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In biology, taxonomy (from Ancient Greek τάξις (taxis), meaning 'arrangement', and -νομία (-nomia), meaning 'method') is the science of naming, defining (circumscribing) and classifying groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super-group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.

With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct.

Definition


The exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception, naming, and classification of groups of organisms.[2] As points of reference, recent definitions of taxonomy are presented below:

The varied definitions either place taxonomy as a sub-area of systematics (definition 2), invert that relationship (definition 6), or appear to consider the two terms synonymous.

  • Systematics: "The study of the identification, taxonomy, and nomenclature of organisms, including the classification of living things with regard to their natural relationships and the study of variation and the evolution of taxa".

A whole set of terms including taxonomy, systematic biology, systematics, biosystematics, scientific classification, biological classification, and phylogenetics have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting.[2][10] The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 by de Candolle, in his Théorie élémentaire de la botanique.[11]

A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular taxon. This analysis may be executed on the basis of any combination of the various available kinds of characters, such as morphological, anatomical, palynological, biochemical and genetic. A monograph or complete revision is a revision that is comprehensive for a taxon for the information given at a particular time, and for the entire world. Other (partial) revisions may be restricted in the sense that they may only use some of the available character sets or have a limited spatial scope. A revision results in a conformation of or new insights in the relationships between the subtaxa within the taxon under study, which may result in a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa.[12]

The term "alpha taxonomy" is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species.[13] In earlier literature, the term had a different meaning, referring to morphological taxonomy, and the products of research through the end of the 19th century.[14]

William Bertram Turrill introduced the term "alpha taxonomy" in a series of papers published in 1935 and 1937 in which he discussed the philosophy and possible future directions of the discipline of taxonomy.[15]

Turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology.

Later authors have used the term in a different sense, to mean the delimitation of species (not subspecies or taxa of other ranks), using whatever investigative techniques are available, and including sophisticated computational or laboratory techniques.[16][13] Thus, Ernst Mayr in 1968 defined "beta taxonomy" as the classification of ranks higher than species.[17]

How species should be defined in a particular group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy.[18][19][13] By extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species.[13]

History


While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, a truly scientific attempt to classify organisms did not occur until the 18th century.

Naming and classifying our surroundings has probably been taking place as long as mankind has been able to communicate.

Organisms were first classified by Aristotle (Greece, 384–322 BC) during his stay on the Island of Lesbos.[24][25][26] He classified beings by their parts, or in modern terms attributes, such as having live birth, having four legs, laying eggs, having blood, or being warm-bodied.[27] He divided all living things into two groups: plants and animals.[25] Some of his groups of animals, such as Anhaima (animals without blood, translated as invertebrates) and Enhaima (animals with blood, roughly the vertebrates), as well as groups like the sharks and cetaceans, are still commonly used today.[28] Theophrastus]](Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his urrently still recognized can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus.[25]

Taxonomy in the Middle Ages was largely based on the Aristotelian system,[27] with additions concerning the philosophical and existential order of creatures. This included concepts such as the Great chain of being in the Western scholastic tradition,[27] again deriving ultimately from Aristotle. Aristotelian system did not classify plants or fungi, due to the lack of microscope at the time,[26] as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder).[25] This, as well, was taken into consideration in the Great chain of being.[25] Advances were made by scholars such as Procopius, Timotheos of Gaza, Demetrios Pepagomenos, and Thomas Aquinas. Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy.[25]

During the Renaissance, the Age of Reason, and the Enlightenment, categorizing organisms became more prevalent,[25] and taxonomic works became ambitious enough to replace the ancient texts.

