Inbiology,taxonomy (from Ancient Greekτάξις (taxis)'arrangement' and -νομία (-nomia)'method') is thescientific study of naming, defining (circumscribing) and classifying groups of biologicalorganisms based on shared characteristics. Organisms are grouped intotaxa (singular: taxon), and these groups are given ataxonomic 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 aredomain,kingdom,phylum (division is sometimes used in botany in place ofphylum),class,order,family,genus, andspecies. The Swedish botanistCarl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known asLinnaean taxonomy for categorizing 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 theevolutionary relationships among 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.[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 a major component ofsystematics) 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 the study of means of formation of species, etc."[5]
"The analysis of an organism's characteristics for the purpose of classification"[6]
"Systematics studiesphylogeny 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 whetherbiological nomenclature is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy.[8][9] 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".
In 1970, Micheneret al. defined "systematic biology" and "taxonomy" in relation to one another as follows:[10]
Systematic biology (hereafter called simply systematics) is the field that
(a) provides scientific names for organisms,
(b) describes them,
(c) preserves collections of them,
(d) provides classifications for the organisms, keys for their identification, and data on their distributions,
(e) investigates their evolutionary histories, and
(f) considers their environmental adaptations.
This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above.
A whole set of terms including taxonomy, systematic biology,systematics, scientific classification, biological classification, andphylogenetics have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting.[1][11] The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 byde Candolle, in hisThéorie élémentaire de la botanique.[12]John Lindley provided an early definition of systematics in 1830, although he wrote of "systematic botany" rather than using the term "systematics".[13] Europeans tend to use the terms "systematics" and "biosystematics" for the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently.[14] However, taxonomy, and in particular alpha taxonomy, is more specifically the identification, description, and naming (i.e., nomenclature) of organisms,[15] while "classification" focuses on placing organisms within hierarchical groups that show their relationships to other organisms.
Monograph and taxonomic revision
Ataxonomic revision ortaxonomic review is a novel analysis of the variation patterns in a particulartaxon. This analysis may be executed on the basis of any combination of the various available kinds of characters, such as morphological,anatomical,palynological,biochemical andgenetic. Amonograph 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
Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (thephylogeny) 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 namingtaxa, 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 thespecies 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 highertaxonomic ranks subgenus and above,[20] or simply in clades that include more than one taxon considered a species, expressed in terms ofphylogenetic nomenclature.[28]
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, with the possible exception of Aristotle, whose works hint at a taxonomy.[29][30] 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", includingLinnaeus'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 ofde Jussieu (1789), de Candolle (1813) andBentham and Hooker (1862–1863). These classifications described empirical patterns and were pre-evolutionary in thinking.
The publication ofCharles Darwin'sOn the Origin of Species (1859) led to a new explanation for classifications, based on evolutionary relationships. This was the concept ofphyletic systems, from 1883 onwards. This approach was typified by those ofEichler (1883) andEngler (1886–1892).
Organisms were first classified byAristotle (Greece, 384–322 BC) during his stay on the island ofLesbos.[35][36][37] He classified beings by their parts, or in modern termsattributes, 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 andanimals.[36]
Some of his groups of animals, such asAnhaima (animals without blood, translated asinvertebrates) andEnhaima (animals with blood, roughly thevertebrates), as well as groups like thesharks andcetaceans, are commonly used.[39][40][41]
Taxonomy in theMiddle Ages was largely based on theAristotelian system,[38] with additions concerning the philosophical and existential order of creatures. This included concepts such as thegreat chain of being in the Westernscholastic tradition,[38] again deriving ultimately from Aristotle.
