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In
biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms, Developmenta ...
, taxonomy () is the
scientific Science (from the Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the area around Rome, known as Latium. Through the power of the ...

scientific
study of naming, defining ( circumscribing) and classifying groups of biological
organism In biology, an organism () is any organic, 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 Multice ...

organism
s based on shared characteristics. Organisms are grouped into
taxa In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...
(singular: taxon) and these groups are given a
taxonomic rank In biological classification In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, ...
; 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 Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a partial function **Domain of holomorphy of a function *Doma ...
,
kingdom Kingdom may refer to: Monarchy * A type of monarchy * A realm ruled by: **A king, during the reign of a male monarch **A queen regnant, during the reign of a female monarch Taxonomy * Kingdom (biology), a category in biological taxonomy Arts an ...
,
phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The plural of a noun typically denotes a q ...
(''division'' is sometimes used in botany in place of ''phylum''),
class Class or The Class may refer to: Common uses not otherwise categorized * Class (biology), a taxonomic rank * Class (knowledge representation), a collection of individuals or objects * Class (philosophy), an analytical concept used differently f ...
,
order Order or ORDER or Orders may refer to: * Orderliness Orderliness is associated with other qualities such as cleanliness Cleanliness is both the abstract state of being clean and free from germs, dirt, trash, or waste, and the habit of achieving a ...
,
family In human society A society is a Social group, group of individuals involved in persistent Social relation, social interaction, or a large social group sharing the same spatial or social territory, typically subject to the same Politics, ...
,
genus Genus (plural genera) is a taxonomic rank Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such classification. The term may also refer to a specific classification s ...
, and
species In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...

species
. The Swedish botanist
Carl Linnaeus Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his Nobility#Ennoblement, ennoblement as Carl von Linné#Blunt, Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalised binomia ...
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 biological classification (taxonomy) set up by Carl Linnaeus Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his Nobility#Ennoblemen ...
for categorizing organisms and
binominal 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 composed ...
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 heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, ...

evolution
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 Biology, 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 (syn ...
) 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 study of means of formation of species, etc." # "The analysis of an organism's characteristics for the purpose of classification" # "Systematics studies
phylogeny , based on completely sequenced genomes. A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolution ...

phylogeny
to provide a pattern that can be translated into the classification and names of the more inclusive field of taxonomy" (listed as a desirable but unusual definition) 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 Biology is the natural science that studies life and living organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, prope ...
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". A whole set of terms including taxonomy,
systematic biology Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tr ...
, systematics,
biosystematics Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tr ...
, scientific classification, biological classification, and
phylogenetics In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms, ...

phylogenetics
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 Augustin Pyramus (or Pyrame) de Candolle (, , ; 4 February 17789 September 1841) was a Swiss Swiss may refer to: * the adjectival form of Switzerland *Swiss people Places *Swiss, Missouri *Swiss, North Carolina *Swiss, West Virginia *Swiss, W ...
, in his ''Théorie élémentaire de la botanique''.


Monograph and taxonomic revision

A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular
taxon In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...
. 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 work A reference work is a work such as a book A book is a medium for recording information Information can be thought of as the resolution of uncertainty; it a ...
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 result in a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa.


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 Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...
, 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 William Bertram Turrill FRS OBE FLS (14 June 1890 – 15 December 1961) was an English botanist. W B Turrill's mathematical classification of leaf shapes Education He was born in Woodstock, Oxfordshire to William Banbury and Thirza Mary (née ...
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 File:Francesco Redi.jpg, Francesco Redi, the founder of biology, is recognized to be one of the greatest biologists of all ti ...
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 problemThe species problem is the set of questions that arises when biologist Francesco Redi, the founder of biology, is recognized to be one of the greatest biologists of all time A biologist is a professional who has specialized knowledge in the fiel ...
. 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 In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, ...
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's system of sexual classification for plants (Of course, Linnaeus's classification of animals was entitled "Systema Naturae" ("the System of Nature"), implying that he, at least, believed that it was more than an "artificial system"). Later came systems based on a more complete consideration of the characteristics of taxa, referred to as "natural systems", such as those of
de JussieuDe Jussieu, the name of a French people, French family which came into prominence towards the close of the sixteenth century, and was known for a century and a half for the botanists it produced. The following are its more eminent members: *Antoine ...