The Swedish botanist Carl Linnaeus (1707–1778)[27] ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735,[35]Systema%20naturae%2C%20sive%20regna%20t]] Species Plantarum[36]Systema Naturae 10th Edition10th Edition]]cies,[38] which proved to be an elegant solution to a chaotic and disorganized taxonomic literature. He not only introduced the standard of class, order, genus, and species, but also made it possible to identify plants and animals from his book, by using the smaller parts of the flower.[38] Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century.[38] Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively).[39] Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar[40]). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.[23]

Modern system of classification


Whereas Linnaeus aimed simply to create readily identifiable taxa, the idea of the Linnaean taxonomy as translating into a sort of dendrogram of the animal and plant kingdoms was formulated toward the end of the 18th century, well before On the Origin of Species was published.[26] Among early works exploring the idea of a transmutation of species were Erasmus Darwin's 1796 Zoönomia and Jean-Baptiste Lamarck's Philosophie Zoologique of 1809.[13] The idea was popularized in the Anglophone world by the speculative but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844.[41]

With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent.[42] Tree of life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds.[43] Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842.[44][45] The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, palaeontologists worked to understand the history of animals through the ages by linking together known groups.[46] With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of the evolution of the major groups was in place. As evolutionary taxonomy is based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use.[47]

The cladistic method has emerged since the 1960s.[42] In 1958, Julian Huxley used the term clade.[13] Later, in 1960, Cain and Harrison introduced the term cladistic.[13] The salient feature is arranging taxa in a hierarchical evolutionary tree, ignoring ranks.[42] A taxon is called monophyletic, if it includes all the descendants of an ancestral form.[48][49] Groups that have descendant groups removed from them are termed paraphyletic,[48] while groups representing more than one branch from the tree of life are called polyphyletic.[48][49] The International Code of Phylogenetic Nomenclature or PhyloCode is intended to regulate the formal naming of clades.[50][51] Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes.[51]

Well before Linnaeus, plants and animals were considered separate Kingdoms.[52] Linnaeus used this as the top rank, dividing the physical world into the plant, animal and mineral kingdoms.

Domains are a relatively new grouping. First proposed in 1977, Carl Woese's three-domain system was not generally accepted until later.[53] One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera),[52] with the Eukaryota for all organisms whose cells contain a nucleus.[54] A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.[52]

Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade that groups together the Archaea and Eucarya, would have evolved from Bacteria, more precisely from Actinobacteria. His 2004 classification treated the archaeobacteria as part of a subkingdom of the kingdom Bacteria, i.e. he rejected the three-domain system entirely.[55] Stefan Luketa in 2012 proposed a five "dominion" system, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains.[56]

Partial classifications exist for many individual groups of organisms and are revised and replaced as new information becomes available; however, comprehensive treatments of most or all life are rarer; two recent examples are that of Adl et al., 2012,[64] which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015,[63] covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives.[63]

Application


Biological taxonomy is a sub-discipline of biology, and is generally practiced by biologists known as "taxonomists", though enthusiastic naturalists are also frequently involved in the publication of new taxa.[66] Because taxonomy aims to describe and organize life, the work conducted by taxonomists is essential for the study of biodiversity and the resulting field of conservation biology.[67][68]

Biological classification is a critical component of the taxonomic process.

The "definition" of a taxon is encapsulated by its description or its diagnosis or by both combined.

The initial description of a taxon involves five main requirements:[72]

However, often much more information is included, like the geographic range of the taxon, ecological notes, chemistry, behavior, etc. How researchers arrive at their taxa varies: depending on the available data, and resources, methods vary from simple quantitative or qualitative comparisons of striking features, to elaborate computer analyses of large amounts of DNA sequence data.[73]

An "authority" may be placed after a scientific name.[74] The authority is the name of the scientist or scientists who first validly published the name.[74] For example, in 1758 Linnaeus gave the Asian elephant the scientific name Elephas maximus, so the name is sometimes written as "Elephas maximus Linnaeus, 1758".[75] The names of authors are frequently abbreviated: the abbreviation L., for Linnaeus,* is commonly used. In botany, there is, in fact, a regulated list of standard abbreviations (see list of botanists by author abbreviation).[76] The system for assigning authorities differs slightly between botany and zoology.[9] However, it is standard that if a species' name or placement has been changed since the original description, the original authority's name is placed in parentheses.[77]

Phenetics


In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships.[13] It results in a measure of evolutionary "distance" between taxa.

Databases


Modern taxonomy uses database technologies to search and catalogue classifications and their documentation.[80] While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life, which attempts to list every documented species.[81] The catalogue listed 1.64 million species for all kingdoms as of April 2016, claiming coverage of more than three quarters of the estimated species known to modern science.[82]

See also


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