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biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of Cell (biology), cells that proce ...
, taxonomy () is the
scientific Science is a systematic endeavor that Scientific method, builds and organizes knowledge in the form of Testability, testable explanations and predictions about the universe. Science may be as old as the human species, and some of the earli ...
study of naming, defining ( circumscribing) and classifying groups of biological
organism In biology, an organism () is any life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), taxonomy into groups such as Multicellular o ...
s based on shared characteristics. Organisms are grouped into
taxa In biology, a taxon (back-formation from ''Taxonomy (biology), taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known ...
(singular: taxon) and these groups are given a
taxonomic rank In biological classification, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system consists of species In biology, a species is the basic unit of Taxonomy (biol ...
; 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 In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (biology), division has been used instead of ph ...
(''division'' is sometimes used in botany in place of ''phylum''), class, order,
family Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its ...
,
genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
, and
species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
. The Swedish botanist
Carl Linnaeus Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his Nobility#Ennoblement, ennoblement in 1761 as Carl von Linné#Blunt, Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalise ...
is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as
Linnaean taxonomy Linnaean taxonomy can mean either of two related concepts: # The particular form of Taxonomy (biology), biological classification (taxonomy) set up by Carl Linnaeus, as set forth in his ''Systema Naturae'' (1735) and subsequent works. In the ta ...
for categorizing organisms and
binomial nomenclature In Taxonomy (biology), taxonomy, binomial nomenclature ("two-term naming system"), also called nomenclature ("two-name naming system") or binary nomenclature, is a formal system of naming species of living things by giving each a name compos ...
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
evolution Evolution is change in the heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to ...
ary 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. 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. # A field of science (and major component of
systematics Biological systematics is the study of the diversification of living forms, both past and present, and the Correlation and dependence, relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: c ...
) that encompasses description, identification, nomenclature, and classification # The science of classification, in biology the arrangement of organisms into a classification # "The science of classification as applied to living organisms, including the study of means of formation of species, etc." # "The analysis of an organism's characteristics for the purpose of classification" # "Systematics studies
phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree (graph theory), tree showing the evolutionary relationships among va ...
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) 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 Nomenclature codes or codes of nomenclature are the various rulebooks that govern biological Taxonomy (biology), taxonomic nomenclature, each in their own broad field of organisms. To an end-user who only deals with names of species, with some awa ...
is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy. For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy: * ''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 Michener ''et al.'' defined "systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) in relationship to one another as follows:
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, biosystematics, scientific classification, biological classification, and
phylogenetics In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...
have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting. 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''.
John Lindley John Lindley Fellow of the Royal Society, FRS (5 February 1799 – 1 November 1865) was an England, English botanist, gardener and orchidology, orchidologist. Early years Born in Old Catton, Catton, near Norwich, England, John Lindley was one ...
provided an early definition of systematics in 1830, although he wrote of "systematic botany" rather than using the term "systematics". 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. However, taxonomy, and in particular
alpha taxonomy In biology, taxonomy () is the science, scientific study of naming, defining (Circumscription (taxonomy), circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxon, taxa (s ...
, is more specifically the identification, description, and naming (i.e. nomenclature) of organisms, while "classification" focuses on placing organisms within hierarchical groups that show their relationships to other organisms.


Monograph and taxonomic revision

A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular
taxon In biology, a taxon (back-formation from ''Taxonomy (biology), taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known ...
. 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 A monograph is a specialist work of writing (in contrast to reference works) or exhibition on a single subject or an aspect of a subject, often by a single author or artist, and usually on a scholarly subject. In Library catalog, library catalo ...
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.


