View source for Taxonomy (biology)

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{{short description|Science of naming, defining and classifying organisms}}
{{Use dmy dates|date=March 2022}}
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{{Evolutionary biology}}
In [[biology]], '''taxonomy''' ({{ety|grc|''[[wikt:τάξις|τάξις]]'' ([[taxis]])|arrangement||''[[wikt:νόμος|-νομία]]'' ([[:wikt:-nomy|-nomia]])|[[Scientific method|method]]}}) is the [[science|scientific]] study of naming, defining ([[Circumscription (taxonomy)|circumscribing]]) and classifying groups of biological [[organism]]s based on shared characteristics. Organisms are grouped into [[taxon|taxa]] (singular: taxon) and these groups are given a [[taxonomic rank]]; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are [[domain (biology)|domain]], [[kingdom (biology)|kingdom]], [[phylum]] (''division'' is sometimes used in botany in place of ''phylum''), [[class (biology)|class]], [[order (biology)|order]], [[family (biology)|family]], [[genus]], and [[species]]. The Swedish botanist [[Carl Linnaeus]] is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as [[Linnaean taxonomy]] for categorizing organisms and [[binomial nomenclature]] for naming organisms.

With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the [[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.<ref name="Wilkins2011">{{Cite web |url= http://evolvingthoughts.net/2011/02/what-is-systematics-and-what-is-taxonomy/ |title=What is systematics and what is taxonomy? |last=Wilkins |first=J. S. |date=5 February 2011 |url-status=live |archive-url= https://web.archive.org/web/20160827124330/http://evolvingthoughts.net/2011/02/what-is-systematics-and-what-is-taxonomy/ |archive-date=27 August 2016 |access-date=21 August 2016}}</ref> 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.<ref name="Judd">{{Cite book |title=Plant Systematics: A Phylogenetic Approach |last1=Judd |first1=W. S. |last2=Campbell |first2=C. S. |last3=Kellogg |first3=E. A. |last4=Stevens |first4=P. F. |last5=Donoghue |first5=M. J. |date=2007 |publisher=Sinauer Associates |edition=3rd |location=Sunderland |chapter=Taxonomy}}</ref>
# A field of science (and a major component of [[systematics]]) that encompasses description, identification, [[nomenclature]], and classification<ref name="Simpson">{{Cite book |title=Plant Systematics |last=Simpson |first=Michael G. |date=2010 |publisher=Academic Press |isbn=9780123743800 |edition=2nd |chapter=Chapter 1 Plant Systematics: an Overview}}</ref>
# The science of classification, in biology the arrangement of organisms into a classification<ref>{{cite book |editor-last1=Kirk |editor-first1=P. M. |editor-last2=Cannon |editor-first2=P. F. |editor-last3=Minter |editor-first3=D. W. |editor-last4=Stalpers |editor-first4=J. A. |date=2008 |chapter=Taxonomy |title=Dictionary of the Fungi |edition=10th |publisher=CABI}}</ref>
# "The science of classification as applied to living organisms, including the study of means of formation of species, etc."<ref>{{Cite book |title=The Wordsworth Dictionary of Science and Technology |date=1988 |publisher=W. R. Chambers Ltd. and Cambridge University Press |editor-last=Walker |editor-first=P. M. B.}}</ref>
# "The analysis of an organism's characteristics for the purpose of classification"<ref name="Henderson">{{Cite book |url= https://books.google.com/books?id=-PLgy6DWe0wC |title=Henderson's Dictionary Of Biology |last=Lawrence |first=E. |date=2005 |publisher=Pearson/Prentice Hall |isbn=9780131273849}}</ref>
# "Systematics studies [[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)<ref>{{Cite journal |last=Wheeler |first=Quentin D.  |title=Taxonomic triage and the poverty of phylogeny |date=2004 |journal=[[Philosophical Transactions of the Royal Society]] |editor1-first=H. C. J. |editor1-last=Godfray |editor2-first=S. |editor2-last=Knapp |volume=359: Taxonomy for the twenty-first century |pages=571–583 |doi=10.1098/rstb.2003.1452 |pmc=1693342 |pmid=15253345 |author-link=Quentin D. Wheeler |issue=1444| issn = 0962-8436}}</ref>

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]] is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy.<ref name="Herbarium">{{Cite web |title=Nomenclature, Names, and Taxonomy |url= http://herbarium.usu.edu:80/teaching/4420/botnom.htm |date=2005 |website=Intermountain Herbarium |publisher=Utah State University |url-status=dead |archive-url= https://web.archive.org/web/20161123030604/http://herbarium.usu.edu/teaching/4420/botnom.htm |archive-date=23 November 2016}}</ref><ref name="Laurin 2023 Advent">{{cite book |last1=Laurin |first1=Michel |title=The Advent of PhyloCode: The Continuing Evolution of Biological Nomenclature |date=3 August 2023 |publisher=CRC Press |location=Boca Raton, Florida |isbn=9781003092827 |pages=xv + 209 |doi=10.1201/9781003092827 |url=https://www.taylorfrancis.com/books/mono/10.1201/9781003092827/advent-phylocode-michel-laurin |access-date=19 September 2023 |archive-date=5 September 2023 |archive-url=https://web.archive.org/web/20230905140719/https://www.taylorfrancis.com/books/mono/10.1201/9781003092827/advent-phylocode-michel-laurin |url-status=live }}</ref> For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy:<ref name="Henderson" />
* ''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 relation to one another as follows:<ref>{{cite book |last1=Michener |first1=Charles D. |first2=John O. |last2=Corliss |first3=Richard S. |last3=Cowan |first4=Peter H. |last4=Raven |first5=Curtis W. |last5=Sabrosky |first6=Donald S. |last6=Squires |first7=G. W. |last7=Wharton |date=1970 |title=Systematics In Support of Biological Research |publisher=Division of Biology and Agriculture, National Research Council |location=Washington, DC}}</ref>
<blockquote>
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.
</blockquote>

A whole set of terms including taxonomy, systematic biology, [[systematics]], scientific classification, biological classification, and [[phylogenetics]] have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting.<ref name="Wilkins2011" /><ref name="Small1989">{{Cite journal |last=Small |first=Ernest |date=1989 |title=Systematics of Biological Systematics (Or, Taxonomy of Taxonomy) |journal=Taxon |volume=38 |issue=3 |pages=335–356 |doi=10.2307/1222265 |jstor=1222265}}</ref> The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 by [[Augustin Pyramus de Candolle|de Candolle]], in his ''[[Théorie élémentaire de la botanique]]''.<ref>{{Cite book |url= https://books.google.com/books?id=In_Lv8iMt24C&pg=PA20 |title=Plant systematics: An integrated approach |last=Singh |first=Gurcharan |date=2004 |publisher=Science Publishers |isbn=9781578083510 |page=20 |via=Google Books}}</ref> [[John Lindley]] provided an early definition of systematics in 1830, although he wrote of "systematic botany" rather than using the term "systematics".<ref>{{cite web |last=Wilkins |first=J. S. |url= http://evolvingthoughts.net/2011/02/what-is-systematics-and-what-is-taxonomy/ |title=What is systematics and what is taxonomy? |work=EvolvingThoughts.net |archive-url= https://web.archive.org/web/20160827124330/http://evolvingthoughts.net/2011/02/what-is-systematics-and-what-is-taxonomy/ |archive-date=27 August 2016}}</ref> 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.<ref>{{cite book |last1=Brusca |first1=R. C. |last2=Brusca |first2=G. J. |date=2003 |title=Invertebrates |edition=2nd |location=Sunderland, Massachusetts |publisher=Sinauer Associates |page=27}}</ref> However, taxonomy, and in particular [[alpha taxonomy]], is more specifically the identification, description, and naming (i.e., nomenclature) of organisms,<ref name="Fortey">{{Cite book |last=Fortey |first=Richard |author-link=Richard Fortey |date=2008 |title=Dry Store Room No. 1: The Secret Life of the Natural History Museum |location=London |publisher=Harper Perennial |isbn=9780007209897}}</ref> 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]]. This analysis may be executed on the basis of any combination of the various available kinds of characters, such as morphological, [[anatomical]], [[palynological]], [[Biochemistry|biochemical]] and [[Genetics|genetic]]. A [[Monograph#In biology|monograph]] or complete revision is a revision that is comprehensive for a taxon for the information given at a particular time, and for the entire world. Other (partial) revisions may be restricted in the sense that they may only use some of the available character sets or have a limited spatial scope. A revision results in a conformation of or new insights in the relationships between the subtaxa within the taxon under study, which may lead to a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa.<ref>{{Cite journal |last=Maxted |first=Nigel |date=1992 |title=Towards Defining a Taxonomic Revision Methodology |journal=Taxon |volume=41 |issue=4 |pages=653–660 |doi=10.2307/1222391 |jstor=1222391}}</ref>

