Taxonomy (biology)

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.[16]

Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (the phylogeny) between taxa are inferred.[17][18] Kinds of taxonomic characters include:[19]

The term "alpha taxonomy" is primarily used to refer to the discipline of finding, describing, and naming taxa, particularly species.[20] 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.[21]

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.[22]

... 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.[22]

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.[23]

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.[24][20] Thus, Ernst Mayr in 1968 defined "beta taxonomy" as the classification of ranks higher than species.[25]

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.[26][27][20] By extension, macrotaxonomy is the study of groups at the higher taxonomic ranks subgenus and above,[20] or simply in clades that include more than one taxon considered a species, expressed in terms of phylogenetic nomenclature.[28]

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.[34]

Description of rare animals (写生珍禽图), by Song dynasty painter Huang Quan (903–965)

Organisms were first classified by Aristotle (Greece, 384–322 BC) during his stay on the Island of Lesbos.[35][36][37] 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.[38] He divided all living things into two groups: plants and animals.[36]

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 commonly used.[39][40][41]

His student Theophrastus (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum. Several plant groups can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus.[36]

Taxonomy in the Middle Ages was largely based on the Aristotelian system,[38] 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,[38] again deriving ultimately from Aristotle.

The Aristotelian system did not classify plants or fungi, due to the lack of microscopes at the time,[37] as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder).[36] This, as well, was taken into consideration in the great chain of being.[36]

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.[36]

During the Renaissance and the Age of Enlightenment, categorizing organisms became more prevalent,[36] 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".[42] His magnum opus De Plantis came out in 1583, and described more than 1500 plant species.[43][44] Two large plant families that he first recognized are in use: the Asteraceae and Brassicaceae.[45]

In the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works.[37] Arguably his greatest accomplishment was Methodus Plantarum Nova (1682),[46] 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).[47] 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.[34]

Title page of Systema Naturae, Leiden, 1735

The Swedish botanist Carl Linnaeus (1707–1778)[38] ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735,[48] Species Plantarum in 1753,[49] and Systema Naturae 10th Edition,[50] he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species,[51] 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).[51]

Plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively).[52] Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar[53]). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.[34]

Modern taxonomy is heavily influenced by technology such as DNA sequencing, bioinformatics, databases, and imaging.

The basic scheme of modern classification. Many other levels can be used; domain, the highest level within life, is both new and disputed.

Well before discovery of Carl Linnaeus (Botanist) plants and animals were considered separate Kingdoms.[67] 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.[68] 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),[67] with the Eukaryota for all organisms whose cells contain a nucleus.[69] A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.[67]

Thomas Cavalier-Smith, who published extensively on the classification of protists, in 2002[70] 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.[71] 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.[72]

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,[80][81] which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015,[82] covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives.[82] A separate compilation (Ruggiero, 2014)[83] 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 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.[87][note 1]

Type specimen for Nepenthes smilesii, a tropical pitcher plant

The "definition" of a taxon is encapsulated by its description or its diagnosis or by both combined. There are no set rules governing the definition of taxa, but the naming and publication of new taxa is governed by sets of rules.[8] In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code).[88] In the fields of phycology, mycology, and botany, the naming of taxa is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN).[89]

The initial description of a taxon involves five main requirements:[90]

1. The taxon must be given a name based on the 26 letters of the Latin alphabet (a binomial for new species, or uninomial for other ranks).
2. The name must be unique (i.e. not a homonym).
3. The description must be based on at least one name-bearing type specimen.
4. It should include statements about appropriate attributes either to describe (define) the taxon or to differentiate it from other taxa (the diagnosis, ICZN Code, Article 13.1.1, ICN, Article 38, which may or may not be based on morphology[91]). Both codes deliberately separate defining the content of a taxon (its circumscription) from defining its name.
5. These first four requirements must be published in a work that is obtainable in numerous identical copies, as a permanent scientific record.

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.[92]

An "authority" may be placed after a scientific name.[93] The authority is the name of the scientist or scientists who first validly published the name.[93] 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".[94] 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).[95] The system for assigning authorities differs slightly between botany and zoology.[8] However, it is standard that if the genus of a species has been changed since the original description, the original authority's name is placed in parentheses.[96]