Editing Linnaean taxonomy (section)

== Rank-based scientific classification ==
{{Main|Taxonomy (biology)}}

This rank-based method of classifying living organisms was originally popularized by (and much later named for) 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 second term, which together uniquely identify each [[species]] of organism within a kingdom. For example, the [[human]] species is uniquely identified within the animal kingdom by the name ''Homo sapiens''. No other species of animal can have this same [[binomen]] (the technical term for a binomial in the case of animals). Prior to Linnaean taxonomy, animals were classified according to their mode of movement.

Linnaeus's use of binomial nomenclature was anticipated by the theory of definition used in [[Scholasticism]]. Scholastic logicians and philosophers of nature defined the species human, for example, as ''Animal rationalis'', where ''animal'' was considered a genus and ''rationalis'' (Latin for "rational") the characteristic distinguishing humans from all other animals. Treating ''animal'' as the immediate genus of the species human, horse, etc. is of little practical use to the biological taxonomist, however. Accordingly, Linnaeus's classification treats ''animal'' as a class including many genera (subordinated to the animal "kingdom" via intermediary classes such as "orders"), and treats ''homo'' as the genus of a species ''Homo sapiens'', with ''sapiens'' (Latin for "knowing" or "understanding") playing a differentiating role analogous to that played, in the Scholastic system, by ''rationalis'' (the word ''homo'', Latin for "human being", was used by the Scholastics to denote a species, not a genus).

A strength of Linnaean taxonomy is that it can be used to organize the different kinds of living [[organism]]s, simply and practically. Every species can be given a unique (and, one hopes, stable) name, as 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 [[Systematics|systematists]] (biologists specializing in taxonomy), not merely of the binomial names themselves, but of the rules governing the use of these names, which are laid down in formal [[nomenclature code]]s.

Species can be placed in a [[taxonomic rank|ranked]] [[hierarchy]], starting with either ''[[Domain (biology)|domains]]'' or ''kingdoms''. Domains are divided into [[Kingdom (biology)|kingdoms]]. Kingdoms are divided into ''[[phylum|phyla]]'' (singular: ''phylum'') — for [[animal]]s; the term ''division'', used for [[plant]]s 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 ''[[Class (biology)|classes]]'', and they, in turn, into ''[[Order (biology)|orders]]'', ''[[Family (biology)|families]]'', ''[[genus|genera]]'' (singular: ''genus''), and ''[[species]]'' (singular: ''species''). There are ranks below species: in zoology, ''subspecies'' (but see ''[[form (zoology)|form]]'' or ''[[morph (zoology)|morph]]''); in botany, ''variety'' (varietas) and ''form'' (forma), etc.

Groups of organisms at any of these ranks are called ''taxa'' (singular: ''[[taxon]]'') or ''taxonomic groups''.

The Linnaean system has proven robust and it remains the only extant working classification system at present that enjoys universal scientific acceptance. However, although the number of ranks is unlimited, in practice any classification becomes more cumbersome the more ranks are added. Among the later subdivisions that have arisen are such entities as phyla, families, and tribes, as well as any number of ranks with prefixes (superfamilies, subfamilies, etc.). The use of newer taxonomic tools such as [[cladistics]] and [[phylogenetic nomenclature]] has led to a different way of looking at evolution (expressed in many nested [[clade]]s) and this sometimes leads to a desire for more ranks. An example of such complexity is the [[Mammal classification#McKenna.2FBell classification|scheme for mammals]] proposed by McKenna and Bell.

=== Alternatives ===
Over time, 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, following the 1859 publication of Charles Darwin's ''[[On the Origin of Species]]''. It then became generally understood that classifications ought to reflect the [[phylogeny]] of organisms, their descent by evolution. This led to [[evolutionary taxonomy]], where the various [[extant taxon|extant]] and [[extinction|extinct]] are linked together to construct a phylogeny. This is largely what is meant by the term 'Linnaean taxonomy' when used in a modern context.
In [[cladistics]], originating in the work of [[Willi Hennig]], 1950 onwards, each taxon is grouped so as to include the common ancestor of the group's members (and thus to avoid [[phylogeny]]). Such taxa may be either [[monophyly|monophyletic]] (including all descendants) such as genus ''[[Homo]]'', or [[paraphyly|paraphyletic]] (excluding some descendants), such as genus ''[[Australopithecus]]''.

Originally, Linnaeus established three kingdoms in his scheme, namely for [[Plant]]s, [[Animal]]s 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 [[prokaryote]]s (i.e., bacteria); [[Protist]]a, for protozoans and most algae; and [[fungus|Fungi]].  This five-kingdom scheme is still far from the [[phylogenetics|phylogenetic]] ideal and has largely been supplanted in modern taxonomic work by a division into three domains: [[Bacterium|Bacteria]] and [[Archaea]], which contain the prokaryotes, and [[Eukaryote|Eukaryota]], comprising the remaining forms. These arrangements should not be seen as definitive. They are based on the [[genome]]s of the organisms; as knowledge on this increases, classifications will change.<ref>{{cite journal|author1=Embley, T. A.  |author2=Martin, W. |name-list-style=amp|date=2006 |title=Eukaryotic evolution, changes and challenges. |journal=Nature |volume=440 |issue=7084 |pages=623–630 |doi=10.1038/nature04546 |pmid=16572163 |s2cid=4396543 |url=http://www.nature.com/scitable/content/eukaryotic-evolution-changes-and-challenges-13997647|url-access=subscription }}</ref>

Representing presumptive evolutionary relationships within the framework of Linnaean taxonomy is sometimes seen as problematic, especially given the wide acceptance of [[cladistic]] methodology and numerous [[molecular phylogenetic|molecular phylogenies]] that have challenged long-accepted classifications. Therefore, some systematists have proposed a [[PhyloCode]] to replace it.