=== Taxonomic characters ===
Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (the [[phylogeny]]) between taxa are inferred.<ref name="Hennig 1965">{{cite journal |last1=Hennig |first1=Willi |title=Phylogenetic Systematics |journal=Annual Review of Entomology |date=January 1965 |volume=10 |issue=1 |pages=97–116 |doi=10.1146/annurev.en.10.010165.000525 |url=https://doi.org/10.1146/annurev.en.10.010165.000525 |issn=0066-4170 |access-date=19 September 2023 |archive-date=13 November 2023 |archive-url=https://web.archive.org/web/20231113101423/https://www.annualreviews.org/doi/10.1146/annurev.en.10.010165.000525 |url-status=live }}</ref><ref>{{cite book |last=Mayr |first=Ernst |author-link=Ernst Mayr |date=1991 |title=Principles of Systematic Zoology |location=New York |publisher=McGraw-Hill |page=159}}</ref> Kinds of taxonomic characters include:<ref>Mayr, Ernst (1991), p. 162.</ref>
{{div col|colwidth=35em}}
* [[Morphology (biology)|Morphological]] characters
** General external [[Morphology (biology)|morphology]]
** Special structures (e.g., [[Sex organ|genitalia]])
** Internal morphology ([[anatomy]])
** [[Embryology]]
** [[Karyotype|Karyology]] and other [[Cell biology|cytological]] factors
* [[Physiology|Physiological]] characters
** [[Metabolism|Metabolic factors]]
** Body secretions
** Genic sterility factors
* [[Molecular biology|Molecular]] characters
** Immunological distance
** Electrophoretic differences
** Amino acid sequences of proteins
** DNA hybridization
** DNA and RNA sequences
** Restriction endonuclease analyses
** Other molecular differences
* [[Behavior|Behavioral]] characters
** Courtship and other ethological isolating mechanisms
** Other behavior patterns
* [[Ecology|Ecological]] characters
** Habit and habitats
** Food
** Seasonal variations
** Parasites and hosts
* [[Geography|Geographic]] characters
** General [[Species distribution|biogeographic distribution]] patterns
** [[Sympatry|Sympatric]]-[[Allopatric speciation|allopatric]] relationship of populations
{{div col end}}

=== Alpha and beta taxonomy ===
{{distinguish|Alpha diversity}}
The term "'''alpha taxonomy'''" is primarily used to refer to the discipline of finding, describing, and naming [[taxon|taxa]], particularly species.<ref name="BiologyDiscussion" /> 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.<ref>{{Cite journal |last1=Rosselló-Mora |first1=Ramon |last2=Amann |first2=Rudolf |date=1 January 2001 |title=The species concept for prokaryotes |journal=FEMS Microbiology Reviews |volume=25 |issue=1 |pages=39–67 |doi=10.1111/j.1574-6976.2001.tb00571.x |issn=1574-6976 |pmid=11152940|doi-access=free}}</ref>

[[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.{{sfn|Turrill|1938}}<blockquote> ... 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.{{sfn|Turrill|1938}}</blockquote>

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.{{sfn|Turrill|1938|pp=365–366}}

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.<ref>{{Cite journal |last=Steyskal |first=G. C. |date=1965 |title=Trend curves of the rate of species description in zoology |journal=Science |volume=149 |issue=3686 |pages=880–882 |bibcode=1965Sci...149..880S |doi=10.1126/science.149.3686.880 |pmid=17737388|s2cid=36277653}}</ref><ref name="BiologyDiscussion" /> Thus, [[Ernst Mayr]] in 1968 defined "'''beta taxonomy'''" as the classification of ranks higher than species.<ref>{{cite journal |last=Mayr |first=Ernst |title=The Role of Systematics in Biology: The study of all aspects of the diversity of life is one of the most important concerns in biology |date=9 February 1968 |journal=Science |volume=159 |issue=3815 |pages=595–599 |bibcode=1968Sci...159..595M |doi=10.1126/science.159.3815.595 |pmid=4886900 |author-link=Ernst Mayr}}</ref><blockquote>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".</blockquote>

=== Microtaxonomy and macrotaxonomy ===
{{Main|Species problem}}
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.<ref>{{Cite book |title=The Growth of Biological Thought: Diversity, Evolution, and Inheritance |last=Mayr |first=Ernst |date=1982 |publisher=Belknap Press of Harvard University Press |isbn=9780674364462 |chapter=Chapter 6: Microtaxonomy, the science of species |chapter-url=https://books.google.com/books?id=pHThtE2R0UQC |access-date=15 September 2017 |archive-date=3 July 2023 |archive-url=https://web.archive.org/web/20230703072557/https://books.google.com/books?id=pHThtE2R0UQC |url-status=live }}</ref><ref>{{Cite web |url= http://www.biological-concepts.com/views/search.php?term=1508 |title=Result of Your Query |website=biological-concepts.com |url-status=live |archive-url= https://web.archive.org/web/20170405170414/http://www.biological-concepts.com/views/search.php?term=1508 |archive-date=5 April 2017}}</ref><ref name="BiologyDiscussion">{{Cite news |url= http://www.biologydiscussion.com/animals-2/taxonomy/taxonomy-meaning-levels-periods-and-role/32373 |title=Taxonomy: Meaning, Levels, Periods and Role |date=27 May 2016 |work=Biology Discussion |url-status=live |archive-url= https://web.archive.org/web/20170405073645/http://www.biologydiscussion.com/animals-2/taxonomy/taxonomy-meaning-levels-periods-and-role/32373 |archive-date=5 April 2017}}</ref> By extension, macrotaxonomy is the study of groups at the higher [[taxonomic rank]]s subgenus and above,<ref name="BiologyDiscussion" /> or simply in clades that include more than one taxon considered a species, expressed in terms of [[phylogenetic nomenclature]].<ref name="Cantino & de Queiroz 2020">{{cite book |last1=Cantino |first1=Philip D. |last2=de Queiroz |first2=Kevin |title=International Code of Phylogenetic Nomenclature (PhyloCode): A Phylogenetic Code of Biological Nomenclature |date=29 April 2020 |publisher=CRC Press |location=Boca Raton, Florida |isbn=978-0429821356 |pages=xl + 149 |url=https://www.routledge.com/International-Code-of-Phylogenetic-Nomenclature-PhyloCode/Queiroz-Cantino/p/book/9781138332829 |access-date=19 September 2023 |archive-date=14 October 2023 |archive-url=https://web.archive.org/web/20231014042402/https://www.routledge.com/International-Code-of-Phylogenetic-Nomenclature-PhyloCode/Queiroz-Cantino/p/book/9781138332829 |url-status=live }}</ref>

