Linnaean taxonomy

Linnaean taxonomy is a method of classifying living things, originally devised by (and named for) Carl Linnaeus, although it has changed considerably since his time. The greatest innovation of Linnaeus, and still the most important aspect of this system, is the general use of binomial nomenclature, the combination of a genus name and a single specific epithet to uniquely identify each species of organism. For example, the human species is uniquely identified by the binomial Homo sapiens. No other species of organism can have this binomial. Prior to Linnaean taxonomy, animals were classified according to their mode of movement.

All species are classified in a ranked hierarchy, originally starting with kingdoms although domains have since been added as a rank above the kingdoms. Kingdoms are divided into phyla (singular: phylum) &mdash; for animals; the term division, used for plants and fungi, is equivalent to the rank of phylum (and the current International Code of Botanical Nomenclature allows the use of either term). Phyla (or divisions) are divided into classes, and they, in turn, into orders, families, genera (singular: genus), and species (singular: species).

Though the Linnaean system has proven robust, expansion of knowledge has led to an expansion of the number of hierarchical levels within the system, increasing the administrative requirements of the system (see, for example, ICZN), though it remains the only extant working classification system at present that enjoys universal scientific acceptance. Among the later subdivisions that have arisen are such entities as phyla, superclasses, superorders, infraorders, families, superfamilies and tribes. Many of these extra hierarchical levels tend to arise in disciplines such as entomology, whose subject matter is replete with species requiring classification. Any biological field that is species rich, or which is subject to a revision of the state of current knowledge concerning those species and their relationships to each other, will inevitably make use of the additional hierarchical levels, particularly when fossil forms are integrated into classifications originally designed for extant living organisms, and when newer classification tools such as cladistics are applied to facilitate this.

There are ranks below species: in zoology, subspecies and morph; in botany, variety (varietas) and form (forma). Many botanists now use "subspecies" instead of "variety" although the two are not, strictly speaking, of equivalent rank, and "form" has largely fallen out of use.

Groups of organisms at any of these ranks are called taxa (singular: taxon), or phyla, or taxonomic groups.

Taxonomic ranks
A summary of this scheme, from most general to most specific, would be:


 * Dominion
 * Domain (or Superkingdom)
 * Kingdom
 * Subkingdom
 * Branch
 * Infrakingdom
 * Superphylum (or Superdivision in botany)
 * Phylum (or Division in botany)
 * Subphylum (or Subdivision in botany)
 * Infraphylum (or Infradivision in botany)
 * Microphylum
 * Supercohort (botany)
 * Cohort (botany)
 * Subcohort (botany)
 * Infracohort (botany)
 * Superclass
 * Class
 * Subclass
 * Infraclass
 * Parvclass
 * Superdivision (zoology)
 * Division (zoology)
 * Subdivision (zoology)
 * Infradivision (zoology)
 * Superlegion (zoology)
 * Legion (zoology)
 * Sublegion (zoology)
 * Infralegion (zoology)
 * Supercohort (zoology)
 * Cohort (zoology)
 * Subcohort (zoology)
 * Infracohort (zoology)
 * Gigaorder (zoology)
 * Magnorder or Megaorder (zoology)
 * Grandorder or Capaxorder (zoology)
 * Mirorder or Hyperorder (zoology)
 * Superorder
 * Series (for fishes)
 * Order
 * Parvorder (position in some zoological classifications)
 * Nanorder (zoology)
 * Hypoorder (zoology)
 * Minorder (zoology)
 * Suborder
 * Infraorder
 * Parvorder (usual position) or Microorder (zoology)
 * Section (zoology)
 * Subsection (zoology)
 * Gigafamily (zoology)
 * Megafamily (zoology)
 * Grandfamily (zoology)
 * Hyperfamily (zoology)
 * Superfamily
 * Epifamily (zoology)
 * Series (for Lepidoptera)
 * Group (for Lepidoptera)
 * Family
 * Subfamily
 * Infrafamily
 * Supertribe
 * Tribe
 * Subtribe
 * Infratribe
 * Genus
 * Subgenus
 * Section (botany)
 * Subsection (botany)
 * Series (botany)
 * Subseries (botany)
 * Superspecies or Species-group
 * Species
 * Subspecies (or Forma Specialis for fungi, or Variety for bacteria )
 * Variety (botany) or Form/Morph (zoology)
 * Subvariety (botany)
 * Form (botany)
 * Subform (botany)

Of these many ranks, the only one that has an exact biological definition is species. The other levels are intended to represent the phylogeny of the organisms under discussion, and are to some extent a matter of judgement. For most groups of organisms, not all the ranks would actually be used; they have been defined to deal with the most complicated cases, such as insects and vertebrates.

