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Science of naming, defining and classifying organisms

In biology, taxonomy is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive 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 ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evolutionary relationships among organisms, both living and extinct.

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 lead to a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa.

The term "alpha taxonomy" is primarily used to refer to the discipline of finding, describing, and naming taxa, particularly species. 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. there is an increasing desire amongst taxonomists to consider their problems from wider viewpoints, to investigate the possibilities of closer co operation with their cytological, ecological and genetics colleagues and to acknowledge that some revision or expansion, perhaps of a drastic nature, of their aims and methods, may be desirable Turrill (1935) has suggested that while accepting the older invaluable taxonomy, based on structure, and conveniently designated "alpha", it is possible to glimpse a far distant taxonomy built upon as wide a basis of morphological and physiological facts as possible, and one in which "place is found for all observational and experimental data relating, even if indirectly, to the constitution, subdivision, origin, and behaviour of species and other taxonomic groups". Ideals can, it may be said, never be completely realized. They have, however, a great value of acting as permanent stimulants, and if we have some, even vague, ideal of an "omega" taxonomy we may progress a little way down the Greek alphabet. Some of us please ourselves by thinking we are now groping in a "beta" taxonomy. 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. He further excludes phylogenetic reconstruction from alpha taxonomy. 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. An understanding of the biological meaning of variation and of the evolutionary origin of groups of related species is even more important for the second stage of taxonomic activity, the sorting of species into groups of relatives ("taxa") and their arrangement in a hierarchy of higher categories. This activity is what the term classification denotes; it is also referred to as "beta taxonomy".

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. By extension, macrotaxonomy is the study of groups at the higher taxonomic ranks subgenus and above,

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, with the possible exception of Aristotle, whose works hint at a taxonomy. 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 for plants (Linnaeus's 1735 classification of animals was entitled "Systema Naturae" ("the System of Nature"), implying that he, at least, believed that it was more than an "artificial system"). 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 classifications described empirical patterns and were pre evolutionary in thinking. The publication of Charles Darwin's On the Origin of Species (1859) led to a new explanation for classifications, 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 cladistic methodology in the 1970s led to classifications based on the sole criterion of monophyly, supported by the presence of synapomorphies. Since then, the evidentiary basis has been expanded with data from molecular genetics that for the most part complements traditional morphology.

Naming and classifying human surroundings likely began with the onset of language. Distinguishing poisonous plants from edible plants is integral to the survival of human communities. 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.

Organisms were first classified by Aristotle (Greece, 384–322 BC) during his stay on the Island of Lesbos. He divided all living things into two groups: plants and animals. His student Theophrastus (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum. Several plant genera can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus. His magnum opus De Plantis came out in 1583, and described more than 1500 plant species. Two large plant families that he first recognized are in use: the Asteraceae and Brassicaceae. In the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works. Arguably his greatest accomplishment was Methodus Plantarum Nova (1682), 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). 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. Species Plantarum in 1753, and Systema Naturae 10th Edition, he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species, 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 (known as the Linnaean system). Names published before these dates are referred to as "pre Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar). Even taxonomic names published by Linnaeus himself before these dates are considered pre Linnaean. With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent. 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. 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. 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. 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. The cladistic method has emerged since the 1960s. Groups that have descendant groups removed from them are termed paraphyletic,

Cladistic classifications are compatible with traditional Linnean taxonomy and the Codes of Zoological and Botanical nomenclature, to a certain extent. An alternative system of nomenclature, the International Code of Phylogenetic Nomenclature or PhyloCode has been proposed, which regulates the formal naming of clades. for over 250 years.

Well before discovery of Carl Linnaeus (Botanist) plants and animals were considered separate Kingdoms. Unreliable source: date=April 2017 Linnaeus used this as the top rank, dividing the physical world into the vegetable, animal and mineral kingdoms. As advances in microscopy made the classification of microorganisms possible, the number of kingdoms increased, five and six kingdom systems being the most common. Domains are a relatively new grouping. First proposed in 1977, Carl Woese's three domain system was not generally accepted until later. 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), A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method. proposed that the Neomura, the clade that groups together the Archaea and Eucarya, would have evolved from Bacteria, more precisely from Actinomycetota. His 2004 classification treated the archaeobacteria as part of a subkingdom of the kingdom Bacteria, i. e., he rejected the three domain system entirely.

Partial classifications exist for many individual groups of organisms and are revised and replaced as new information becomes available; however, comprehensive, published treatments of most or all life are rarer; recent examples are that of Adl et al., 2012 and 2019, which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015, covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives. covers extant taxa to the rank of Family. Other, database driven treatments include the Encyclopedia of Life, the Global Biodiversity Information Facility, the NCBI taxonomy database, the Interim Register of Marine and Nonmarine Genera, the Open Tree of Life, and the Catalogue of Life. The Paleobiology Database is a resource for fossils.

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. 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.

Biological classification is a critical component of the taxonomic process. As a result, it informs the user as to what the relatives of the taxon are hypothesized to be. Biological classification uses taxonomic ranks, including among others (in order from most inclusive to least inclusive): Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species, and Strain. This ranking system, except for "Strain", can be remembered by the mnemonic "Do Kings Play Chess On Fine Glass Sets?"

An "authority" may be placed after a scientific name. The authority is the name of the scientist or scientists who first validly published the name. The names of authors are often 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). The system for assigning authorities differs slightly between botany and zoology.

In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships. However, certain phenetic methods, such as neighbor joining, have persisted, as rapid estimators of relationships when more advanced methods (such as Bayesian inference) are too computationally expensive.

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