== History ==
While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, a truly scientific attempt to classify organisms did not occur until the 18th century, with the possible exception of Aristotle, whose works hint at a taxonomy.<ref name="Voultsiadou & Vafidis 2007">{{cite journal |last1=Voultsiadou |first1=Eleni |last2=Vafidis |first2=Dimitris |title=Marine invertebrate diversity in Aristotle's zoology |journal=Contributions to Zoology |date=1 January 2007 |volume=76 |issue=2 |pages=103–120 |doi=10.1163/18759866-07602004 |url=https://doi.org/10.1163/18759866-07602004 |issn=1875-9866 |access-date=19 September 2023 |archive-date=25 April 2023 |archive-url=https://web.archive.org/web/20230425063507/https://brill.com/view/journals/ctoz/76/2/article-p103_4.xml |url-status=live }}</ref><ref name="Voultsiadou et al. 2017">{{cite journal |last1=Voultsiadou |first1=Eleni |last2=Gerovasileiou |first2=Vasilis |last3=Vandepitte |first3=Leen |last4=Ganias |first4=Kostas |last5=Arvanitidis |first5=Christos |title=Aristotle's scientific contributions to the classification, nomenclature and distribution of marine organisms |journal=Mediterranean Marine Science |date=2017 |volume=18 |issue=3 |pages=468–478 |doi=10.12681/mms.13874 |issn=1791-6763 |doi-access=free }}</ref> 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 [[Carl Linnaeus|Linnaeus]]'s system of sexual classification for plants (Linnaeus's 1735 classification of animals was entitled "[[Systema Naturae]]" ("the System of Nature"), implying that he, at least, believed that it was more than an "artificial system"). 

Later came systems based on a more complete consideration of the characteristics of taxa, referred to as "natural systems", such as those of [[Antoine Laurent de Jussieu|de Jussieu]] (1789), de Candolle (1813) and [[Bentham and Hooker]] (1862–1863). These classifications described empirical patterns and were pre-[[evolution]]ary in thinking. 

The publication of [[Charles Darwin]]'s ''[[On the Origin of Species]]'' (1859) led to a new explanation for classifications, based on evolutionary relationships. This was the concept of [[phyletic]] systems, from 1883 onwards. This approach was typified by those of [[August Eichler|Eichler]] (1883) and [[Adolf Engler|Engler]] (1886–1892). 

The advent of [[cladistic]] methodology in the 1970s led to classifications based on the sole criterion of [[monophyly]], supported by the presence of [[synapomorphies]]. Since then, the evidentiary basis has been expanded with data from [[molecular genetics]] that for the most part complements traditional [[Morphology (biology)|morphology]].{{sfn|Datta|1988}}{{page needed|date=July 2019}}{{sfn|Stace|1989}}{{page needed|date=July 2019}}{{sfn|Stuessy|2009}}{{page needed|date=July 2019}}

=== Pre-Linnaean ===

==== Early taxonomists ====
Naming and classifying human surroundings likely began with the onset of language. Distinguishing poisonous plants from edible plants is integral to the survival of human communities. Medicinal plant illustrations show up in Egyptian wall paintings from {{Circa|1500 BC}}, indicating that the uses of different species were understood and that a basic taxonomy was in place.<ref name="Manktelow">{{cite web |last=Manktelow |first=M. |date=2010 |url= http://atbi.eu/summerschool/files/summerschool/Manktelow_Syllabus.pdf |title=History of Taxonomy |archive-url= https://web.archive.org/web/20150529020546/http://atbi.eu/summerschool/files/summerschool/Manktelow_Syllabus.pdf |archive-date=29 May 2015 |publisher=Dept. of Systematic Biology, [[Uppsala University]]}}</ref>

==== Ancient times ====

{{further|Aristotle's biology#Classification}}

[[File:Huang-Quan-Xie-sheng-zhen-qin-tu.jpg|thumb|upright=1.7|''Description of rare animals'' (写生珍禽图), by [[Song dynasty]] painter [[Huang Quan (painter)|Huang Quan]] (903–965)]]

Organisms were first classified by [[Aristotle]] ([[Greece]], 384–322 BC) during his stay on the [[Lesbos|Island of Lesbos]].<ref>{{cite book |last=Mayr |first=Ernst |author-link=Ernst Mayr |date=1982 |title=The Growth of Biological Thought |publisher=Belknap Press of Harvard University Press |location=Cambridge, Massachusetts}}</ref><ref name="Palaeos">{{Cite web |url= http://palaeos.com/taxonomy/history.html |title= History of Taxonomy |website=Palaeos |url-status=dead |archive-url= https://web.archive.org/web/20170331022648/http://palaeos.com/taxonomy/history.html |archive-date=31 March 2017}}</ref><ref name="Britannica – Taxonomy" /> 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.<ref name="Roanoke">{{Cite web |url= http://www.cbs.dtu.dk/courses/genomics_course/roanoke/bio101ch20.htm |title=Biology 101, Ch 20 |date=23 March 1998 |website=cbs.dtu.dk |url-status=live |archive-url= https://web.archive.org/web/20170628023508/http://www.cbs.dtu.dk/courses/genomics_course/roanoke/bio101ch20.htm |archive-date=28 June 2017}}</ref> He divided all living things into two groups: [[plant]]s and [[animal]]s.<ref name="Palaeos" /> 

Some of his groups of animals, such as ''Anhaima'' (animals without blood, translated as [[invertebrate]]s) and ''Enhaima'' (animals with blood, roughly the [[vertebrate]]s), as well as groups like the [[shark]]s and [[cetacean]]s, are commonly used.<ref>{{Cite book |title=The Lagoon: How Aristotle Invented Science |title-link=Aristotle's Lagoon |last=Leroi |first=Armand Marie |date=2014 |publisher=Bloomsbury |isbn=9781408836224 |pages=384–395 |author-link=Armand Marie Leroi}}</ref><ref name="von Lieven & Humar 2008">{{cite journal |last1=von Lieven |first1=Alexander Fürst |last2=Humar |first2=Marcel |title=A Cladistic Analysis of Aristotle's Animal Groups in the "Historia animalium" |journal=History and Philosophy of the Life Sciences |date=2008 |volume=30 |issue=2 |pages=227–262 |jstor=23334371 |pmid=19203017 |url=https://www.jstor.org/stable/23334371 |issn=0391-9714 |access-date=19 September 2023 |archive-date=27 November 2022 |archive-url=https://web.archive.org/web/20221127081940/https://www.jstor.org/stable/23334371 |url-status=live }}</ref><ref name="Laurin & Humar 2022">{{cite journal |last1=Laurin |first1=Michel |last2=Humar |first2=Marcel |title=Phylogenetic signal in characters from Aristotle's History of Animals |journal=Comptes Rendus Palevol |date=2022 |volume=21 |issue=1 |pages=1–16 |doi=10.5852/cr-palevol2022v21a1 |language=fr |doi-access=free }}</ref>

His student [[Theophrastus]] (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his ''[[Historia Plantarum (Theophrastus)|Historia Plantarum]]''. Several plant [[Genus|genera]] can be traced back to Theophrastus, such as ''[[Cornus (genus)|Cornus]]'', ''[[Crocus]]'', and ''[[Narcissus (plant)|Narcissus]]''.<ref name="Palaeos" />

==== Medieval ====
Taxonomy in the [[Middle Ages]] was largely based on the [[Aristotelian system]],<ref name="Roanoke" /> with additions concerning the philosophical and existential order of creatures. This included concepts such as the [[great chain of being]] in the Western [[scholasticism|scholastic]] tradition,<ref name="Roanoke" /> again deriving ultimately from Aristotle. 

