Editing Domain (biology)

{{short description|Taxonomic rank}}
{{Biological classification}}
{{Use dmy dates|date=April 2016}}
In [[Biology|biological]] [[Taxonomy (biology)|taxonomy]], a '''domain''' ({{IPAc-en|d|ə|ˈ|m|eɪ|n}} or {{IPAc-en|d|oʊ|ˈ|m|eɪ|n}}) ([[Latin]]: ''regio''<ref name=Woese1990/>), also '''dominion''',<ref name=Moore1974/> '''superkingdom''', '''realm''', or '''empire''', is the highest [[taxonomic rank]] of all [[organism]]s taken together. It was introduced in the [[three-domain system]] of taxonomy devised by [[Carl Woese]], [[Otto Kandler]] and [[Mark Wheelis]] in 1990.<ref name=Woese1990/>

According to the domain system, the [[tree of life (biology)|tree of life]] consists of either three domains, [[Archaea]], [[Bacteria]], and [[Eukarya]],<ref name=Woese1990>{{cite journal |vauthors=Woese C, Kandler O, Wheelis M |year=1990 |title=Towards a natural system of organisms: Proposal for the domain Archaea, Bacteria, and Eucarya |journal=[[Proc Natl Acad Sci USA]] |volume=87 |issue=12 |pages=4576–4579 |pmid=2112744 |doi=10.1073/pnas.87.12.4576 |pmc=54159 |bibcode=1990PNAS...87.4576W |doi-access=free }}</ref> or [[Two-domain system|two domains]], Archaea and Bacteria, with Eukarya included in Archaea.<ref name=":02">{{cite journal |last1=Nobs |first1=Stephanie-Jane |last2=MacLeod |first2=Fraser I. |last3=Wong |first3=Hon Lun |last4=Burns |first4=Brendan P. |year=2022 |title=Eukarya the chimera: Eukaryotes, a secondary innovation of the two domains of life? |journal=Trends in Microbiology |lang=en |volume=30 |issue=5 |pages=421–431 |doi=10.1016/j.tim.2021.11.003 |pmid=34863611 |s2cid=244823103 |url=https://linkinghub.elsevier.com/retrieve/pii/S0966842X21002699}}</ref><ref name=":3">{{cite journal |last=Doolittle |first=W. Ford |year=2020 |title=Evolution: Two domains of life or three? |journal=Current Biology |lang=en |volume=30 |issue=4 |pages=R177–R179 |doi=10.1016/j.cub.2020.01.010 |doi-access=free |pmid=32097647}}</ref> In the three-domain [[model]], the first two are [[prokaryote]]s, [[Unicellular organism|single-celled]] [[microorganism]]s without a [[nuclear envelope|membrane-bound]] [[cell nucleus|nucleus]]. All [[organism]]s that have a cell nucleus and other [[membrane-bound organelle]]s are included in Eukarya and called [[Eukaryote|eukaryotes]].

[[Non-cellular life]], most notably the [[virus]]es, is not included in this system. Alternatives to the three-domain system include the earlier [[two-empire system]] (with the empires Prokaryota and Eukaryota), and the [[eocyte hypothesis]] (with two domains of Bacteria and Archaea, with Eukarya included as a branch of Archaea).

== Terminology ==
The term ''domain'' was proposed by [[Carl Woese]], [[Otto Kandler]], and [[Mark Wheelis]] (1990) in a [[three-domain system]]. This term represents a synonym for the category of dominion (Lat. ''dominium''), introduced by [[Royall T. Moore|Moore]] in 1974.<ref name=Moore1974>{{cite journal |author=Moore R.T. |author-link=Royall T. Moore |year=1974 |title=Proposal for the recognition of super ranks |journal=Taxon |volume=23 |issue=4 |pages=650–652 |doi=10.2307/1218807 |jstor=1218807 |url=http://www.iapt-taxon.org/historic/Congress/IBC_1975/Prop034bis-037.pdf}}</ref>

== Development of the domain system ==
[[Carl Linnaeus]] made the classification "domain" popular in the famous [[taxonomy]] system he created in the middle of the eighteenth century. This system was further improved by the studies of [[Charles Darwin]] later on but could not classify [[bacteria]] easily, as they have very few observable features to compare to the other domains.<ref>{{Cite web |title=Domains of Life, Genomics {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/topicpage/the-two-empires-and-three-domains-of-14432998/ |access-date=2022-12-01 |website=www.nature.com |language=en}}</ref> 