Taxonomic characters

Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (the
phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree (graph theory), tree showing the evolutionary relationships among va ...
) between taxa are inferred. Kinds of taxonomic characters include: * Morphological characters ** General external morphology ** Special structures (e.g. genitalia) ** Internal morphology (anatomy) ** Embryology ** Karyology and other cytological factors * Physiological characters ** Metabolic factors ** Body secretions ** Genic sterility factors * Molecular characters ** Immunological distance ** Electrophoretic differences ** Amino acid sequences of proteins ** DNA hybridization ** DNA and RNA sequences ** Restriction endonuclease analyses ** Other molecular differences * Behavioral characters ** Courtship and other ethological isolating mechanisms ** Other behavior patterns * Ecological characters ** Habit and habitats ** Food ** Seasonal variations ** Parasites and hosts * Geographic characters ** General biogeographic distribution patterns ** Sympatric-allopatric relationship of populations


Alpha and beta taxonomy

The term "alpha taxonomy" is primarily used today to refer to the discipline of finding, describing, and naming
taxa In biology, a taxon (back-formation from ''Taxonomy (biology), taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known ...
, particularly species. 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. 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. Thus,
Ernst Mayr Ernst Walter Mayr (; 5 July 1904 – 3 February 2005) was one of the 20th century's leading evolutionary biologists. He was also a renowned Taxonomy (biology), taxonomist, tropical explorer, ornithologist, Philosophy of biology, philosopher o ...
in 1968 defined "beta taxonomy" as the classification of ranks higher than species.
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".


Microtaxonomy and macrotaxonomy

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 rank In biological classification, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system consists of species In biology, a species is the basic unit of Taxonomy (biol ...
s subgenus and above.


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 Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his Nobility#Ennoblement, ennoblement in 1761 as Carl von Linné#Blunt, Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalise ...
's system of sexual classification for plants (Linnaeus's 1735 classification of animals was entitled "
Systema Naturae ' (originally in Latin language, Latin written ' with the Orthographic ligature, ligature æ) is one of the major works of the Sweden, Swedish botanist, zoologist and physician Carl Linnaeus (1707–1778) and introduced the Linnaean taxonomy. Al ...
" ("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-
evolution Evolution is change in the heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to ...
ary in thinking. The publication of
Charles Darwin Charles Robert Darwin ( ; 12 February 1809 – 19 April 1882) was an English naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all species of life have descended ...
's ''
On the Origin of Species ''On the Origin of Species'' (or, more completely, ''On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life''),The book's full original title was ''On the Origin of Species by Me ...
'' (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 Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived ...
methodology in the 1970s led to classifications based on the sole criterion of
monophyly In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic grou ...
, supported by the presence of
synapomorphies In phylogenetics, an apomorphy (or derived trait) is a novel Phenotypic trait, character or character state that has evolution, evolved from its ancestral form (or Plesiomorphy and symplesiomorphy, plesiomorphy). A synapomorphy is an apomorphy sh ...
. Since then, the evidentiary basis has been expanded with data from
molecular genetics Molecular genetics is a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the ...
that for the most part complements traditional morphology.


Pre-Linnaean


Early taxonomists

Naming and classifying human surroundings likely begun 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.Manktelow, M. (2010
History of Taxonomy
. Lecture from Dept. of Systematic Biology,
Uppsala University Uppsala University ( sv, Uppsala universitet) is a public university, public research university in Uppsala, Sweden. Founded in 1477, it is the List of universities in Sweden, oldest university in Sweden and the Nordic countries still in opera ...
.