The Aristotelian system did not classify plants or [[fungi]], due to the lack of microscopes at the time,<ref name="Britannica – Taxonomy" /> as his ideas were based on arranging the complete world in a single continuum, as per the ''scala naturae'' (the Natural Ladder).<ref name="Palaeos" /> This, as well, was taken into consideration in the great chain of being.<ref name="Palaeos" /> 

Advances were made by scholars such as [[Procopius]], [[Timotheus of Gaza]], [[Demetrios Pepagomenos]], and [[Thomas Aquinas]]. Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy.<ref name="Palaeos" />

==== Renaissance and early modern ====

During the [[Renaissance]] and the [[Age of Enlightenment]], categorizing organisms became more prevalent,<ref name="Palaeos" />
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".<ref>{{Cite encyclopedia |url= https://www.britannica.com/biography/Andrea-Cesalpino |title=Andrea Cesalpino {{!}} Italian physician, philosopher, and botanist |url-status=live |archive-url= https://web.archive.org/web/20170405075220/https://www.britannica.com/biography/Andrea-Cesalpino |archive-date=5 April 2017 |encyclopedia=Encyclopedia Britannica}}</ref> His [[Masterpiece|magnum opus]] ''De Plantis'' came out in 1583, and described more than 1,500 plant species.<ref>{{Cite book |url= https://archive.org/details/deplantislibrixv00cesa |title=De plantis libri XVI |last1=Cesalpino |first1=Andrea |last2=Marescotti |first2=Giorgio |date=1583 |publisher=Apud Georgium Marescottum |location=Florence |via=Internet Archive}}</ref><ref>{{Cite encyclopedia |url= https://www.britannica.com/biography/Andrea-Cesalpino#ref130098 |title=Andrea Cesalpino {{!}} Italian physician, philosopher, and botanist |url-status=live |archive-url= https://web.archive.org/web/20170405075220/https://www.britannica.com/biography/Andrea-Cesalpino#ref130098 |archive-date=5 April 2017 |encyclopedia=Encyclopedia Britannica}}</ref> Two large plant families that he first recognized are in use: the [[Asteraceae]] and [[Brassicaceae]].<ref>{{Cite book |title=International Edition Vegetables I: Asteraceae, Brassicaceae, Chenopodicaceae, and Cucurbitaceae (Handbook of Plant Breeding) |last=Jaime |first=Prohens |date=2010 |publisher=Springer |isbn=9781441924742}}</ref> 

In the 17th century, [[John Ray]] ([[England]], 1627–1705) wrote many important taxonomic works.<ref name="Britannica – Taxonomy">{{Cite encyclopedia |url= https://www.britannica.com/science/taxonomy |title=taxonomy {{!}} biology |url-status=live |archive-url= https://web.archive.org/web/20170405075451/https://www.britannica.com/science/taxonomy |archive-date=5 April 2017 |encyclopedia=Encyclopedia Britannica}}</ref> Arguably his greatest accomplishment was ''Methodus Plantarum Nova'' (1682),<ref>{{Cite book |last=John |first=Ray |url= https://www.biodiversitylibrary.org/item/84226#page/7/mode/1up |title=Methodus plantarum nova |publisher=impensis Henrici Faithorne & Joannis Kersey, ad insigne Rofæ Coemeterio D. Pauli |date=1682 |language=la |trans-title=New Method of Plants |archive-url= https://web.archive.org/web/20170929060003/http://www.biodiversitylibrary.org/item/84226#page/7/mode/1up |archive-date=29 September 2017 |url-status=live}}</ref> in which he published details of over 18,000 plant species. At the time, his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. 

The next major taxonomic works were produced by [[Joseph Pitton de Tournefort]] (France, 1656–1708).<ref>{{Cite encyclopedia |url= https://www.britannica.com/biography/Joseph-Pitton-de-Tournefort |title=Joseph Pitton de Tournefort {{!}} French botanist and physician |url-status=live |archive-url= https://web.archive.org/web/20170405075951/https://www.britannica.com/biography/Joseph-Pitton-de-Tournefort |archive-date=5 April 2017 |encyclopedia=Encyclopedia Britannica}}</ref> His work from 1700, ''Institutiones Rei Herbariae'', included more than 9,000 species in 698 genera, which directly influenced Linnaeus, as it was the text he used as a young student.<ref name="Manktelow" />

=== Linnaean era ===
{{Main|Linnaean taxonomy}}
[[File:Linné-Systema Naturae 1735.jpg|thumb|upright|Title page of ''[[Systema Naturae]]'', Leiden, 1735]]
The Swedish botanist [[Carl Linnaeus]] (1707–1778)<ref name="Roanoke" /> ushered in a new era of taxonomy. With his major works ''[[Systema Naturae]]'' 1st Edition in 1735,<ref>{{cite book |last=Linnaeus |first=Carl |author-link=Carl Linnaeus |date=1735 |title=Systema naturae, sive regna tria naturae systematice proposita per classes, ordines, genera, & species |language=la |publisher=Haak |location=Leiden}}</ref> ''[[Species Plantarum]]'' in 1753,<ref>{{cite book |last=Linnaeus |first=Carl |author-link=Carl Linnaeus |date=1753 |title=Species Plantarum |language=la |location=Stockholm}}</ref> and [[10th edition of Systema Naturae|''Systema Naturae'' 10th Edition]],<ref>{{cite book |last=Linnaeus |first=Carl |author-link=Carl Linnaeus |date=1758 |title=Systema naturae, sive regna tria naturae systematice proposita per classes, ordines, genera, & species |edition=10th |language=la |publisher=Haak |location=Leiden}}</ref> he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species,<ref name="Britannica – Linnaean">{{Cite encyclopedia |url= https://www.britannica.com/science/taxonomy/The-Linnaean-system |title=taxonomy – The Linnaean system {{!}} biology |url-status=live |archive-url= https://web.archive.org/web/20170405074215/https://www.britannica.com/science/taxonomy/The-Linnaean-system |archive-date=5 April 2017 |encyclopedia=Encyclopedia Britannica}}</ref> 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&nbsp;species, but also made it possible to identify plants and animals from his book, by using the smaller parts of the flower (known as the [[Linnaean system]]).<ref name="Britannica – Linnaean" />

Plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively).<ref>{{Cite journal |last=Donk |first=M. A. |date=December 1957 |title=Typification and later starting-points |url= http://www.iapt-taxon.org/historic/Congress/IBC_1959/Prop018-019.pdf |url-status=live |journal=Taxon |volume=6 |issue=9 |pages=245–256 |doi=10.2307/1217493 |jstor=1217493 |archive-url= https://web.archive.org/web/20150518091529/http://www.iapt-taxon.org/historic/Congress/IBC_1959/Prop018-019.pdf |archive-date=18 May 2015}}</ref> Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in ''[[Svenska Spindlar]]''<ref>{{Cite book |last1=Carl |first1=Clerck |last2=Carl |first2=Bergquist |last3=Eric |first3=Borg |last4=L. |first4=Gottman |last5=Lars |first5=Salvius |url= https://www.biodiversitylibrary.org/item/209583#page/7/mode/1up |title=Svenska spindlar |publisher=Literis Laur. Salvii |date=1757 |language=sv |trans-title=Swedish Spiders |archive-url= https://web.archive.org/web/20171201181959/https://www.biodiversitylibrary.org/item/209583#page/7/mode/1up |archive-date=1 December 2017 |url-status=live}}</ref>). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.<ref name="Manktelow" />

=== The digital era of taxonomy ===
Modern taxonomy is heavily influenced by technology such as [[DNA sequencing]], [[bioinformatics]], [[Biological database|databases]], and [[imaging]].