Carl Woese made a revolutionary breakthrough when, in 1977, he compared the [[nucleotide]] sequences of the [[16S ribosomal RNA|16s ribosomal RNA]] and discovered that the [[Rank (taxonomy)|rank]] "domain" contained three branches, not two as scientists had previously thought. Initially, due to their physical similarities, [[Archaea]] and [[Bacteria]] were classified together and called "archaebacteria". However, scientists now know that these two domains are hardly similar and are internally distinctly different.<ref>{{Cite web |title=Taxonomy I {{!}} Biology |url=https://www.visionlearning.com/en/library/Biology/2/Taxonomy-I/70 |access-date=2022-12-01 |website=Visionlearning |language=en}}</ref>

== Characteristics of the three domains ==
{{PhylomapB|align = left|size=300px|caption=A speculatively rooted tree for [[RNA]] [[gene]]s, showing major branches Bacteria, Archaea, and Eukaryota}}
[[File:Two domain tree.png|200px|thumb|The three-domain tree and the [[eocyte hypothesis]] (two-domain tree), 2008.<ref>{{cite journal |author1=Cox, C.J. |author2=Foster, P.G. |author3=Hirt, R.P. |author4=Harris, S.R. |author5=Embley, T.M. |author-link5=Martin Embley |year=2008 |title=The archaebacterial origin of eukaryotes |journal=[[Proc Natl Acad Sci USA]] |volume=105 |issue=51 |pages=20356–61 |doi=10.1073/pnas.0810647105 |pmid=19073919 |pmc=2629343 |bibcode=2008PNAS..10520356C |doi-access=free }}</ref>]]
[[File:Collapsed tree labels simplified.png|thumb|200px|[[Phylogenetic tree]] showing the relationship between the eukaryotes and other forms of life, 2006.<ref>{{cite journal |vauthors=Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P |title=Toward automatic reconstruction of a highly resolved tree of life |journal=Science |volume=311 |issue=5765 |pages=1283–7 |year=2006 |pmid=16513982 |doi=10.1126/science.1123061 |bibcode=2006Sci...311.1283C|url=http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf |citeseerx=10.1.1.381.9514 |s2cid=1615592 }}</ref> Eukaryotes are colored red, archaea green, and bacteria blue.]]
{{main|Three-domain system}}

Each of these three domains contains unique [[ribosomal RNA]]. This forms the basis of the three-domain system. While the presence of a [[nuclear envelope|nuclear membrane]] differentiates the [[Eukarya]] from the [[Archaea]] and [[Bacteria]], both of which lack a [[nuclear envelope]], the Archaea and Bacteria are distinct from each other due to differences in the [[biochemistry]] of their [[cell membrane]]s and [[RNA]] markers.<ref name="Woese1990"/>

{{clear left}}
===Archaea===
{{further|Archaea}}
Archaea are  prokaryotic cells, typically characterized by membrane lipids that are branched [[hydrocarbon]] chains attached to glycerol by ether linkages. The presence of these ether linkages in Archaea adds to their ability to withstand extreme temperatures and highly [[acid]]ic conditions, but many archaea live in mild environments. [[Halophile]]s (organisms that thrive in highly salty environments) and [[hyperthermophiles]] (organisms that thrive in extremely hot environments) are examples of Archaea.<ref name="Woese1990"/>

Archaea are relatively small. They range from 0.1&nbsp;μm to 15&nbsp;μm diameter and up to 200&nbsp;μm long, about the size of bacteria and the [[mitochondria]] found in eukaryotic cells. Members of the genus ''[[Thermoplasma]]'' are the smallest Archaea.<ref name="Woese1990"/>

===Bacteria===
{{further|Bacteria}}
[[Cyanobacteria]] and [[mycoplasmas]] are two examples of bacteria.
Even though bacteria are prokaryotic cells like Archaea, their [[cell membranes]] are instead made of [[phospholipid bilayers]], with none of the ether linkages that Archaea have. Internally, bacteria have different RNA structures in their [[ribosomes]], hence they are grouped into a different category. In the two- and three-domain systems, this puts them into a separate domain.