Ancient times

Organisms were first classified by
Aristotle Aristotle (; grc-gre, Ἀριστοτέλης ''Aristotélēs'', ; 384–322 BC) was a Greek philosopher and polymath during the Classical Greece, Classical period in Ancient Greece. Taught by Plato, he was the founder of the Peripatet ...
(
Greece Greece,, or , romanized: ', officially the Hellenic Republic, is a country in Southeast Europe. It is situated on the southern tip of the Balkans, and is located at the crossroads of Europe, Asia, and Africa. Greece shares land borders with ...
, 384–322 BC) during his stay on the Island of Lesbos. 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. He divided all living things into two groups: plants and animals. Some of his groups of animals, such as ''Anhaima'' (animals without blood, translated as
invertebrate Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chordata, ...
s) and ''Enhaima'' (animals with blood, roughly the
vertebrate Vertebrates () comprise all animal Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually ...
s), as well as groups like the
shark Sharks are a group of elasmobranch fish characterized by a Chondrichthyes#Skeleton, cartilaginous skeleton, five to seven gill slits on the sides of the head, and pectoral fins that are not fused to the head. Modern sharks are classified with ...
s and
cetacean Cetacea (; , ) is an infraorder of aquatic mammals that includes whales, dolphins, and porpoises. Key characteristics are their fully aquatic lifestyle, streamlined body shape, often large size and exclusively carnivorous diet. They propel th ...
s, are still commonly used today. His student
Theophrastus Theophrastus (; grc-gre, Θεόφραστος ; c. 371c. 287 BC), a Greek philosopher and the successor to Aristotle in the Peripatetic school. He was a native of Eresos in Lesbos Island, Lesbos.Gavin Hardy and Laurence Totelin, ''Ancient Bota ...
(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 ''Crocus'' (; plural: crocuses or croci) is a genus of seasonal flowering plants in the family Iridaceae (iris family) comprising about 100 species of perennial plant, perennials growing from corms. They are low growing plants, whose flower stem ...
'', and '' Narcissus''.


Medieval

Taxonomy in the
Middle Ages In the history of Europe, the Middle Ages or medieval period lasted approximately from the late 5th to the late 15th centuries, similar to the Post-classical, post-classical period of World history (field), global history. It began with t ...
was largely based on the Aristotelian system, 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, again deriving ultimately from Aristotle. The Aristotelian system did not classify plants or
fungi A fungus (plural, : fungi or funguses) is any member of the group of Eukaryote, eukaryotic organisms that includes microorganisms such as yeasts and Mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified ...
, due to the lack of microscopes at the time, as his ideas were based on arranging the complete world in a single continuum, as per the ''scala naturae'' (the Natural Ladder). This, as well, was taken into consideration in the great chain of being. Advances were made by scholars such as
Procopius Procopius of Caesarea ( grc-gre, Προκόπιος ὁ Καισαρεύς ''Prokópios ho Kaisareús''; la, Procopius Caesariensis; – after 565) was a prominent late antique Greek scholar from Caesarea Maritima. Accompanying the Roman ge ...
, Timotheos of Gaza, Demetrios Pepagomenos, and
Thomas Aquinas Thomas Aquinas, Dominican Order, OP (; it, Tommaso d'Aquino, lit=Thomas of Aquino, Italy, Aquino; 1225 – 7 March 1274) was an Italian Dominican Order, Dominican friar and Catholic priest, priest who was an influential List of Catholic philo ...
. Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy.


Renaissance and early modern

During the
Renaissance The Renaissance ( , ) , from , with the same meanings. is a Periodization, period in History of Europe, European history marking the transition from the Middle Ages to modernity and covering the 15th and 16th centuries, characterized by an e ...
and the
Age of Enlightenment The Age of Enlightenment or the Enlightenment; german: Aufklärung, "Enlightenment"; it, L'Illuminismo, "Enlightenment"; pl, Oświecenie, "Enlightenment"; pt, Iluminismo, "Enlightenment"; es, La Ilustración, "Enlightenment" was an intel ...
, categorizing organisms became more prevalent, 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". 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 still in use today: the
Asteraceae The family (biology), family Asteraceae, alternatively Compositae, consists of over 32,000 known species of flowering plants in over 1,900 genera within the Order (biology), order Asterales. Commonly referred to as the aster, daisy, composite, ...
and
Brassicaceae Brassicaceae () or (the older) Cruciferae () is a medium-sized and economically important Family (biology), family of flowering plants commonly known as the mustards, the crucifers, or the cabbage family. Most are herbaceous plants, while some ar ...
. Then in the 17th century
John Ray John Ray Fellow of the Royal Society, FRS (29 November 1627 – 17 January 1705) was a Christian England, English Natural history, naturalist widely regarded as one of the earliest of the English parson-naturalists. Until 1670, he wrote his na ...
(
England England is a Countries of the United Kingdom, country that is part of the United Kingdom. It shares land borders with Wales to its west and Scotland to its north. The Irish Sea lies northwest and the Celtic Sea to the southwest. It is separa ...
, 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 Joseph Pitton de Tournefort (5 June 165628 December 1708) was a French botanist, notable as the first to make a clear definition of the concept of genus for plants. Botanist Charles Plumier was his pupil and accompanied him on his voyages. Lif ...
(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.


