]
Division/Phylum	-phyta		-mycota
Subdivision/Subphylum	-phytina		-mycotina
Class	-opsida	-phyceae	-mycetes		-ia
Subclass	-idae	-phycidae	-mycetidae		-idae
Superorder	-anae
Order	-ales				-ales
Suborder	-ineae				-ineae
Infraorder	-aria
Superfamily	-acea			-oidea
Epifamily				-oidae
Family	-aceae			-idae	-aceae
Subfamily	-oideae			-inae	-oideae
Infrafamily				-odd
Tribe	-eae			-ini	-eae
Subtribe	-inae			-ina	-inae
Infratribe				-ad

Table notes:

In botany and mycology names at the rank of family and below are based on the name of a genus, sometimes called the type genus of that taxon, with a standard ending. For example, the rose family Rosaceae is named after the genus Rosa, with the standard ending "-aceae" for a family. Names above the rank of family are formed from a family name, or are descriptive (like Gymnospermae or Fungi).

For animals, there are standard suffixes for taxa only up to the rank of superfamily.^[4]

The taxonomic system is based on the rules of Latin, so forming a name based on a generic name may be not straightforward. For example, the Latin "homo" has the genitive "hominis", thus the genus "Homo" (human) is in the Hominidae, not "Homidae".

The ranks of epifamily, infrafamily and infratribe (in animals) are used where the complexities of phyletic branching require finer-than-usual distinctions. Although they fall below the rank of superfamily, they are not regulated under the International Code of Zoological Nomenclature and hence do not have formal standard endings. The suffixes listed here are regular, but informal.^[5]

A Sample Taxonomy

Below is a sample taxonomy provided to show how various taxonomic ranks are used. It is used here for illustrative purposes only and may not be current or complete.

Kingdom Protista

Phylum Protozoa

Subphylum Plasmodroma

Class Mastigophora

Subclass Phytomastigina

Order Chloromonadina
Order Cryptomonadina
Order Dinoflagellata
Order Euglenoidina
Order Phytomonadina

Subclass Zoomastigina

Order Hypermastigina
Order Polymastigina
Order Protomonadina
Order Rhizomastigina

Class Sporozoa

Subclass Cnidosporidia

Order Actinomyxidia
Order Helicosporidia
Order Microsporidia
Order Myxosporidia

Subclass Haplosporidia
Subclass Sarcosporidia
Subclass Telosporidia

Order Coccidia
Order Gregarinida
Order Haemosporidia

Class Sarcodina

Order Amoebina
Order Foraminifera
Order Heliozoa
Order Mycetozoa
Order Proteomyxa
Order Radiolaria
Order Testacea

Subphylum Ciliophora

Class Ciliata

Subclass Protociliata
Subclass Euciliata

Order Chonotricha
Order Holotricha

Suborder Apostomea
Suborder Astomata
Suborder Gymnostomata
Suborder Hymenostomata
Suborder Thigmostomata

Order Peritricha

Suborder Sessilia
Suborder Mobilia

Order Spirotricha

Suborder Ctenostomata
Suborder Heterotricha
Suborder Hypotricha
Suborder Oligotricha

Class Suctoria

Kingdom Animalia

Phylum Porifera

Class Calcarea

Order Homocoela
Order Heterocoela

Class Hexactinellida

Order Hexasterophora
Order Amphidicophora

Class Demospongiae

Subclass Tetractinellida
Subclass Monaxonida
Subclass Keratosa

Phylum Coelenterata

Class Hydrozoa

Order Hydroida

Suborder Anthomedusae
Suborder Leptomedusae
Suborder Limnomedusae

Order Hydrocorallina

Suborder Milleporina
SuborderStylasterina

Order Trachylina

Suborder Trachymedusae
Suborder Narcomedusae
Suborder Pteromedusae

Order Siphonophora

Class Scyphozoa

Order Stauromedusae
Order Cubomedusae
Order Coronatae
Order Discomedusae

Suborder Semaeostomae
Suborder Rhizostomae

Class Anthozoa

Subclass Alcyonaria

Order Alcyonacea
Order Coenothecalia
Order Gorgonacea
Order Pennatulacea
Order Stolonifera
Order Telestacea

Subclass Zoantharia

Order Actiniaria

Suborder Actinaria
Suborder Ptychodactiaria
Suborder Corallimorpharia

Order Madreporaria
Order Zonanthidea
Order Antipatharia
Order Ceriantharia

References

↑ McKenna, Malcolm C., and Bell, Susan K. 1997. Classification of Mammals Above the Species Level. Columbia University Press, New York, 631 pp. ISBN 0-231-11013-8
↑ Mammal classification at Wikipedia
↑ SP Lapage, PHA Sneath, EF Lessel, VBD Skerman, HPR Seeliger, and WA Clark (editors). 1992. International Code of Nomenclature of Bacteria (Bacteriological Code, 1990 Revision). Washington (DC): ASM Press. ISBN-10: 1-55581-039-X Bacteriologocal Code (1990 Revision)
↑ ICZN article 27.2
↑ As supplied by Eugene S. Gaffney & Peter A. Meylan (1988), "A phylogeny of turtles", in M.J. Benton (ed.), The Phylogeny and Classification of the Tetrapods, Volume 1: Amphibians, Reptiles, Birds 157-219 (Oxford: Clarendon Press).

Examples of Linnaean Taxonomy

Terminations of names (suffixes)

A Sample Taxonomy

References

Further reading and resources