There is a great deal of diversity in the domain [[Bacteria]]. That diversity is further confounded by the [[horizontal gene transfer|exchange of genes]] between different bacterial lineages. The occurrence of duplicate genes between otherwise distantly-related bacteria makes it nearly impossible to distinguish bacterial species, count the bacterial species on the Earth, or organize them into a tree-like structure (unless the structure includes cross-connections between branches, making it a "network" instead of a "tree").<ref name=Woese1990/>

===Eukarya===
{{further|Eukaryote}}
Members of the domain Eukarya—called ''eukaryotes''—have membrane-bound organelles (including a nucleus containing genetic material) and are represented by five [[Kingdom (biology)|kingdoms]]: [[Plantae]], [[Protozoa]], [[Animalia]], [[Chromista]], and [[Fungi]].<ref name="Woese1990"/>

==Exclusion of viruses and prions==
{{Main article|Non-cellular life}}
{{Further|Virus|Prion}}

The three-domain system includes no form of non-cellular [[life]]. Stefan Luketa proposed a five-dominion system in 2012, adding [[Prion]]obiota (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 S.|year=2012|title=New views on the megaclassification of life|url=http://protistology.ifmo.ru/num7_4/luketa_protistology_7-4.pdf|journal=Protistology|volume=7|issue=4|pages=218–237|access-date=4 October 2016|archive-date=2 April 2015|archive-url=https://web.archive.org/web/20150402150257/http://protistology.ifmo.ru/num7_4/luketa_protistology_7-4.pdf|url-status=dead}}</ref>

==Alternative classifications==
{{Biological classification with acellular}}
Alternative classifications of life include:
* The [[two-empire system]] or '''superdomain system''', proposed by [[Ernst Mayr|Mayr]] (1998), with top-level groupings of Prokaryota (or [[Monera]]) and Eukaryota.<ref name=Mayr1998>{{cite journal |author=Mayr, E. |author-link=Ernst Mayr |year=1998 |title=Two empires or three? |journal=PNAS |volume=95 |issue=17 |pages=9720–9723 |pmid=9707542 |doi=10.1073/pnas.95.17.9720 |doi-access=free |pmc=33883 |bibcode=1998PNAS...95.9720M }}</ref><ref name="CavalierSmith2004">{{cite journal |last=Cavalier-Smith |first=T. |author-link=Thomas Cavalier-Smith |year=2004 |title=Only six kingdoms of life |journal=Proc. R. Soc. Lond. B |volume=271 |issue=1545 |pages=1251–1262 |doi=10.1098/rspb.2004.2705 |pmid=15306349 |pmc=1691724 |url=http://www.cladocera.de/protozoa/cavalier-smith_2004_prs.pdf |access-date=2010-04-29}}</ref>
* The [[eocyte hypothesis]], proposed by [[James A. Lake|Lake]] ''et al''. (1984),<ref name=Lake/> which posits two domains, Bacteria and Archaea, with Eukaryota included as a subordinate clade branching from Archaea.<ref name=Archibald>{{cite journal |first1=John M. |last1=Archibald |date=23 December 2008 |title=The eocyte hypothesis and the origin of eukaryotic cells |journal=PNAS |volume=105 |issue=51 |pages=20049–20050 |doi=10.1073/pnas.0811118106 |doi-access=free |pmid=19091952 |pmc=2629348 |bibcode=2008PNAS..10520049A}}</ref><ref name=Lake>{{cite journal |first1=J.A. |last1=Lake |author1-link=James A. Lake |first2=Eric |last2=Henderson |first3=Melanie |last3=Oakes |first4=Michael W. |last4=Clark |date=June 1984 |title=Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes |journal=PNAS |volume=81 |issue=12 |pages=3786–3790 |doi=10.1073/pnas.81.12.3786 |doi-access=free |pmid=6587394 |pmc=345305|bibcode=1984PNAS...81.3786L}}</ref><ref name=2domains>{{cite journal |first1=Tom A. |last1= Williams |first2=Peter G. |last2=Foster |first3=Cymon J. |last3=Cox |first4=T. Martin |last4=Embley |author4-link=Martin Embley |date=December 2013 |title=An archaeal origin of eukaryotes supports only two primary domains of life |journal=Nature |volume=504 |issue=7479 |pages=231–236 |doi=10.1038/nature12779 |pmid=24336283|bibcode=2013Natur.504..231W |s2cid= 4461775 |url=https://eprint.ncl.ac.uk/fulltext.aspx?url=199146/704E71B4-8D68-4F3C-93BA-E73C50449593.pdf&pub_id=199146 }}</ref>

== See also ==
* [[Biological dark matter]]
* [[Neomura]], which is the two domains of life of Archaea and Eukaryota
* [[Phylogenetics]]
* [[Protein structure]]
* [[Realm (virology)]], an equivalent rank for non-cellular life
* [[Systematics]]

== References ==
{{Reflist}}

== External links ==
* {{YouTube|id=gSuRoDGpKWw|title=Learn Biology: Classification-Domains}}

{{Taxonomic ranks}}
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[[Category:Domains (biology)| ]]