Linnaean era

The Swedish botanist
Carl Linnaeus Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his Nobility#Ennoblement, ennoblement in 1761 as Carl von Linné#Blunt, Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalise ...
(1707–1778) ushered in a new era of taxonomy. With his major works ''
Systema Naturae ' (originally in Latin language, Latin written ' with the Orthographic ligature, ligature æ) is one of the major works of the Sweden, Swedish botanist, zoologist and physician Carl Linnaeus (1707–1778) and introduced the Linnaean taxonomy. Al ...
'' 1st Edition in 1735, ''
Species Plantarum ' (Latin for "The Species of Plants") is a book by Carl Linnaeus, originally published in 1753, which lists every species of plant known at the time, classified into genus, genera. It is the first work to consistently apply binomial nomenclature ...
'' 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. Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century. Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively). 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.


Modern system of classification

A pattern of groups nested within groups was specified by Linnaeus' classifications of plants and animals, and these patterns began to be represented as dendrograms of the animal and plant kingdoms toward the end of the 18th century, well before Charles Darwin's ''On the Origin of Species'' was published. 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 a
transmutation of species Transmutation of species and transformism are unproven 18th and 19th-century evolutionary ideas about the change of one species into another that preceded Charles Darwin's theory of natural selection. The French ''Transformisme'' was a term used ...
were
Erasmus Darwin Erasmus Robert Darwin (12 December 173118 April 1802) was an English physician. One of the key thinkers of the Midlands Enlightenment, he was also a natural philosophy, natural philosopher, physiology, physiologist, Society for Effecting the ...
's (Charles Darwin's grandfather's) 1796 '' Zoönomia'' and
Jean-Baptiste Lamarck Jean-Baptiste Pierre Antoine de Monet, chevalier de Lamarck (1 August 1744 – 18 December 1829), often known simply as Lamarck (; ), was a French naturalist, biologist, academic, and soldier. He was an early proponent of the idea that biologi ...
's '' Philosophie Zoologique'' of 1809. 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. With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of
common descent Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. All living beings are in fact descendants of a unique ancestor commonly referred to as the last universal comm ...
.
Tree of life The tree of life is a fundamental archetype in many of the world's mythology, mythological, religion, religious, and philosophy, philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The ...
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 ''Archaeopteryx'' (; ), sometimes referred to by its German name, "" ( ''Primeval Bird''), is a genus of bird-like dinosaurs. The name derives from the ancient Greek (''archaīos''), meaning "ancient", and (''ptéryx''), meaning "feather" ...
'' and '' Hesperornis'',
Thomas Henry Huxley Thomas Henry Huxley (4 May 1825 – 29 June 1895) was an English biologist and anthropologist specialising in comparative anatomy. He has become known as "Darwin's Bulldog" for his advocacy of Charles Darwin Charles Robert Darwin ...
pronounced that they had evolved from dinosaurs, a group formally named by
Richard Owen Sir Richard Owen (20 July 1804 – 18 December 1892) was an English biologist, comparative anatomy, comparative anatomist and paleontology, paleontologist. Owen is generally considered to have been an outstanding naturalist with a remarkable ...
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 Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived ...
method has emerged since the 1960s. In 1958,
Julian Huxley Sir Julian Sorell Huxley (22 June 1887 – 14 February 1975) was an English evolutionary biologist, Eugenics, eugenicist, and Internationalism (politics), internationalist. He was a proponent of natural selection, and a leading figure in the m ...
used the term ''clade''. Later, in 1960, Cain and Harrison introduced the term ''cladistic''. The salient feature is arranging taxa in a hierarchical
evolutionary tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree (graph theory), tree showing the evolutionary relationships among va ...
, with the desideratum that all named taxa are monophyletic. A taxon is called monophyletic if it includes all the descendants of an ancestral form. Groups that have descendant groups removed from them are termed
paraphyletic In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and most of its descendants, excluding a few monophyletic subgroups. The group is said to be paraphyletic ''with respect to'' the excluded subgroups. In ...
, while groups representing more than one branch from the tree of life are called
polyphyletic A polyphyletic group is an assemblage of organisms or other evolving elements that is of mixed evolutionary origin. The term is often applied to groups that share similar features known as Homoplasy, homoplasies, which are explained as a result ...
. Monophyletic groups are recognized and diagnosed on the basis of
synapomorphies In phylogenetics, an apomorphy (or derived trait) is a novel Phenotypic trait, character or character state that has evolution, evolved from its ancestral form (or Plesiomorphy and symplesiomorphy, plesiomorphy). A synapomorphy is an apomorphy sh ...
, shared derived character states. Cladistic classifications are compatible with traditional Linnean taxonomy and the Codes of
Zoological Zoology ()The pronunciation of zoology as is usually regarded as nonstandard, though it is not uncommon. is the branch of biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unify ...
and
Botanical nomenclature Botanical nomenclature is the formal, scientific naming of plants. It is related to, but distinct from Alpha taxonomy, taxonomy. Plant taxonomy is concerned with grouping and classifying plants; botanical nomenclature then provides names for the ...
. An alternative system of nomenclature, the '' International Code of Phylogenetic Nomenclature'' or ''PhyloCode'' has been proposed, whose intent is to regulate the formal naming of clades. Linnaean ranks will be optional under the ''PhyloCode'', which is intended to coexist with the current, rank-based codes. It remains to be seen whether the systematic community will adopt the ''PhyloCode'' or reject it in favor of the current systems of nomenclature that have been employed (and modified as needed) for over 250 years.