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 heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, ...

evolution
ary in thinking. The publication of
Charles Darwin Charles Robert Darwin (; ; 12 February 1809 – 19 April 1882) was an English natural history#Before 1900, naturalist, geologist and biologist, best known for his contributions to the science of evolution. His proposition that all spe ...

Charles Darwin
'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 Mea ...
'' (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 Taxonomy (biology), 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 ...
methodology in the 1970s led to classifications based on the sole criterion of
monophyly Image:Monophyly, paraphyly, polyphyly.png, 300px, A cladogram of the primates, showing a ''monophyletic'' taxon: ''the simians'' (in yellow); a ''paraphyletic'' taxon: ''the prosimians'' (in cyan, including the red patch); and a ''polyphyletic'' ...
, supported by the presence of
synapomorphies 279px, trait states. In phylogenetics, apomorphy and synapomorphy refer to derived characters of a clade A clade (; from grc, , ''klados'', "branch"), also known as a monophyletic group or natural group, is a group of organisms that are mon ...
. 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 Morphology, from the Greek and meaning "study of shape", may refer to: Disciplines * Morphology (archaeology), study of the shapes or forms of artifacts * Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies ...
.


Pre-Linnaean


Early taxonomists

Naming and classifying human surroundings likely begun with the onset of
language A language is a structured system of communication used by humans, including speech (spoken language), gestures (Signed language, sign language) and writing. Most languages have a writing system composed of glyphs to inscribe the original soun ...

language
. Distinguishing poisonous plants from edible plants is integral to the survival of . 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 research university in Uppsala, Sweden Sweden (; sv, Sverige ), officially the Kingdom of Sweden ( sv, links=no, Konungariket Sverige ), is a Nordic countries, Nordic country in Northern ...
.


Ancient times

Organisms were first classified by
Aristotle Aristotle (; grc-gre, Ἀριστοτέλης ''Aristotélēs'', ; 384–322 BC) was a Greek philosopher A philosopher is someone who practices philosophy. The term ''philosopher'' comes from the grc, φιλόσοφος, , translit ...

Aristotle
(
Greece Greece ( el, Ελλάδα, Elláda, ), officially the Hellenic Republic, is a country located in Southeastern Europe Southeast Europe or Southeastern Europe () is a geographical region of Europe Europe is a continent A contin ...

Greece
, 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 animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This includes all animals apart from the subphylum vertebrate, Vertebrata. Familiar example ...
s) and ''Enhaima'' (animals with blood, roughly the
vertebrate Vertebrates () comprise all species of animal Animals (also called Metazoa) are multicellular eukaryotic organisms that form the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic ma ...
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 within ...

shark
s and
cetacean Cetaceans (from la, cetus Cetus () is a constellation, sometimes called 'the whale' in English. The Cetus (mythology), Cetus was a sea monster in Greek mythology which both Perseus and Heracles needed to slay. Cetus is in the region of the s ...
s, are still commonly used today. His student
Theophrastus Theophrastus (; grc-gre, Θεόφραστος ''Theόphrastos''; c. 371c. 287 BC), a Greek native of Eresos in Lesbos,Gavin Hardy and Laurence Totelin, ''Ancient Botany'', Routledge, 2015, p. 8. was the successor to Aristotle in the Peripatet ...

Theophrastus
(Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his '' Historia Plantarum''. Again, several plant groups currently still recognized can be traced back to Theophrastus, such as ''
Cornus '' Cornus mas'' Mature and immature flowers of ''Cornus canadensis'', Bonnechere Provincial Park, Ontario ''Cornus'' is a genus of about 30–60 species of woody plants in the family (biology), family Cornaceae, commonly known as dogwoo ...
'', ''
Crocus ''Crocus'' (English plural: crocuses or croci) is a genus Genus (plural genera) is a taxonomic rank Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such classifi ...
'', and ''
Narcissus Narcissus may refer to: Biology * Narcissus (plant), ''Narcissus'' (plant), a genus containing daffodils and others People * Narcissus (mythology), Greek mythological character * Narcissus (wrestler) (2nd century), assassin of the Roman emperor Co ...
''.


