domain (biology)

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 Moore in 1974.{{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}}

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.{{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}}

Carl Woese made a revolutionary breakthrough when, in 1977, he compared the nucleotide sequences of the 16s ribosomal RNA and discovered that the 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.{{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}}

{{PhylomapB|align = left|size=300px|caption=A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota}}

File:Two domain tree.png (two-domain tree), 2008.{{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 }}]]

File:Collapsed tree labels simplified.png showing the relationship between the eukaryotes and other forms of life, 2006.{{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 }} 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 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 membranes and RNA markers.

{{clear left}}

{{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 acidic conditions, but many archaea live in mild environments. Halophiles (organisms that thrive in highly salty environments) and hyperthermophiles (organisms that thrive in extremely hot environments) are examples of Archaea.

Archaea are relatively small. They range from 0.1 μm to 15 μm diameter and up to 200 μm long, about the size of bacteria and the mitochondria found in eukaryotic cells. Members of the genus Thermoplasma are the smallest Archaea.

{{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 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").

{{further|Eukaryote}}

Members of the domain Eukarya—called eukaryotes—have membrane-bound organelles (including a nucleus containing genetic material) and are represented by five kingdoms: Plantae, Protozoa, Animalia, Chromista, and Fungi.

{{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 Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains.{{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}}

{{Biological classification with acellular}}

Alternative classifications of life include:

• The two-empire system or superdomain system, proposed by Mayr (1998), with top-level groupings of Prokaryota (or Monera) and Eukaryota.{{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 }}{{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}}
• The eocyte hypothesis, proposed by Lake et al. (1984), which posits two domains, Bacteria and Archaea, with Eukaryota included as a subordinate clade branching from Archaea.{{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}}{{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}}{{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 }}

• 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

{{Reflist}}

• {{YouTube|id=gSuRoDGpKWw|title=Learn Biology: Classification-Domains}}

{{Taxonomic ranks}}

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