== Modern system of classification ==
{{Main|Evolutionary taxonomy|Phylogenetic nomenclature}}
[[File:Spindle diagram.jpg|thumb|upright=1.25|Evolution of the [[vertebrates]] at class level, width of spindles indicating number of families. Spindle diagrams are typical for [[evolutionary taxonomy]].]]
[[File:Cladogram vertebrata.jpg|thumb|upright=1.25|The same relationship, expressed as a [[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.<ref name="Britannica – Taxonomy" /> 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]] were ''[[Zoonomia]]'' in 1796 by [[Erasmus Darwin]] (Charles Darwin's grandfather), and [[Jean-Baptiste Lamarck]]'s ''[[Philosophie zoologique]]'' of 1809.<ref name="BiologyDiscussion" /> 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 (publisher, born 1802)|Robert Chambers]] in 1844.<ref>{{Cite book |url= http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/14098.ctl |title=Victorian Sensation: The Extraordinary Publication, Reception, and Secret Authorship of Vestiges of the Natural History of Creation |last=Secord |first=James A. |date=2000 |publisher=[[University of Chicago Press]] |isbn=9780226744100 |author-link=James A. Secord |archive-url= https://web.archive.org/web/20080516224806/http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/14098.ctl |archive-date=16 May 2008 |url-status=dead}}</ref>

With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of [[common descent]].<ref name="Britannica – since Linnaeus">{{Cite encyclopedia |url= https://www.britannica.com/science/taxonomy/Classification-since-Linnaeus |title=taxonomy – Classification since Linnaeus {{!}} biology |url-status=live |archive-url= https://web.archive.org/web/20170405075916/https://www.britannica.com/science/taxonomy/Classification-since-Linnaeus |archive-date=5 April 2017 |encyclopedia=Encyclopedia Britannica}}</ref> [[Tree of life (science)|Tree of life]] representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds.<ref>{{cite magazine |last=Black |first=Riley |date=7 December 2010 |title=Thomas Henry Huxley and the Dinobirds |url=https://www.smithsonianmag.com/science-nature/thomas-henry-huxley-and-the-dinobirds-88519294/ |magazine=Smithsonian Magazine |location=Washington, DC |publisher=[[Smithsonian Institution]] |access-date=10 November 2023 |archive-date=10 November 2023 |archive-url=https://web.archive.org/web/20231110094503/https://www.smithsonianmag.com/science-nature/thomas-henry-huxley-and-the-dinobirds-88519294/ |url-status=live }}</ref> Using the then newly discovered fossils of ''[[Archaeopteryx]]'' and ''[[Hesperornis]]'', [[Thomas Henry Huxley]] pronounced that they had evolved from dinosaurs, a group formally named by [[Richard Owen]] in 1842.<ref>{{cite book |author-link=Thomas Henry Huxley |last=Huxley |first=Thomas Henry |date=1876 |chapter=Lectures on Evolution |title=Collected Essays |volume=IV |pages=46–138 |url= http://aleph0.clarku.edu/huxley/CE4/LecEvol.html |archive-url= https://web.archive.org/web/20110628224543/http://aleph0.clarku.edu/huxley/CE4/LecEvol.html |archive-date=28 June 2011}} Original text w/ figures. First published as ''New York Tribune'', Extra no. 36.</ref><ref>{{Cite encyclopedia |url= https://www.britannica.com/biography/Thomas-Henry-Huxley |title=Thomas Henry Huxley {{!}} British biologist |url-status=live |archive-url= https://web.archive.org/web/20180206114405/https://www.britannica.com/biography/Thomas-Henry-Huxley |archive-date=6 February 2018 |encyclopedia=Encyclopedia Britannica}}</ref> The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of [[Evolutionary taxonomy|evolutionary taxonomic]] thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, [[paleontology|palaeontologists]] worked to understand the history of animals through the ages by linking together known groups.<ref>{{Cite book |title=The Meaning of Fossils: Episodes in the History of Palaeontology |url=https://books.google.com/books?id=-NuYXr8BszwC&pg=PA24 |last=Rudwick |first=M. J. S. |date=1985 |publisher=University of Chicago Press |isbn=9780226731032 |page=24}}</ref> With the [[modern synthesis (20th century)|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.<ref>{{Cite journal |last=Paterlini |first=Marta |date=September 2007 |title=There shall be order. The legacy of Linnaeus in the age of molecular biology |journal=EMBO Reports |volume=8 |issue=9 |pages=814–816 |doi=10.1038/sj.embor.7401061 |doi-access=free |pmc=1973966 |pmid=17767191}}</ref>

The [[cladistic]] method has emerged since the 1960s.<ref name="Britannica – since Linnaeus" /> In 1958, [[Julian Huxley]] used the term ''clade''.<ref name="BiologyDiscussion" /> Later, in 1960, Cain and Harrison introduced the term ''cladistic''.<ref name="BiologyDiscussion" /> The salient feature is arranging taxa in a hierarchical [[evolutionary tree]], with the desired objective of all named taxa being monophyletic.<ref name="Britannica – since Linnaeus" /> A taxon is called monophyletic if it includes all the descendants of an ancestral form.<ref name="Mike Taylor">{{Cite web |url= http://www.miketaylor.org.uk/dino/faq/s-class/phyletic/ |date=17 July 2003 |title=What do terms like monophyletic, paraphyletic and polyphyletic mean? |last=Taylor |first=Mike |website=miketaylor.org.uk |url-status=live |archive-url= https://web.archive.org/web/20100801072310/http://www.miketaylor.org.uk/dino/faq/s-class/phyletic/ |archive-date=1 August 2010}}</ref><ref name="NCSE">{{Cite web |url= https://ncse.com/book/export/html/2206 |title=Polyphyletic vs. Monophyletic |website=National Center for Science Education |url-status=dead |archive-url= https://web.archive.org/web/20170405170039/https://ncse.com/book/export/html/2206 |archive-date=5 April 2017}}</ref> Groups that have descendant groups removed from them are termed [[paraphyletic]],<ref name="Mike Taylor" /> while groups representing more than one branch from the tree of life are called [[polyphyletic]].<ref name="Mike Taylor" /><ref name="NCSE" /> Monophyletic groups are recognized and diagnosed on the basis of [[synapomorphies]], shared derived character states.<ref>{{cite book |last1=Brower |first1=Andrew V. Z. |first2=Randall T. |last2=Schuh |date=2021 |title=Biological Systematics: Principles and Applications |edition=3rd |publisher=Cornell University Press |location=Ithaca, New York |page=13}}</ref>

Cladistic classifications are compatible with traditional Linnean taxonomy and the Codes of [[Zoological nomenclature|Zoological]] and [[Botanical nomenclature]], to a certain extent.<ref>{{cite journal |last=Schuh |first=Randall T. |title=The Linnaean system and its 250-year persistence |journal=The Botanical Review |volume=69 |issue=1 |date=2003 |page=59|doi=10.1663/0006-8101(2003)069[0059:TLSAIY]2.0.CO;2 }}</ref> An alternative system of nomenclature, the ''[[PhyloCode|International Code of Phylogenetic Nomenclature]]'' or ''PhyloCode'' has been proposed, which regulates the formal naming of clades.<ref>{{Cite web |url= https://www.ohio.edu/phylocode/ |title=The PhyloCode |last1=Queiroz |first1=Philip D. |last2=de Cantino |first2=Kevin |website=Ohio.edu |url-status=dead |archive-url= https://web.archive.org/web/20160510200022/https://www.ohio.edu/phylocode/ |archive-date=10 May 2016}}</ref><ref name="Cantino & de Queiroz 2020" /><ref name="Laurin 2023 Advent" /> Linnaean ranks are optional and have no formal standing under the ''PhyloCode'', which is intended to coexist with the current, rank-based codes.<ref name="Cantino & de Queiroz 2020" /> While popularity of phylogenetic nomenclature has grown steadily in the last few decades,<ref name="Laurin 2023 Advent" /> it remains to be seen whether a majority of systematists will eventually adopt the ''PhyloCode'' or continue using the current systems of nomenclature that have been employed (and modified, but arguably not as much as some systematists wish)<ref name="Dubois 2007">{{cite journal |last1=Dubois |first1=Alain |title=Naming taxa from cladograms: A cautionary tale |journal=Molecular Phylogenetics and Evolution |date=1 February 2007 |volume=42 |issue=2 |pages=317–330 |doi=10.1016/j.ympev.2006.06.007 |pmid=16949307 |bibcode=2007MolPE..42..317D |url=https://doi.org/10.1016/j.ympev.2006.06.007 |issn=1055-7903 |access-date=21 October 2023 |archive-date=13 November 2023 |archive-url=https://web.archive.org/web/20231113101502/https://www.sciencedirect.com/science/article/abs/pii/S1055790306002375?via%3Dihub |url-status=live }}</ref><ref name="Dubois et al. 2019">{{cite journal |last1=Dubois |first1=Alain |last2=Bauer |first2=Aaron M. |last3=Ceríaco |first3=Luis M. P. |last4=Dusoulier |first4=François |last5=Frétey |first5=Thierry |last6=Löbl |first6=Ivan |last7=Lorvelec |first7=Olivier |last8=Ohler |first8=Annemarie |last9=Stopiglia |first9=Renata |last10=Aescht |first10=Erna |title=The Linz Zoocode project: A set of new proposals regarding the terminology, the Principles and Rules of zoological nomenclature. First report of activities (2014‒2019) |journal=Bionomina |date=17 December 2019 |volume=17 |issue=1 |pages=1–111 |doi=10.11646/BIONOMINA.17.1.1|doi-access=free }}</ref> for over 250 years.