Medieval

Taxonomy in the
Middle Ages In the history of Europe, the Middle Ages or medieval period lasted approximately from the 5th to the late 15th centuries, similarly to the Post-classical, Post-classical period of global history. It began with the fall of the Western Roma ...
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 The Great Chain of Being is a hierarchical structure of all matter and life, thought by medieval Christianity Christianity is an Abrahamic religions, Abrahamic Monotheism, monotheistic religion based on the Life of Jesus in the New Testament, ...
in the Western scholastic tradition, again deriving ultimately from Aristotle. The Aristotelian system did not classify plants or
fungi A fungus (plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The plural of a noun typically denotes a quantity great ...

fungi
, 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 Greek may refer to: Greece Anything of, from, or related t ...
,
Timotheos of GazaTimotheus of Gaza ( el, Τιμόθεος ὁ Γαζαῖος), sometimes referred to as Timothy of Gaza, was a Greek grammarian active during the reign of Anastasius, i.e. 491-518. He is the author of a book on animals which may have been one of th ...
, Demetrios Pepagomenos, and
Thomas Aquinas Thomas Aquinas (; it, Tommaso d'Aquino, lit=Thomas of Aquino, Italy, Aquino; 1225 – 7 March 1274) was an Italian Dominican Order, Dominican friar, Philosophy, philosopher, Catholic priest, and Doctor of the Church. An immensely influential ...

Thomas Aquinas
. 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 period Period may refer to: Common uses * Era, a length or span of time * Full stop (or period), a punctuation mark Arts, entertainment, and media * Period (music), a concept in m ...

Renaissance
and the
Age of Enlightenment The Age of Enlightenment (also known as the Age of Reason or simply the Enlightenment); ger, Aufklärung, "Enlightenment"; it, L'Illuminismo, "Enlightenment"; pl, Oświecenie , "Enlightenment"; pt, Iluminismo, "Enlightenment"; es, link=n ...
, 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 Andrea Cesalpino ( Latinized as Andreas Cæsalpinus) (6 June 1524 – 23 February 1603) was an Italian physician A physician (American English), medical practitioner (English in the Commonwealth of Nations, Commonwealth English), medical d ...
(1519–1603), who has been called "the first taxonomist". His
magnum opus 's ''The Creation of Adam'' (c. 1512), part of the Sistine Chapel ceiling The Sistine Chapel ceiling ( it, Volta della Cappella Sistina), painted by Michelangelo Michelangelo di Lodovico Buonarroti Simoni (; 6 March 1475 – 18 Febr ...

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, or ...
and
Brassicaceae Brassicaceae () or 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, some shrubs, with simple, ...
. Then in the 17th century
John Ray John Ray FRS (29 November 1627 – 17 January 1705) was an English naturalist Natural history is a domain of inquiry involving organisms, including animals, fungus, fungi, and plants, in their natural environment, leaning more towards ob ...

John Ray
(
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 of England and the Celtic Sea to the southwest. En ...

England
, 1627–1705) wrote many important taxonomic works. Arguably his greatest accomplishment was ''Methodus Plantarum Nova'' (1682), in which he published details of over 18,000 plant species. At the time, his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. The next major taxonomic works were produced by
Joseph Pitton de Tournefort Joseph Pitton de Tournefort (5 June 1656 – 28 December 1708) was a French botanist Botany, also called , plant biology or phytology, is the science Science (from the Latin word ''scientia'', meaning "knowledge") is a systematic ent ...
(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 as Carl von Linné#Blunt, Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalised binomia ...
(1707–1778) ushered in a new era of taxonomy. With his major works ''
Systema Naturae ' (originally in Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the area around Rome, known as Latium. Through the power of the Rom ...
'' 1st Edition in 1735, ''
Species Plantarum ' (Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the area around Rome, known as Latium. Through the power of the Roman Republic, i ...
'' 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 The book ' or ' ( Swedish and Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the area around Rome, known as Latium. Through the powe ...
''). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.


Modern system of classification

upright=1.25, The same relationship, expressed as a cladogram_typical_for_cladistics_.html" ;"title="cladistics.html" ;"title="cladogram typical for cladistics">cladogram typical for cladistics ">cladistics.html" ;"title="cladogram typical for cladistics">cladogram typical for cladistics 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 Kingdom (biology), 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 19th-century evolutionary ideas for the altering of one species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well a ...
were
Erasmus Darwin Erasmus Darwin (12 December 173118 April 1802) was an English physician. One of the key thinkers of the Midlands Enlightenment, he was also a natural philosopher, physiologist, slave-trade abolitionist, inventor, and poet. His poems includ ...
'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 Natural history is a domain of inquiry involving organisms, including animals, fu ...