Kingdoms and domains

Well before discovery of Carl Linnaeus (Botanist) plants and animals were considered separate Kingdoms. 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 Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain (biology), domain of life) in 1977 through a pioneering phylogenetic taxonomy (biol ...
's three-domain system was not generally accepted until later. One main characteristic of the three-domain method is the separation of
Archaea Archaea ( ; singular archaeon ) is a Domain (biology), domain of Unicellular organism, single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially Taxonomy (biology), classified as bacter ...
and
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometre The micrometre (Amer ...
, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera), with the
Eukaryota Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
for all organisms whose cells contain a
nucleus Nucleus (plural, : nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA ...
. A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.
Thomas Cavalier-Smith Thomas (Tom) Cavalier-Smith, Royal Society, FRS, Royal Society of Canada, FRSC, Natural Environment Research Council, NERC Professorial Fellow (21 October 1942 – 19 March 2021), was a professor of evolutionary biology in the Departme ...
, who published extensively on the classification of
protist A protist () is any eukaryotic organism (that is, an organism whose Cell (biology), cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a Common descent, common ancestor (the last eukary ...
s, in 2002 proposed that the Neomura, the clade that groups together the Archaea and Eucarya, would have evolved from Bacteria, more precisely from
Actinomycetota The ''Actinomycetota'' (synonym ''Actinobacteria'') are a phylum of mostly Gram-positive bacteria. They can be terrestrial animal, terrestrial or aquatic animal, aquatic. They are of great economic importance to humans because agriculture and fo ...
. His 2004 classification treated the archaeobacteria as part of a subkingdom of the kingdom Bacteria, i.e., he rejected the three-domain system entirely. Stefan Luketa in 2012 proposed a five "dominion" system, adding
Prion Prions are Proteinopathy, misfolded proteins that have the ability to transmit their misfolded shape onto normal variants of the same protein. They characterize several fatal and transmissible neurodegenerative diseases in humans and many othe ...
obiota (
acellular Non-cellular life, or acellular life is life Life is a quality that distinguishes matter that has biological processes, such as Cell signaling, signaling and self-sustaining processes, from that which does not, and is defined by the ca ...
and without
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all Organism, known forms of life. They are composed of nucleotides, which are the monomers made of three components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. ...
) and
Virus A virus is a wikt:submicroscopic, submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and ...
obiota (acellular but ''with'' nucleic acid) to the traditional three domains.


