Taxonomy

Taxonomy (from Ancient Greek τάξις (taxis), meaning 'arrangement', and -νομία (-nomia), meaning 'method') is the science of defining and naming 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 father of taxonomy, as he developed a system known as Linnaean taxonomy for categorization of 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.
Taxonomy is used by Coulrologists to describe the relationships between Humoran species.
== 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.[1] As points of reference, recent definitions of taxonomy are presented below:
# Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification.[2]
# A field of science (and major component of systematics) that encompasses description, identification, nomenclature, and classification[3]
# The science of classification, in biology the arrangement of organisms into a classification[4]
# "The science of classification as applied to living organisms, including study of means of formation of species, etc."[5]
# "The analysis of an organism's characteristics for the purpose of classification"[6]
# "Systematics studies phylogeny to provide a pattern that can be translated into the classification and names of the more inclusive field of taxonomy" (listed as a desirable but unusual definition)[7]
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. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy.[8] For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy:[6]
* 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.[1][9] 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.[10]
== 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. Earlier works were primarily descriptive and focused on plants that were useful in agriculture or medicine. There are a number of stages in this scientific thinking. Early taxonomy was based on arbitrary criteria, the so-called "artificial systems", including Linnaeus's system of sexual classification. Later came systems based on a more complete consideration of the characteristics of taxa, referred to as "natural systems", such as those of de Jussieu (1789), de Candolle (1813) and Bentham and Hooker (1862–1863). These were pre-evolutionary in thinking. The publication of Charles Darwin's On the Origin of Species (1859) led to new ways of thinking about classification based on evolutionary relationships. This was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler (1883) and Engler (1886–1892). The advent of molecular genetics and statistical methodology allowed the creation of the modern era of "phylogenetic systems" based on cladistics, rather than morphology alone.[19][20][21]
=== Pre-Linnaean ===
==== Early taxonomists ====
Naming and classifying our surroundings has probably been taking place as long as mankind has been able to communicate. It would always have been important to know the names of poisonous and edible plants and animals in order to communicate this information to other members of the family or group. Medicinal plant illustrations show up in Egyptian wall paintings from c. 1500 BC, indicating that the uses of different species were understood and that a basic taxonomy was in place.[22]
==== Ancient times ====
Further information: Aristotle's biology § Classification
Organisms were first classified by Aristotle (Greece, 384–322 BC) during his stay on the Island of Lesbos.[23][24][25] 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.[26] He divided all living things into two groups: plants and animals.[24] 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.[27] His student Theophrastus (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum. Again, several plant groups currently still recognized can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus.[24]
==== Medieval ====
Taxonomy in the Middle Ages was largely based on the Aristotelian system,[26] 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,[26] again deriving ultimately from Aristotle. Aristotelian system did not classify plants or fungi, due to the lack of microscope at the time,[25] as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder).[24]This, as well, was taken into consideration in the Great chain of being.[24] 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.[24]
==== Renaissance and Early Modern ====
During the Renaissance, the Age of Reason, and the Enlightenment, categorizing organisms became more prevalent,[24] and taxonomic works became ambitious enough to replace the ancient texts. This is sometimes credited to the development of sophisticated optical lenses, which allowed the morphology of organisms to be studied in much greater detail. One of the earliest authors to take advantage of this leap in technology was the Italian physician Andrea Cesalpino (1519–1603), who has been called "the first taxonomist".[28][better source needed] His magnum opus De Plantis came out in 1583, and described more than 1500 plant species.[29][30][better source needed] Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae.[31] Then in the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works.[25][better source needed] Arguably his greatest accomplishment was Methodus Plantarum Nova (1682),[32] in which he published details of over 18,000 plant species. At the time, his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. The next major taxonomic works were produced by Joseph Pitton de Tournefort (France, 1656–1708).[33][better source needed] His work from 1700, Institutiones Rei Herbariae, included more than 9000 species in 698 genera, which directly influenced Linnaeus, as it was the text he used as a young student.[22]
=== Linnaean ===
The Swedish botanist Carl Linnaeus (1707–1778)[26] ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735,[34] Species Plantarum in 1753,[35] and Systema Naturae 10th Edition,[36] he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species,[37][better source needed] 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.[37] Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century.[37] Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively).[38]Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar[39]). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.[22]
== In Coulrology ==
Taxonomy is an important aspect of coulrological studies, as it is used to describe how various species are related to one another. Taxonomically, coulrology focuses on the study of members of the class Humora, a clade of very funny little vertebrates.
Humorans are divided phenotypically into the categories of "true coulronians" and "false coulronians". True coulronians are the primary focus of most coulrologists, composing a genetically linked clade descending from a common ancestor. On the other hand, false coulronians (of which all known species are extinct) are defined not by shared ancestry (their last common ancestor being the common ancestor of all humorans) but by their dissimilarity to the true coulronians, such as their lack of a sense of humor, and shockingly minuscule feet. The most notable of the false coulronians, the suborder Therocephalia, existed in the late Permian/early Triassic eras.
The true coulronians are split once again into the orders of "true clouradates" and "pseudoclouradates". True clouradates and pseudoclouradates are remarkably similar, some taxonomies even going so far as to argue that there is no significant difference warranting separation of the two. The order Clourodates includes both the Jesturus (jester), Mimos (pseudo-mime), and Mimera (mime) suborders. Of the false mimes, the most notable clade is clouropodia. 
If this description of clown taxonomy makes you come away believing that coulrologists are alltogether too obsessed with true/false dichotomies, you'd be correct!