Jean-Baptiste Lamarck
'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 ''Vestiges of the Natural History of Creation'' is an 1844 work of speculative natural history Natural history is a domain of inquiry involving organisms, including animals, fungus, fungi, and plants, in their natural environment, leaning mor ...
'', 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 Evolutionary biology is the subfield of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chem ...
.
Tree of life The tree of life is a fundamental widespread mytheme or archetype in many of the world's mythology, mythologies, religion, religious and philosophy, philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Ma ...
representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was
birds Birds are a group of warm-blooded vertebrates constituting the class (biology), class Aves , characterised by feathers, toothless beaked jaws, the Oviparity, laying of Eggshell, hard-shelled eggs, a high Metabolism, metabolic rate, a four-c ...

birds
. Using the then newly discovered fossils of ''
Archaeopteryx ''Archaeopteryx'' ( "old wing"), sometimes referred to by its German name, ' ("original bird" or "first bird"), is a genus Genus (plural genera) is a taxonomic rank Taxonomy (general) is the practice and science of classification of thi ...

Archaeopteryx
'' and ''
Hesperornis ''Hesperornis'' (meaning "western bird") is a genus Genus (plural genera) is a taxonomic rank Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such classification ...

Hesperornis
'',
Thomas Henry Huxley Thomas Henry Huxley (4 May 1825 – 29 June 1895) was an English biologist Francesco Redi, the founder of biology, is recognized to be one of the greatest biologists of all time A biologist is a professional who has specialized knowledge ...

Thomas Henry Huxley
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 anatomist and paleontologist. Despite being a controversial figure, Owen is generally considered to have been an outstanding naturalist with a remark ...

Richard Owen
in 1842. The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries,
palaeontologists Paleontology (), also spelled palaeontology or palæontology, is the scientific study of life that existed prior to, and sometimes including, the start of the Holocene The Holocene ( ) is the current Geologic time scale, geological epoch. ...
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 Taxonomy (biology), 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 ...
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, eugenicist, and internationalist. He was a proponent of natural selection Natural selection is the differential survival and reprodu ...
used the term ''clad''e. Later, in 1960, Cain and Harrison introduced the term ''cladistic''. The salient feature is arranging taxa in a hierarchical
evolutionary tree , based on completely sequenced genomes. 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 ...
, 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 all descendants of that ancestor excluding a few—typically only one or two—Monophyly, monophyletic subgroups. The group is said to be paraphyleti ...

paraphyletic
, while groups representing more than one branch from the tree of life are called
polyphyletic File:Monophyly, paraphyly, polyphyly.png, 300px, Cladogram of the primates, showing a monophyly (the simians, in yellow), a paraphyly (the prosimians, in cyan, including the red patch), and a polyphyly (the night-active primates, the lorises and th ...

polyphyletic
. Monophyletic groups are recognized and diagnosed on the basis of
synapomorphies 279px, trait states. In phylogenetics, apomorphy and synapomorphy refer to derived characters of a clade A clade (; from grc, , ''klados'', "branch"), also known as a monophyletic group or natural group, is a group of organisms that are mon ...
, shared derived character states. Cladistic classifications are compatible with traditional Linnean taxonomy and the Codes of
Zoological Zoology ()The pronunciation of zoology as is typically regarded as nonstandard, though it is not uncommon. is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical s ...
and
Botanical Nomenclature Botanical nomenclature is the formal, scientific naming of plants. It is related to, but distinct from taxonomy Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such c ...
. 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 Linnaeus, 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 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 by phylogenetic taxonomy (biology), taxonomy of 16 ...

Carl Woese
's
three-domain system The three-domain system is a biological classification In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, ...
was not generally accepted until later. One main characteristic of the three-domain method is the separation of
Archaea Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

Archaea
and
Bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a Bacte ...

Bacteria
, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called
Monera Monera (/məˈnɪərə/) (Greek - μονήρης (monḗrēs), "single", "solitary") is a biological kingdom that is made up of prokaryote A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus, a ...
), with the
Eukaryota Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...
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, FRS, FRSC, Natural Environment Research Council, NERC Professorial Fellow (21 October 1942 - 19 March 2021), was a Professor of Evolutionary Biology in the Department of Zoology, at the University of Oxford. His res ...
, 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 eukaryo ...
s, recently proposed that the Neomura, the clade that groups together the Archaea and , would have evolved from Bacteria, more precisely from
Actinobacteria The Actinobacteria are a phylum of mostly Gram-positive bacteria File:Gram stain 01.jpg, 300px, Violet-stained gram-positive cocci and pink-stained gram-negative bacillus (shape), bacilli In bacteriology, gram-positive bacteria are bacteria tha ...
. 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 misfolded protein Protein folding is the physical process Physical changes are changes affecting the form of a chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter ...