Example classification: humans
As an example, consider the Linnaean classification for modern humans:


 * Dominion: Terroa (uses double-helix DNA to store hereditary information and creates proteins using the twenty left-handed amino acids)
 * Domain: Eukaryota (organisms which have cells with a nucleus)
 * Kingdom: Animalia (with eukaryotic cells having cell membrane but lacking cell wall, multicellular, heterotrophic)
 * Phylum: Chordata (animals with a notochord, dorsal nerve cord, and pharyngeal gill slits, which may be vestigial)
 * Subphylum: Vertebrata (possessing a backbone, which may be cartilaginous, to protect the dorsal nerve cord)
 * Class: Mammalia (endothermic vertebrates with hair and mammary glands which, in females, secrete milk to nourish young)
 * Cohort: Placentalia (giving birth to live young after a full internal gestation period)
 * Order: Primates (collar bone, eyes face forward, grasping hands with fingers, and two types of teeth: incisors and molars)
 * Family: Hominidae (upright posture, large brain, stereoscopic vision, flat face, hands and feet have different specializations)
 * Genus: Homo (s-curved spine, "man")
 * Species: Homo sapiens (high forehead, well-developed chin, skull bones thin)

(Note that this makes use of the customary visible diagnostic characters.)

Nomenclature
A strength of Linnaean taxonomy is that it can be used to develop a simple and practical system for organizing the different kinds of living organisms. Every species is given a unique and stable name (compared with common names that are often neither unique nor consistent from place to place and language to language). This uniqueness and stability are, of course, a result of the acceptance by working systematists (biologists specializing in taxonomy); not merely of the binomial nomenclature in itself, but of much more complex codes of rules and procedures governing the use of these names.

These rules are governed by formal codes of biological nomenclature. The rules governing the nomenclature and classification of plants and fungi are contained in the International Code of Botanical Nomenclature, maintained by the International Association for Plant Taxonomy. The current code, the "Saint Louis Code" was adopted in 1999 and supersedes the "Tokyo code". The corresponding code for animals is the International Code of Zoological Nomenclature (ICZN], also last revised in 1999, and maintained by the International Commission on Zoological Nomenclature. The code for bacteria is the International Code of Nomenclature of Bacteria (ICNB), last revised in 1990, and maintained by the International Committee on Systematics of Prokaryotes (ICSP).  There is also a code for virus nomenclature, the Universal Virus Database of the International Committee on Taxonomy of Viruses (ICTVdB) although it is organized on somewhat different principles, as the evolutionary history of these forms is not understood.

Later developments since Linnaeus
Over time, our understanding of the relationships between living things has changed. Linnaeus could only base his scheme on the structural similarities of the different organisms. The greatest change was the widespread acceptance of evolution as the mechanism of biological diversity and species formation. It then became generally understood that classifications ought to reflect the phylogeny of organisms, by grouping each taxon so as to include the common ancestor of the group's members (and thus to avoid polyphyly). Such taxa may be either monophyletic (including all descendants) such as genus Homo, or paraphyletic (excluding some descendants), such as genus Australopithecus.

Originally, Linnaeus established three kingdoms in his scheme, namely Plantae, Animalia and an additional group for minerals, which has long since been abandoned. Since then, various life forms have been moved into three new kingdoms: Monera, for prokaryotes (i.e., bacteria); Protista, for protozoans and most algae; and Fungi. This five kingdom scheme is still far from the phylogenetic ideal and has largely been supplanted in modern taxonomic work by a division into three domains: Bacteria and Archaea, which contain the prokaryotes, and Eukaryota, comprising the remaining forms. This change was precipitated by the discovery of the Archaea. These arrangements should not be seen as definitive. They are based on the genomes of the organisms; as knowledge on this increases, so will the categories change.

Reflecting truly evolutionary relationships, especially given the wide acceptance of cladistic methodology and numerous molecular phylogenies that have challenged long-accepted classifications, has proved problematic within the framework of Linnaean taxonomy. Therefore, some systematists have proposed a Phylocode to replace it.

Quotations

 * "Taxonomy (the science of classification) is often undervalued as a glorified form of filing&mdash;with each species in its prescribed place in an album; but taxonomy is a fundamental and dynamic science, dedicated to exploring the causes of relationships and similarities among organisms. Classifications are theories about the basis of natural order, not dull catalogues compiled only to avoid chaos." Stephen Jay Gould (1990, p.98)