Domain (biology)

In biological taxonomy, a domain [/də(ʊ)ˈmeɪn/] (Latin: regio[1]), also superkingdom or empire,[2] is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese et.al. in 1990[1].

According to this system, the tree of life consists of three domains: Archaea, Bacteria, and Eukarya.[1] The first two are all prokaryotic microorganisms, or single-celled organisms whose cells have no nucleus. All life that has a nucleus and membrane-bound organelles, and multicellular organisms, is included in the Eukarya.

Taxonomic Rank Graph
Main taxonomic ranks: Domain, kingdom, phylum, class, order, family, genus, and species.
LifeDomainKingdomPhylumClassOrderFamilyGenusSpecies
The hierarchy of biological classification's eight major taxonomic ranks. Life is divided into domains, which are subdivided into further groups. Intermediate minor rankings are not shown.

Domain / Dominion

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.[3] However, only Stefan Luketa uses the term "dominion".[4] He created two additional domains ("dominions") for Prions and Viruses.

Characteristics of the Three Domains

BacteriaArchaeaEucaryotaAquifexThermotogaCytophagaBacteroidesBacteroides-CytophagaPlanctomycesCyanobacteriaProteobacteriaSpirochetesGram-positive bacteriaGreen filantous bacteriaPyrodicticumThermoproteusThermococcus celerMethanococcusMethanobacteriumMethanosarcinaHalophilesEntamoebaeSlime moldAnimalFungusPlantCiliateFlagellateTrichomonadMicrosporidiaDiplomonad
A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota
Two domain tree
The three-domains tree and the Eocyte hypothesis (Two domains tree), 2008.[5]
Collapsed tree labels simplified
Phylogenetic tree showing the relationship between the eukaryotes and other forms of life, 2006[6] Eukaryotes are colored red, archaea green, and bacteria blue.

Each of these three domains contains unique rRNA. 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 membrane, distinct biochemical and RNA markers differentiate the Archaea and Bacteria from each other.[1]

Archaea

Archaea are prokaryota cells, typically characterized by membrane lipids that are branched hydrocarbon chains attached to glycerol by ether linkages. The presence of these other linkages in Archaea adds to their ability to withstand extreme temperatures and highly acidic conditions, but many archeae 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.[1]

Archaea evolved many cell sizes, but all are relatively small. Their size ranges from 0.1 μm to 15 μm diameter and up to 200 μm long. They are about the size of bacteria, or similar in size to the mitochondria found in eukaryotic cells. Members of the genus Thermoplasma are the smallest of the Archaea.[1]

Bacteria

Even though bacteria are prokaryotic cells just like Archaea, their membranes are made of oligonucleotide acid attached to glycerol by ester linkages. Cyanobacteria and mycoplasmas are two examples of bacteria. They characteristically do not have ether linkages like Archaea, and they are grouped into a different category—and hence a different domain. There is a great deal of diversity in this domain. Confounded by that diversity and horizontal gene transfer, it is next to impossible to determine how many species of bacteria exist on the planet, or to organize them in a tree-structure, without cross-connections between branches.[1]

Eukarya

Members of the domain Eukarya—called eukaryotes—have membrane-bound organelles (including a nucleus containing genetic material) and are represented by five kingdoms: Plantae, Protista, Animalia, Chromista, and Fungi.[1]

Exclusion of viruses and prions

The three-domain system does not include any form of non-cellular life. As of 2011 there was talk about nucleocytoplasmic large DNA viruses possibly being a fourth domain of life, a view supported by researchers in 2012.[7] Stefan Luketa proposed a five-domain system in 2012, adding Prionobiota (acellular and without nucleic acid) and Virobiota (acellular but with nucleic acid) to the traditional three domains.[4]

Alternative classifications

Alternative classifications of life include:

See also

References

  1. ^ a b c d e f g h Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proc Natl Acad Sci USA. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744. Retrieved 11 February 2010.
  2. ^ "The Scientific Taxonomy and Classification of all Creatures". Retrieved 19 October 2015.
  3. ^ Moore R. T. (1974). "Proposal for the recognition of super ranks" (PDF). Taxon. 23 (4): 650–652. doi:10.2307/1218807. JSTOR 1218807.
  4. ^ a b Luketa S. (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237.
  5. ^ Cox, C. J.; Foster, P. G.; Hirt, R. P.; Harris, S. R.; Embley, T. M. (2008). "The archaebacterial origin of eukaryotes". Proc Natl Acad Sci USA. 105 (51): 20356–61. Bibcode:2008PNAS..10520356C. doi:10.1073/pnas.0810647105. PMC 2629343. PMID 19073919.
  6. ^ Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006). "Toward automatic reconstruction of a highly resolved tree of life" (PDF). Science. 311 (5765): 1283–7. Bibcode:2006Sci...311.1283C. CiteSeerX 10.1.1.381.9514. doi:10.1126/science.1123061. PMID 16513982.
  7. ^ Nasir, A; Kim, KM; Caetano-Anolles, G (2012). "Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria, and Eukarya". BMC Evol. Biol. 12: 156. doi:10.1186/1471-2148-12-156. PMC 3570343. PMID 22920653.
  8. ^ Mayr, Ernst (1998). "Two empires or three?". PNAS. 95 (17): 9720–9723. Bibcode:1998PNAS...95.9720M. doi:10.1073/pnas.95.17.9720. PMC 33883. PMID 9707542.
  9. ^ Cavalier-Smith, T. (2004). "Only six kingdoms of life" (PDF). Proc. R. Soc. Lond. B. 271 (1545): 1251–1262. doi:10.1098/rspb.2004.2705. PMC 1691724. PMID 15306349. Retrieved 29 April 2010.
  10. ^ Archibald, John M. (23 December 2008). "The eocyte hypothesis and the origin of eukaryotic cells". PNAS. 105 (51): 20049–20050. Bibcode:2008PNAS..10520049A. doi:10.1073/pnas.0811118106. PMC 2629348. PMID 19091952.
  11. ^ Lake, James A.; Henderson, Eric; Oakes, Melanie; Clark, Michael W. (June 1984). "Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes". PNAS. 81 (12): 3786–3790. Bibcode:1984PNAS...81.3786L. doi:10.1073/pnas.81.12.3786. PMC 345305. PMID 6587394.
  12. ^ Williams, Tom A.; Foster, Peter G.; Cox, Cymon J.; Embley, T. Martin (December 2013). "An archaeal origin of eukaryotes supports only two primary domains of life". Nature. 504 (7479): 231–236. Bibcode:2013Natur.504..231W. doi:10.1038/nature12779. PMID 24336283.

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Two-empire system

The two-empire system (two-superkingdom system) was the top-level biological classification system in general use before the establishment of the three-domain system. It classified life into Prokaryota and Eukaryota. When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

Some prominent scientists, such as Thomas Cavalier-Smith, still hold to the two-empire system. The late Ernst Mayr, one of the 20th century's leading evolutionary biologists, wrote dismissively of the three-domain system, "I cannot see any merit at all in a three empire cladification." Additionally, the scientist Radhey Gupta argues for a return to the two-empire system, claiming that the primary division within prokaryotes should be among those surrounded by a single membrane (monoderm), including gram-positive bacteria and archaebacteria, and those with an inner and outer cell membrane (diderm), including gram-negative bacteria.

This system was preceded by Haeckel's three-kingdom system: Animalia, Plantae and Protista.

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