The Aristotelian system did not classify plants orfungi, 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 thescala naturae (the Natural Ladder).[36] This, as well, was taken into consideration in the great chain of being.[36]
During theRenaissance and theAge 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 physicianAndrea Cesalpino (1519–1603), who has been called "the first taxonomist".[42] Hismagnum opusDe Plantis came out in 1583, and described more than 1,500 plant species.[43][44] Two large plant families that he first recognized are in use: theAsteraceae andBrassicaceae.[45]
In the 17th century,John Ray (England, 1627–1705) wrote many important taxonomic works.[37] Arguably his greatest accomplishment wasMethodus 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 byJoseph Pitton de Tournefort (France, 1656–1708).[47] His work from 1700,Institutiones Rei Herbariae, included more than 9,000 species in 698 genera, which directly influenced Linnaeus, as it was the text he used as a young student.[34]
The Swedish botanistCarl Linnaeus (1707–1778)[38] ushered in a new era of taxonomy. With his major worksSystema Naturae 1st Edition in 1735,[48]Species Plantarum in 1753,[49] andSystema 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 theLinnaean 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 inSvenska Spindlar[53]). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.[34]
Evolution of thevertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical forevolutionary taxonomy.The same relationship, expressed as acladogram typical forcladistics
A pattern of groups nested within groups was specified by Linnaeus' classifications of plants and animals, and these patterns began to be represented asdendrograms of the animal and plantkingdoms toward the end of the 18th century, well before Charles Darwin'sOn the Origin of Species was published.[37] The pattern of the "Natural System" did not entail a generating process, such as evolution, but may have implied it, inspiring early transmutationist thinkers. Among early works exploring the idea of atransmutation of species wereZoonomia in 1796 byErasmus Darwin (Charles Darwin's grandfather), andJean-Baptiste Lamarck'sPhilosophie zoologique of 1809.[20] The idea was popularized in the Anglophone world by the speculative but widely readVestiges of the Natural History of Creation, published anonymously byRobert Chambers in 1844.[54]
With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle ofcommon descent.[55]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.[56] Using the then newly discovered fossils ofArchaeopteryx andHesperornis,Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named byRichard Owen in 1842.[57][58] The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark ofevolutionary 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.[59] With themodern 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.[60]
Thecladistic method has emerged since the 1960s.[55] In 1958,Julian Huxley used the termclade.[20] Later, in 1960, Cain and Harrison introduced the termcladistic.[20] The salient feature is arranging taxa in a hierarchicalevolutionary tree, with the desired objective of all named taxa being monophyletic.[55] A taxon is called monophyletic if it includes all the descendants of an ancestral form.[61][62] Groups that have descendant groups removed from them are termedparaphyletic,[61] while groups representing more than one branch from the tree of life are calledpolyphyletic.[61][62] Monophyletic groups are recognized and diagnosed on the basis ofsynapomorphies, shared derived character states.[63]
Cladistic classifications are compatible with traditional Linnean taxonomy and the Codes ofZoological andBotanical nomenclature, to a certain extent.[64] An alternative system of nomenclature, theInternational Code of Phylogenetic Nomenclature orPhyloCode has been proposed, which regulates the formal naming of clades.[65][28][9] Linnaean ranks are optional and have no formal standing under thePhyloCode, which is intended to coexist with the current, rank-based codes.[28] While popularity of phylogenetic nomenclature has grown steadily in the last few decades,[9] it remains to be seen whether a majority of systematists will eventually adopt thePhyloCode or continue using the current systems of nomenclature that have been employed (and modified, but arguably not as much as some systematists wish)[66][67] for over 250 years.
The basic scheme of modern classification. Many other levels can be used; domain, the highest level within life, is both new and disputed.
Domains are a relatively new grouping. First proposed in 1977,Carl Woese'sthree-domain system was not generally accepted until later.[68] One main characteristic of the three-domain method is the separation ofArchaea andBacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes calledMonera),[69] with theEukaryota for all organisms whose cells contain anucleus.[70] A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.[69]
Thomas Cavalier-Smith, who published extensively on the classification ofprotists, in 2002[71] proposed that theNeomura, the clade that groups together the Archaea andEucarya, would have evolved from Bacteria, more precisely fromActinomycetota. His 2004 classification treated thearchaeobacteria as part of a subkingdom of the kingdom Bacteria, i.e., he rejected the three-domain system entirely.[72] Stefan Luketa in 2012 proposed a five "dominion" system, addingPrionobiota (acellular and withoutnucleic acid) andVirusobiota (acellular butwith nucleic acid) to the traditional three domains.[73]
Biological taxonomy is a sub-discipline ofbiology, and is generally practiced by biologists known as "taxonomists", although enthusiasticnaturalists are also frequently involved in the publication of new taxa.[85] Because taxonomy aims to describe and organizelife, the work conducted by taxonomists is essential for the study ofbiodiversity and the resulting field ofconservation biology.[86][87]
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, andstrain.[88][note 1]
The description must be based on at least one name-bearingtype specimen.
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[92]). Both codes deliberately separate defining the content of a taxon (itscircumscription) from defining its name.
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 simplequantitative orqualitative comparisons of striking features, to elaborate computer analyses of large amounts ofDNA sequence data.[93]
An "authority" may be placed after a scientific name.[94] The authority is the name of the scientist or scientists who first validly published the name.[94] For example, in 1758, Linnaeus gave theAsian elephant the scientific nameElephas maximus, so the name is sometimes written as "Elephas maximus Linnaeus, 1758".[95] The names of authors are often abbreviated: the abbreviationL., forLinnaeus, is commonly used. In botany, there is, in fact, a regulated list of standard abbreviations (seelist of botanists by author abbreviation).[96] The system for assigning authorities differs slightly betweenbotany andzoology.[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.[97]
A comparison of phylogenetic and phenetic (character-based) concepts
In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships.[20] It results in a measure of hypergeometric "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded bycladistic analyses, as phenetic methods do not distinguish shared ancestral (orplesiomorphic) traits from shared derived (orapomorphic) traits.[98] However, certain phenetic methods, such asneighbor joining, have persisted, as rapid estimators of relationships when more advanced methods (such asBayesian inference) are too computationally expensive.[99]
Modern taxonomy usesdatabase technologies to search and catalogue classifications and their documentation.[100] While there is no commonly used database, there are comprehensive databases such as theCatalogue of Life, which attempts to list every documented species.[101] The catalogue listed 1.64 million species for all kingdoms as of April 2016[update], claiming coverage of more than three-quarters of the estimated species known to modern science.[102]
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