Linnaean taxonomy

Linnaean taxonomy is a method of classifying living things originally devised by, and named for, Carl von Linn&eacute; (born Carl Linn&aelig;us), 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 animal can have this binomial appellation. Prior to Linnaeus, animals were classified according to their mode of movement.

All species are classified in a ranked hierarchy, originally starting with kingdoms, although the domain has since been added as a rank above kingdoms. There are three domains: Eukarya, Archaea, and Bacteria (the latter two are both made up of prokaryotes, but having them in one Prokarya kingdom would just be too simple and easy-to-understand for biologists). Kingdoms are divided into phyla (singular: phylum) &mdash; for animals; the term division, used for plants, 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, 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 (singular: phylum), 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 extant knowledge concerning those species and their relationships to each other, will inevitably make use of the additional hierarchical levels, particularly if integration of living organisms with fossils is performed, and the application of newer classification tools such as cladistics to facilitate this takes place.

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.

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


 * Domain: Eukarya (cells with a nucleus inside)
 * Kingdom: Animalia (with eukaryotic cells having cell membrane but lacking a cell wall, multicellular, heterotrophic)
 * Superphylum: Deuterostomia (Embryo develops an anus followed by a mouth)
 * 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)
 * Infraphylum: Gnathostomata (has a jaw)
 * Superclass: Tetrapoda (having limbs with digits and breathing air through lungs)
 * Class: Mammalia (warm-blooded vertebrates with hair and mammary glands which, in females, secrete milk to nourish young, also with middle ear bones, dentary-squamosal jaw joints instead of articular-quadrate, prismatic enamel, 2 occipital condyles, and a neocortex in the brain)
 * Subclass: Placentalia (giving birth to live young after a full internal gestation period, lacking an epipubic bone, having wide pelvises, possessing a corpus callosum in their brains, and having a malleolus at the bottom of the fibula)
 * Superorder: Euarchontoglires (posessing a vermiform appendix and notched incisors)
 * 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)
 * Subspecies: Homo sapiens sapiens (behavioral modernity)

(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 the genus Homo, or paraphyletic (excluding some descendants), such as genus Australopithecus. In the field of phylogenetics, only monophyletic groups are considered legitimate, while paraphyletic groups require taxonomic revision.

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. 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. Even with evolutionary relationships straightened out, there is some debate over how to group organisms to best reflect those relationships. For example, some scientists advocate placing chimpanzees into the genus Homo, as they are more closely related to humans than to other great apes.

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)

Appendix: taxonomic ranks
A summary of this scheme, from most general to most specific, is laid out below. Note that the links are to Wikipedia, not RationalWiki pages.


 *  (or )
 * Branch
 *  (or )
 * (zoology)
 * Division (zoology)
 * (zoology)
 * (turtles)
 * (turtles)
 * (turtles)
 * (turtles)
 * (mammals)
 * (or Series for fishes)
 * (position in some zoological classifications)
 * (zoology)
 * (zoology)
 * (zoology)
 * (usual position)
 * (zoology)
 * Division (zoology)
 * Subdivision (zoology)
 * Section (zoology)
 * Subsection (zoology)
 * (zoology)
 * (zoology)
 * (zoology)
 * (zoology)
 * (zoology)
 * Series (for Lepidoptera)
 * Group (for Lepidoptera)
 * Section (botany)
 * Subsection (botany)
 * Species
 * (botany)
 * (botany)
 * (zoology)
 * (bacteria)
 * (fungi)
 * (zoology)
 * (zoology)
 * (usual position)
 * (zoology)
 * Division (zoology)
 * Subdivision (zoology)
 * Section (zoology)
 * Subsection (zoology)
 * (zoology)
 * (zoology)
 * (zoology)
 * (zoology)
 * (zoology)
 * Series (for Lepidoptera)
 * Group (for Lepidoptera)
 * Section (botany)
 * Subsection (botany)
 * Species
 * (botany)
 * (botany)
 * (zoology)
 * (bacteria)
 * (fungi)
 * Section (botany)
 * Subsection (botany)
 * Species
 * (botany)
 * (botany)
 * (zoology)
 * (bacteria)
 * (fungi)
 * (botany)
 * (botany)
 * (zoology)
 * (bacteria)
 * (fungi)
 * (fungi)
 * (fungi)
 * (fungi)

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.