Prion
obiota (
acellular Non-cellular life, or acellular life is life Life is a characteristic that distinguishes physical entities that have biological processes, such as signaling and self-sustaining processes, from those that do not, either because such func ...
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. T ...

nucleic acid
) and
Virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals and plants to microorganisms, including bacte ...

Virus
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 collaborative encyclopedia intended to document all of the 1.9 million living species In biology, a species is the basic unit of biological classification, classification and a taxon ...
, the
Global Biodiversity Information Facility The Global Biodiversity Information Facility (GBIF) is an international organisation that focuses on making scientific data on biodiversity Biodiversity is the biological variety and Genetic variability, variability of life, life on Earth. Bio ...

Global Biodiversity Information Facility
, the NCBI taxonomy database, the
Interim Register of Marine and Nonmarine Genera The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database which attempts to cover published genus names for all domains of life from 1758 in zoology (1753 in botany) up to the present, arranged in a single, internally c ...
, the Open Tree of Life, and the
Catalogue of Life The Catalogue of Life is an online databaseAn online database is a database A database is an organized collection of data Data are units of information Information can be thought of as the resolution of uncertainty; it answers the q ...
. 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 Paleofa ...
is a resource for fossils.


Application

Biological taxonomy is a sub-discipline of
biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms, Developmenta ...
, and is generally practiced by biologists known as "taxonomists", though enthusiastic
naturalists Natural history is a domain of inquiry involving organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, properties of life. ...

naturalists
are also frequently involved in the publication of new taxa. Because taxonomy aims to describe and organize
life Life is a characteristic that distinguishes physical entities that have biological processes, such as Cell signaling, signaling and self-sustaining processes, from those that do not, either because such functions have ceased (they have Death ...

life
, the work conducted by taxonomists is essential for the study of
biodiversity Biodiversity is the biological variety and Genetic variability, variability of life, life on Earth. Biodiversity is a measure of variation at the Genetics, genetic, species, and ecosystem level. Terrestrial biodiversity is usually greater near t ...

biodiversity
and the resulting field of
conservation biology Conservation biology is the study of the conservation of nature and of Earth Earth is the third planet from the Sun and the only astronomical object known to harbour and support life. 29.2% of Earth's surface is land consisting of continen ...
.


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 (biology), Domain, Kingdom (biology), Kingdom, Phylum, Class (biology), Class, Order (biology), Order, Family (biology), Family, Genus, Species, and Strain (biology), 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, the nomenclature for the more commonly used ranks (Superfamily (taxonomy), superfamily to subspecies), is regulated by the ''International Code of Zoological Nomenclature'' (''ICZN Code''). 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''). 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 nomenclature, binomial for new species, or uninomial for other ranks). # The name must be unique (i.e. not a homonym (biology), homonym). # The description must be based on at least one name-bearing Type (biology), type 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). Both codes deliberately separate defining the content of a taxon (its circumscription (taxonomy), 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 property, quantitative or Qualitative property, qualitative comparisons of striking features, to elaborate computer analyses of large amounts of DNA sequence 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 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 Author citation (botany), botany and Author citation (zoology), zoology. 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 evolutionary "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by cladistic analyses, as phenetic methods do not distinguish common ancestral (or plesiomorphic) traits from new common (or apomorphic) traits. However, certain phenetic methods, such as neighbor joining, have found their way into cladistics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference) are too computationally expensive.


Databases

Modern taxonomy uses database technologies to search and catalogue classifications and their documentation. While there is no commonly used database, there are comprehensive databases such as the ''
Catalogue of Life The Catalogue of Life is an online databaseAn online database is a database A database is an organized collection of data Data are units of information Information can be thought of as the resolution of uncertainty; it answers the q ...
'', 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 * Cladogram * Cladistics * Cluster analysis * Consortium for the Barcode of Life * Consortium of European Taxonomic Facilities * Dendrogram * Genetypes * Glossary of scientific naming * Identification (biology) * ''Incertae sedis'' * Open Tree of Life * Parataxonomy * Phenogram * Set theory * Taxonomy (general) * Virus classification


Notes


References


Bibliography

* * * *


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 Taxonomy (biology), Biological nomenclature Biological classification, *