Recent comprehensive classifications

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
prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
s to the rank of Order, although both exclude fossil representatives. A separate compilation (Ruggiero, 2014) covers extant taxa to the rank of Family. Other, database-driven treatments include the
Encyclopedia of Life The ''Encyclopedia of Life'' (''EOL'') is a free, online encyclopedia intended to document all of the 1.9 million Life, living species known to science. It is compiled from existing trusted databases curated by experts and with the assistance of ...
, the
Global Biodiversity Information Facility The Global Biodiversity Information Facility (GBIF) is an international organisation that focuses on making scientific data on biodiversity available via the Internet using web services. The data are provided by many institutions from around the ...
, 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 The Paleobiology Database is an online resource for information on the distribution and classification of fossil animals, plants, and microorganisms. History The Paleobiology Database (PBDB) originated in the NCEAS-funded Phanerozoic Marine Paleo ...
is a resource for fossils.


Application

Biological taxonomy is a sub-discipline of
biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of Cell (biology), cells that proce ...
, 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 Life is a quality that distinguishes matter that has biological processes, such as Cell signaling, signaling and self-sustaining processes, from that which does not, and is defined by the capacity for Cell growth, growth, reaction to Stimu ...
, the work conducted by taxonomists is essential for the study of
biodiversity Biodiversity or biological diversity is the variety and variability of life, life on Earth. Biodiversity is a measure of variation at the Genetics, genetic (''genetic variability''), species (''species diversity''), and ecosystem (''ecosystem d ...
and the resulting field of
conservation biology Conservation biology is the study of the conservation of nature and of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions. It is an int ...
.


Classifying organisms

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 In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (biology), division has been used instead of ph ...
, Class, Order,
Family Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its ...
,
Genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
,
Species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
, and Strain.


Taxonomic descriptions

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. In
zoology Zoology ()The pronunciation of zoology as is usually regarded as nonstandard, though it is not uncommon. is the branch of biology that studies the Animal, animal kingdom, including the anatomy, structure, embryology, evolution, Biological clas ...
, the
nomenclature Nomenclature (, ) is a system of names or terms, or the rules for forming these terms in a particular field of arts or sciences. The principles of naming vary from the relatively informal conventions of everyday speech to the internationally ag ...
for the more commonly used ranks ( superfamily to
subspecies In Taxonomy (biology), biological classification, subspecies is a rank below species, used for populations that live in different areas and vary in size, shape, or other physical characteristics (Morphology (biology), morphology), but that ca ...
), is regulated by the ''
International Code of Zoological Nomenclature The International Code of Zoological Nomenclature (ICZN) is a widely accepted Convention (norm), convention in zoology that rules the formal scientific name, scientific naming of organisms treated as animals. It is also informally known as the I ...
'' (''ICZN Code''). In the fields of phycology,
mycology Mycology is the branch of biology concerned with the study of fungus, fungi, including their genetics, genetic and biochemistry, biochemical properties, their Taxonomy (biology), taxonomy and ethnomycology, their use to humans, including as a so ...
, and
botany Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek wo ...
, the naming of taxa is governed by the ''
International Code of Nomenclature for algae, fungi, and plants The ''International Code of Nomenclature for algae, fungi, and plants'' (ICN) is the set of rules and recommendations dealing with the formal botanical names that are given to plants, fungi and a few other groups of organisms, all those "trad ...
'' (''ICN''). The initial description of a taxon involves five main requirements: # 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). # The name must be unique (i.e. not a
homonym In linguistics, homonyms are words which are homographs (words that share the same spelling, regardless of pronunciation), or homophones (equivocal words, that share the same pronunciation, regardless of spelling), or both. Using this definition, ...
). # The description must be based on at least one name-bearing
type specimen In biology, a type is a particular wiktionary:en:specimen, specimen (or in some cases a group of specimens) of an organism to which the scientific name of that organism is formally attached. In other words, a type is an example that serves to a ...
. # 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). Both codes deliberately separate defining the content of a taxon (its circumscription) 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 simple quantitative or qualitative comparisons of striking features, to elaborate computer analyses of large amounts of
DNA sequence DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The ...
data.


