Editing Taxonomy (biology) (section)

== 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=dead |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" 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|bibcode=1989Taxon..38..335S }}</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 |date=5 February 2011 |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|bibcode=1992Taxon..41..653M }}</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>