=== Kingdoms and domains ===
[[File:Biological classification L Pengo vflip.svg|thumb|upright|The basic scheme of modern classification. Many other levels can be used; domain, the highest level within life, is both new and disputed.]]
{{Main|Kingdom (biology)|Domain (biology)}}

Well before Linnaeus, plants and animals were considered separate Kingdoms.<ref name="Kingdom classification">{{Cite news |url= http://www.biologydiscussion.com/biology/kingdom-classification-of-living-organism/5542 |title=Kingdom Classification of Living Organism |date=2 December 2014 |work=Biology Discussion |url-status=live |archive-url= https://web.archive.org/web/20170405073641/http://www.biologydiscussion.com/biology/kingdom-classification-of-living-organism/5542 |archive-date=5 April 2017}}</ref>{{unreliable source?|date=April 2017}} Linnaeus used this as the top rank, dividing the physical world into the vegetable, animal and mineral kingdoms. As advances in microscopy made the classification of microorganisms possible, the number of kingdoms increased, five- and six-kingdom systems being the most common.

[[Domain (biology)|Domains]] are a relatively new grouping. First proposed in 1977, [[Carl Woese]]'s [[three-domain system]] was not generally accepted until later.<ref>{{Cite web |url= http://www.igb.illinois.edu/about/archaea |title=Carl Woese {{!}} Carl R. Woese Institute for Genomic Biology |website=www.igb.Illinois.edu |url-status=dead |archive-url= https://web.archive.org/web/20170428163950/http://www.igb.illinois.edu/about/archaea |archive-date=28 April 2017}}</ref> One main characteristic of the three-domain method is the separation of [[Archaea]] and [[Bacteria]], previously grouped into the single kingdom Bacteria (a kingdom also sometimes called [[Monera]]),<ref name="Kingdom classification" /> with the [[Eukaryota]] for all organisms whose cells contain a [[Nucleus (biology)|nucleus]].<ref>{{cite book |editor1-link=Joel Cracraft |editor1-last=Cracraft |editor1-first=Joel |editor2-last=Donaghue |editor2-first=Michael J. |date=2004 |title=Assembling the Tree of Life |publisher=Oxford University Press |isbn=0195172345 |pages=45, 78, 555}}</ref> A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.<ref name="Kingdom classification" />

[[Thomas Cavalier-Smith]], who published extensively on the classification of [[protist]]s, in 2002<ref name="pmid11931142">{{cite journal |last=Cavalier-Smith |first=T. |title=The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa |journal=International Journal of Systematic and Evolutionary Microbiology |volume=52 |issue=Pt 2 |pages=297–354 |date=March 2002 |pmid=11931142 |doi=10.1099/00207713-52-2-297 |url=http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=11931142 |access-date=21 November 2022 |archive-date=29 July 2017 |archive-url=https://web.archive.org/web/20170729113756/http://ijs.microbiologyresearch.org/content/journal/ijsem |url-status=live }}</ref> proposed that the [[Neomura]], the clade that groups together the Archaea and [[Eukaryote|Eucarya]]<!--yeah, Woese used a 'c' here-->, would have evolved from Bacteria, more precisely from [[Actinomycetota]]. His 2004 classification treated the [[archaeobacteria]] as part of a subkingdom of the kingdom Bacteria, i.e., he rejected the three-domain system entirely.<ref name="CavalierSmith2004" /> Stefan Luketa in 2012 proposed a five "dominion" system, adding [[Prion]]obiota ([[Non-cellular life|acellular]] and without [[nucleic acid]]) and [[Virus]]obiota (acellular but ''with'' nucleic acid) to the traditional three domains.<ref name="Luketa2012">{{Cite journal |last=Luketa |first=S. |date=2012 |title=New views on the megaclassification of life |url= http://protistology.ifmo.ru/num7_4/luketa_protistology_7-4.pdf |url-status=live |journal=Protistology |volume=7 |issue=4 |pages=218–237 |archive-url= https://web.archive.org/web/20150402150257/http://protistology.ifmo.ru/num7_4/luketa_protistology_7-4.pdf |archive-date=2 April 2015}}</ref>
{{center|{{Biological systems}}}}

=== 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,<ref name="Adl-et-al-2012">{{Cite journal |last1=Adl |first1=S. M. |last2=Simpson |first2=A. G. B. |last3=Lane |first3=C. E. |last4=Lukeš |first4=J. |last5=Bass |first5=D. |last6=Bowser |first6=S. S. |display-authors=etal |date=December 2015 |title=The revised classification of eukaryotes |journal=Journal of Eukaryotic Microbiology |volume=59 |issue=5 |pages=429–493 |doi=10.1111/j.1550-7408.2012.00644.x |pmc=3483872 |pmid=23020233}}</ref><ref name="Adl-et-al-2019">{{Cite journal |last1=Adl |first1=S. M. |last2=Bass |first2=D. |last3=Lane |first3=C. E. |last4=Lukeš |first4=J. |last5=Schoch |first5=C. L. |last6=Smirnov |first6=A. |display-authors=etal |date=2019 |title=Revisions to the classification, nomenclature, and diversity of eukaryotes |journal=Journal of Eukaryotic Microbiology |volume=66 |issue=1 |pages=4–119 |doi=10.1111/jeu.12691 |pmc= 6492006|pmid=30257078|doi-access=free}}</ref> which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015,<ref name="Ruggiero-et-al-2015">{{Cite journal |last1=Ruggiero |first1=Michael A. |last2=Gordon |first2=D. P. |last3=Orrell |first3=T. M. |last4=Bailly |first4=N. |last5=Bourgoin |first5=T. |last6=Brusca |first6=R. C. |display-authors=etal |date=2015 |title=A higher level classification of all living organisms |journal=PLOS ONE |volume=10 |issue=4 |pages=e0119248 |bibcode=2015PLoSO..1019248R |bibcode-access=free |doi=10.1371/journal.pone.0119248 |pmc=4418965 |pmid=25923521|doi-access=free}}</ref> covering both eukaryotes and [[prokaryote]]s to the rank of Order, although both exclude fossil representatives.<ref name="Ruggiero-et-al-2015" /> A separate compilation (Ruggiero, 2014)<ref>{{Cite journal |last=Döring |first=Markus |title=Families of Living Organisms (FALO) |url=https://www.gbif.org/dataset/8067e0a2-a26d-4831-8a1e-21b9118a299c |website=GBIF |date=August 13, 2015 |doi=10.15468/tfp6yv |access-date=11 March 2020 |archive-date=2 March 2020 |archive-url=https://web.archive.org/web/20200302232032/https://www.gbif.org/dataset/8067e0a2-a26d-4831-8a1e-21b9118a299c |url-status=live }}</ref> covers extant taxa to the rank of Family. Other, database-driven treatments include the [[Encyclopedia of Life]], the [[Global Biodiversity Information Facility]], the [[NCBI taxonomy database]], the [[Interim Register of Marine and Nonmarine Genera]], the [[Open Tree of Life]], and the [[Catalogue of Life]]. The [[Paleobiology Database]] is a resource for fossils.