Author citation

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. For example, in 1758 Linnaeus gave the
Asian elephant The Asian elephant (''Elephas maximus''), also known as the Asiatic elephant, is the only living species of the genus ''Elephas'' and is distributed throughout the Indian subcontinent and Southeast Asia, from India in the west, Nepal in the no ...
the scientific name ''Elephas maximus'', so the name is sometimes written as "''Elephas maximus'' Linnaeus, 1758". 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). The system for assigning authorities differs slightly between
botany Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek wo ...
and
zoology Zoology ()The pronunciation of zoology as is usually regarded as nonstandard, though it is not uncommon. is the branch of biology that studies the Animal, animal kingdom, including the anatomy, structure, embryology, evolution, Biological clas ...
. 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.


Phenetics

In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships. It results in a measure of hypergeometric "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by
cladistic Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived ...
analyses, as phenetic methods do not distinguish shared ancestral (or plesiomorphic) traits from shared derived (or apomorphic) traits. However, certain phenetic methods, such as neighbor joining, have persisted, as rapid estimators of relationship when more advanced methods (such as
Bayesian inference Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. Bayesian inference is an important technique in statistics, and e ...
) are too computationally expensive.


Databases

Modern taxonomy uses
database In computing, a database is an organized collection of Data (computing), data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The Databas ...
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 April 2016, claiming coverage of more than three quarters of the estimated species known to modern science.


See also

* Automated species identification * Bacterial taxonomy *
Cluster analysis Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters). It is a main task of ...
*
Consortium for the Barcode of Life The Consortium for the Barcode of Life (CBOL) was an international initiative dedicated to supporting the development of DNA barcoding as a global standard for species identification. CBOL's Secretariat Office is hosted by the National Museum of ...
* Consortium of European Taxonomic Facilities *
Genetypes Genetypes is a taxonomic concept proposed in 2010 to describe any genetic sequence, genetic sequences from type (biology), type specimens. This nomenclature integrates molecular systematics and terms used in Taxonomy (biology), biological taxonomy ...
*
Glossary of scientific naming This is a list of terms and symbols used in scientific name In taxonomy, binomial nomenclature ("two-term naming system"), also called nomenclature ("two-name naming system") or binary nomenclature, is a formal system of naming species ...
* Identification (biology) * ''
Incertae sedis ' () or ''problematica'' is a term used for a taxonomy (biology), taxonomic group where its broader relationships are unknown or undefined. Alternatively, such groups are frequently referred to as "enigmatic taxa". In the system of open nomen ...
'' * Open Tree of Life * Parataxonomy * Phenogram *
Set theory Set theory is the branch of mathematical logic that studies Set (mathematics), sets, which can be informally described as collections of objects. Although objects of any kind can be collected into a set, set theory, as a branch of mathematics, ...
*
Taxonomy (general) Taxonomy is the practice and science of categorization or classification (general theory), classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are ...
*
Virus classification Virus classification is the process of naming viruses and placing them into a Alpha taxonomy, taxonomic system similar to the classification systems used for cell (biology), cellular organisms. Viruses are classified by phenotypic characteristics, ...


Notes


References


Bibliography

* * * * * Wiley, Edward O. and Bruce S. Lieberman. 2011. "Phylogenetics: Theory and Practice of Phylogenetic Systematics", 2nd edn.


External links


What is taxonomy?
at th
''Natural History Museum London''

Taxonomy
a
NCBI
the ''National Center for Biotechnology Information''
Taxonomy
a
UniProt
the ''Universal Protein Resource''
ITIS
the ''Integrated Taxonomic Information System''
CETaF
the ''Consortium of European Taxonomic Facilities''
Wikispecies
''free species directory''

{{Branches of biology Biological nomenclature Biological classification