== Application ==
Biological taxonomy is a sub-discipline of [[biology]], and is generally practiced by biologists known as "taxonomists", though enthusiastic [[Natural history|naturalists]] are also frequently involved in the publication of new taxa.<ref>{{Cite web |url=https://www.smithsonianmag.com/science-nature/the-big-ugly-problem-heart-of-taxonomy-180964629/ |first1=Benjamin |last1=Jones |date=September 7, 2017 |title=A Few Bad Scientists Are Threatening to Topple Taxonomy |website=Smithsonian |access-date=24 February 2019 |archive-date=8 February 2019 |archive-url=https://web.archive.org/web/20190208041357/https://www.smithsonianmag.com/science-nature/the-big-ugly-problem-heart-of-taxonomy-180964629/ |url-status=live }}</ref> Because taxonomy aims to describe and organize [[life]], the work conducted by taxonomists is essential for the study of [[biodiversity]] and the resulting field of [[conservation biology]].<ref>{{Cite web |url= http://www.nhm.ac.uk/nature-online/science-of-natural-history/taxonomy-systematics/what-is-taxonomy/index.html |title=What is taxonomy? |publisher=Natural History Museum |location=London |url-status=dead |archive-url= https://web.archive.org/web/20131001152618/http://www.nhm.ac.uk/nature-online/science-of-natural-history/taxonomy-systematics/what-is-taxonomy/index.html |archive-date=1 October 2013 |access-date=23 December 2017}}</ref><ref>{{Cite journal |last=McNeely |first=Jeffrey A. |date=2002 |title=The role of taxonomy in conserving biodiversity |url= https://pdfs.semanticscholar.org/7b06/e3d09692ef9f2b464fbfb7807ff32a35ce47.pdf |url-status=dead |journal=Journal for Nature Conservation |volume=10 |issue=3 |pages=145–153 |doi=10.1078/1617-1381-00015 |bibcode=2002JNatC..10..145M |s2cid=16953722 |s2cid-access=free |archive-url= https://web.archive.org/web/20171224155349/https://pdfs.semanticscholar.org/7b06/e3d09692ef9f2b464fbfb7807ff32a35ce47.pdf |archive-date=24 December 2017 |via=Semantic Scholar}}</ref>

=== Classifying organisms ===
{{Main|Taxonomic rank}}

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]].<ref>{{Cite news |url= https://www.mnemonic-device.com/biology/taxonomy/domain-kingdom-phylum-class-order-family-genus-species/ |title=Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species |website=Mnemonic Device |url-status=live |archive-url= https://web.archive.org/web/20170606171902/https://www.mnemonic-device.com/biology/taxonomy/domain-kingdom-phylum-class-order-family-genus-species/ |archive-date=6 June 2017}}</ref>{{NoteTag|This ranking system, except for "Strain", can be remembered by the mnemonic "Do Kings Play Chess On Fine Glass Sets?"}}

=== Taxonomic descriptions ===
{{See also|Species description}}
[[File:Nepenthes smilesii type specimen.jpg|thumb|upright|[[Type (biology)|Type]] specimen for ''[[Nepenthes smilesii]]'', a tropical [[pitcher plant]]]]

The "definition" of a taxon is encapsulated by its description or its diagnosis or by both combined. There are no set rules governing the definition of taxa, but the naming and publication of new taxa is governed by sets of rules.<ref name="Herbarium" /> 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'').<ref>{{Cite web |url= http://www.animalbase.uni-goettingen.de/zooweb/servlet/AnimalBase/loadcachedpage?url=animalbase-code.html |title=ICZN Code |website=AnimalBase |access-date=8 April 2017 |archive-date=3 October 2022 |archive-url= https://web.archive.org/web/20221003055350/http://www.animalbase.uni-goettingen.de/zooweb/servlet/AnimalBase/loadcachedpage?url=animalbase-code.html |url-status=dead }}</ref> 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'').<ref>{{Cite web |title=International Code of Nomenclature for algae, fungi, and plants |url= http://www.iapt-taxon.org/nomen/main.php |work=IAPT-Taxon.org |publisher=[[International Association for Plant Taxonomy]] |url-status=live |archive-url= https://web.archive.org/web/20130111104255/http://www.iapt-taxon.org/nomen/main.php |archive-date=11 January 2013}}</ref>

The initial description of a taxon involves five main requirements:<ref>{{Cite web |title=How can I describe new species? |url= http://iczn.org/content/how-can-i-describe-new-species |work=ICZN.org |publisher=[[International Commission on Zoological Nomenclature]] |url-status=dead |archive-url= https://web.archive.org/web/20120306133052/http://iczn.org/content/how-can-i-describe-new-species |archive-date=6 March 2012 |access-date=21 May 2020}}</ref>

# 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 species|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, which may or may not be based on morphology<ref>{{Cite journal |last1=Lawley |first1=Jonathan W. |last2=Gamero-Mora |first2=Edgar |last3=Maronna |first3=Maximiliano M. |last4=Chiaverano |first4=Luciano M. |last5=Stampar |first5=Sérgio N. |last6=Hopcroft |first6=Russell R. |last7=Collins |first7=Allen G. |last8=Morandini |first8=André C. |date=19 September 2022 |title=Morphology is not always useful for diagnosis, and that's ok: Species hypotheses should not be bound to a class of data. Reply to Brown and Gibbons (S Afr J Sci. 2022;118(9/10), Art. #12590) |url=https://sajs.co.za/article/view/14495 |journal=South African Journal of Science |volume=118 |issue=9/10 |doi=10.17159/sajs.2022/14495 |s2cid=252562185 |issn=1996-7489 |doi-access=free |access-date=20 October 2022 |archive-date=20 October 2022 |archive-url=https://web.archive.org/web/20221020063714/https://sajs.co.za/article/view/14495 |url-status=live }}</ref>). 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.<ref>{{Cite encyclopedia |title=Taxonomy – Evaluating taxonomic characters |url= https://www.britannica.com/science/taxonomy/Evaluating-taxonomic-characters |url-status=live |archive-url= https://web.archive.org/web/20190422143927/https://www.britannica.com/science/taxonomy/Evaluating-taxonomic-characters |archive-date=22 April 2019 |encyclopedia=[[Encyclopædia Britannica]]}}</ref>

=== Author citation ===
{{Main|Author citation (botany)|Author citation (zoology)}}
An "authority" may be placed after a scientific name.<ref name="AJE">{{Cite web |url= http://www.aje.com/en/arc/editing-tip-scientific-names-species/ |title=Editing Tip: Scientific Names of Species |publisher=American Journal Experts, Research Square Company |website=AJE.com |url-status=live |archive-url= https://web.archive.org/web/20170409021714/http://www.aje.com/en/arc/editing-tip-scientific-names-species/ |archive-date=9 April 2017}}</ref> The authority is the name of the scientist or scientists who first validly published the name.<ref name="AJE" /> 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".<ref>{{Cite web |url= http://study.com/academy/lesson/carolus-linnaeus-classification-taxonomy-contributions-to-biology.html |title=Carolus Linnaeus: Classification, Taxonomy & Contributions to Biology – Video & Lesson Transcript |website=Study.com |url-status=live |archive-url= https://web.archive.org/web/20170409021600/http://study.com/academy/lesson/carolus-linnaeus-classification-taxonomy-contributions-to-biology.html |archive-date=9 April 2017}}</ref> The names of authors are often abbreviated: the abbreviation ''L.'', for ''Linnaeus,'' is commonly used. In botany, there is, in fact, a regulated list of standard abbreviations (see [[list of botanists by author abbreviation]]).<ref>{{Cite web |url= http://www.biocyclopedia.com/index/biological_classification.php |title=Biological Classification |last=Biocyclopedia.com |website=biocyclopedia.com |url-status=live |archive-url= https://web.archive.org/web/20170514164313/http://www.biocyclopedia.com/index/biological_classification.php |archive-date=14 May 2017}}</ref> The system for assigning authorities differs slightly between [[Author citation (botany)|botany]] and [[Author citation (zoology)|zoology]].<ref name="Herbarium" /> 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.<ref>{{Cite web |url= http://www.annelida.net/zootax-tutor.html |title=Zoological nomenclature: a basic guide for non-taxonomist authors |website=Annelida.net |url-status=live |archive-url= https://web.archive.org/web/20170316112709/http://www.annelida.net/zootax-tutor.html |archive-date=16 March 2017}}</ref>

== Phenetics ==
[[File:Phylogenetics.svg|thumb|300px|A comparison of phylogenetic and phenetic (character-based) concepts]]
{{Main|Phenetics}}
In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships.<ref name="BiologyDiscussion" /> It results in a measure of hypergeometric "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by [[Cladistics|cladistic]] analyses, as phenetic methods do not distinguish shared ancestral (or [[plesiomorph]]ic) traits from shared derived (or [[apomorphic]]) traits.<ref>{{Cite web |title=Classification |url= https://projects.ncsu.edu/project/evoresources/Evolutionary%20medicine/classification/classification16.htm |publisher=[[North Carolina State University]] |url-status=live |archive-url= https://web.archive.org/web/20170414163250/https://projects.ncsu.edu/project/evoresources/Evolutionary%20medicine/classification/classification16.htm |archive-date=14 April 2017 |access-date=27 April 2017}}</ref> However, certain phenetic methods, such as [[neighbor joining]], have persisted, as rapid estimators of relationships when more advanced methods (such as [[Bayesian inference]]) are too computationally expensive.<ref>{{Cite web |title=Molecular Marker Glossary |url= http://www.uwyo.edu/dbmcd/molmark/mcdgloss.html |last=McDonald |first=David |date=Fall 2008 |publisher=[[University of Wyoming]] |url-status=live |archive-url= https://web.archive.org/web/20070610123503/http://www.uwyo.edu/dbmcd/molmark/McDGloss.html |archive-date=10 June 2007}}</ref>

== Databases ==
{{Main|Taxonomic database}}
Modern taxonomy uses [[database]] technologies to search and catalogue classifications and their documentation.<ref>{{Cite journal |last1=Wood |first1=Dylan |last2=King |first2=Margaret |last3=Landis |first3=Drew |last4=Courtney |first4=William |last5=Wang |first5=Runtang |last6=Kelly |first6=Ross |last7=Turner |first7=Jessica A. |last8=Calhoun |first8=Vince D. |date=26 August 2014 |title=Harnessing modern web application technology to create intuitive and efficient data visualization and sharing tools |journal=Frontiers in Neuroinformatics |volume=8 |pages=71 |doi=10.3389/fninf.2014.00071 |issn=1662-5196 |pmc=4144441 |pmid=25206330|doi-access=free}}</ref> While there is no commonly used database, there are comprehensive databases such as the ''[[Catalogue of Life]]'', which attempts to list every documented species.<ref>{{Cite web |url= http://www.theplantlist.org/about/ |title= About – The Plant List |website= theplantlist.org |access-date= 8 April 2017 |archive-date= 21 June 2017 |archive-url= https://web.archive.org/web/20170621190909/http://www.theplantlist.org/about/ |url-status= live }}</ref> The catalogue listed 1.64&nbsp;million species for all kingdoms {{as of|2016|4|lc=on}}, claiming coverage of more than three-quarters of the estimated species known to modern science.<ref name="About the Catalogue of Life">{{Cite web |url= http://www.catalogueoflife.org/annual-checklist/2016/info/about |title=About the Catalogue of Life: 2016 Annual Checklist |website=Catalogue of Life |publisher=[[Integrated Taxonomic Information System]] (ITIS) |url-status=live |archive-url= https://web.archive.org/web/20160515032942/http://www.catalogueoflife.org/annual-checklist/2016/info/about |archive-date=15 May 2016 |access-date=22 May 2016}}</ref>

== See also ==
{{Div col|small=yes}}
* [[Automated species identification]]
* [[Bacterial taxonomy]]
* [[Cluster analysis]]
* [[Consortium for the Barcode of Life]]
* [[Consortium of European Taxonomic Facilities]]
* [[Genetypes]]
* [[Glossary of scientific naming]]
* [[Identification (biology)]]
* ''[[Incertae sedis]]''
* [[Open Tree of Life]]
* [[Parataxonomy]]
* [[Phenogram]]
* [[Set theory]]
* [[Taxonomy]] (general)
* [[Virus classification]]
{{div col end}}

== Notes ==
{{NoteFoot}}

== References ==
{{Reflist}}

== Bibliography ==
{{refbegin}}
* {{Cite book |url=https://books.google.com/books?id=X7lfMACvjs4C |title=Systematic Botany |last=Datta |first=Subhash Chandra |date=1988 |publisher=New Age International |isbn=9788122400137 |edition=4 |location=New Delhi |access-date=25 January 2015 |archive-date=13 November 2023 |archive-url=https://web.archive.org/web/20231113101351/https://books.google.com/books?id=X7lfMACvjs4C |url-status=live }}
* {{Cite book |url=https://books.google.com/books?id=VfQnuwh3bw8C |title=Plant taxonomy and biosystematics |last=Stace |first=Clive A. |date=1989 |publisher=[[Cambridge University Press]] |isbn=9780521427852 |edition=2nd. |location=Cambridge |author-link=Clive A. Stace |access-date=19 April 2015 |orig-year=1980 |archive-date=13 January 2023 |archive-url=https://web.archive.org/web/20230113180249/https://books.google.com/books?id=VfQnuwh3bw8C |url-status=live }}
* {{Cite book |url=https://books.google.com/books?id=0bYs8F0Mb9gC |title=Plant Taxonomy: The Systematic Evaluation of Comparative Data |last=Stuessy |first=Tod F. |date=2009 |publisher=Columbia University Press |isbn=9780231147125 |access-date=6 February 2014 |archive-date=13 November 2023 |archive-url=https://web.archive.org/web/20231113101356/https://books.google.com/books?id=0bYs8F0Mb9gC |url-status=live }}
*{{Cite journal |last=Turrill |first=W. B. |date=1938 |title=The Expansion Of Taxonomy With Special Reference To Spermatophyta |journal=Biological Reviews |volume=13 |issue=4 |pages=342–373 |doi=10.1111/j.1469-185X.1938.tb00522.x|s2cid=84905335}}
* {{cite book |last1=Wiley |first1=Edward O. |first2=Bruce S. |last2=Lieberman |date=2011 |title=Phylogenetics: Theory and Practice of Phylogenetic Systematics |publisher=John Wiley & Sons |edition=2nd |isbn=9780470905968}}
{{refend}}

== External links ==
* [http://www.nhm.ac.uk/nature-online/science-of-natural-history/taxonomy-systematics/what-is-taxonomy/index.html What is taxonomy?] at the [http://www.nhm.ac.uk/ ''Natural History Museum London'']
* [https://www.ncbi.nlm.nih.gov/Taxonomy/ Taxonomy] at [https://www.ncbi.nlm.nih.gov/ NCBI] the ''National Center for Biotechnology Information''
* [https://www.uniprot.org/taxonomy/ Taxonomy] at [https://www.uniprot.org/ UniProt] the ''Universal Protein Resource''
* [https://www.itis.gov/ ITIS] the ''Integrated Taxonomic Information System''
* [http://www.cetaf.org/ CETaF] the ''Consortium of European Taxonomic Facilities''
* [http://species.wikimedia.org/ Wikispecies] ''free species directory''
* [https://www.thescienceclass.online/2019/10/biological-classification.html Biological classification.] {{Webarchive |url= https://web.archive.org/web/20200813180358/https://www.thescienceclass.online/2019/10/biological-classification.html |date=13 August 2020}}

{{Branches of biology}}
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[[Category:Taxonomy (biology)| ]]
[[Category:Biological nomenclature]]
[[Category:Biological classification]]
[[Category:Neo-Latin terminology]]