Domain (biology)
<imagemap> File:Biological_classification_L_Pengo_vflip.svg|thumb|right|150px|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. rect 100 15 225 57 Life rect 100 78 225 120 Domain rect 100 142 225 184 Kingdom rect 100 205 225 247 Phylum rect 100 268 225 310 Class rect 100 332 225 374 Order rect 100 395 225 437 Family rect 100 459 225 501 Genus rect 100 522 225 564 Species
default File:Biological classification L Pengo vflip.svg desc none </imagemap> In biological taxonomy, a domain (/dəˈmeɪn/ or /doʊˈmeɪn/) (Latin: regio[1]), also dominion,[2] superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990.[1]
According to the domain system, the tree of life consists of either three domains, Archaea, Bacteria, and Eukarya,[1] or two domains, Archaea and Bacteria, with Eukarya included in Archaea.[3][4] In the three-domain model, the first two are prokaryotes, single-celled microorganisms without a membrane-bound nucleus. All organisms that have a cell nucleus and other membrane-bound organelles are included in Eukarya and called eukaryotes.
Non-cellular life, most notably the viruses, 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 Moore in 1974.[2]
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.[5]
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 wildly different.[6]
Characteristics of the three domains
<imagemap> File:Phylogenetic tree.svg|left|A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota|300px|thumb rect 248 3 520 77 Bacteria rect 816 3 1088 77 Archaea rect 1296 3 1622 77 Eukaryota rect 26 775 180 826 Aquifex rect 26 695 248 746 Thermotoga rect 19 574 248 667 Bacteroides–Cytophaga rect 11 467 283 518 Planctomyces rect 32 410 304 451 "Cyanobacteria" rect 171 338 443 389 Proteobacteria rect 247 198 470 248 Spirochetes rect 467 262 647 351 Gram-positives rect 645 195 857 246 Chloroflexi rect 644 485 934 571 Thermoproteus–Pyrodictium rect 686 410 958 485 Thermococcus celer rect 705 359 1027 410 Methanococcus rect 690 309 1110 359 Methanobacterium rect 819 258 1104 309 Methanosarcina rect 1080 313 1316 364 Haloarchaea rect 1045 195 1288 246 Entamoebae rect 1337 181 1461 271 Slime molds rect 1518 198 1682 249 Animals rect 1575 256 1694 306 Fungi rect 1575 342 1704 392 Plants rect 1573 401 1719 452 Ciliates rect 1569 492 1772 542 Flagellates rect 1559 575 1825 626 Trichomonads rect 1544 668 1809 718 Microsporidia rect 1534 759 1788 810 Diplomonads </imagemap>
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.[1]
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.[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
Cyanobacteria and mycoplasmas are two examples of bacteria. Even though bacteria are prokaryotic cells just like Archaea, their cell membranes are instead made of phospholipid bilayers. Bacteria cell membranes are distinct from Archean membranes: They characteristically have 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").[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, Protozoa, Animalia, Chromista, and Fungi.[1]
Exclusion of viruses and prions
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.[9]
Alternative classifications
| Taxonomical root node | Two superdomains (controversial) | Two empires | Three domains | Five Dominiums[10] | Five kingdoms | Six kingdoms | Eocyte hypothesis |
|---|---|---|---|---|---|---|---|
| Biota / Vitae / Life | Acytota / Aphanobionta non-cellular life |
Virusobiota (Viruses, Viroids) | |||||
| Prionobiota (Prions) | |||||||
| Cytota cellular life |
Prokaryota / Procarya (Monera) |
Bacteria | Bacteria | Monera | Eubacteria | Bacteria | |
| Archaea | Archaea | Archaebacteria | Archaea including eukaryotes | ||||
| Eukaryota / Eukarya | Protista | ||||||
| Fungi | |||||||
| Plantae | |||||||
| Animalia | |||||||
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.[11][12]
- The eocyte hypothesis, proposed by Lake et al. (1984),[13] which posits two domains, Bacteria and Archaea, with Eukaryota included as a subordinate clade branching from Archaea.[14][13][15]
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
- ^ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 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): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
- ^ 2.0 2.1 Moore R.T. (1974). "Proposal for the recognition of super ranks" (PDF). Taxon. 23 (4): 650–652. doi:10.2307/1218807. JSTOR 1218807.
- ^ Nobs, Stephanie-Jane; MacLeod, Fraser I.; Wong, Hon Lun; Burns, Brendan P. (2022). "Eukarya the chimera: Eukaryotes, a secondary innovation of the two domains of life?". Trends in Microbiology. 30 (5): 421–431. doi:10.1016/j.tim.2021.11.003. PMID 34863611. S2CID 244823103.
- ^ Doolittle, W. Ford (2020). "Evolution: Two domains of life or three?". Current Biology. 30 (4): R177–R179. doi:10.1016/j.cub.2020.01.010. PMID 32097647.
- ^ "Domains of Life, Genomics | Learn Science at Scitable". www.nature.com. Retrieved 1 December 2022.
- ^ "Taxonomy I | Biology". Visionlearning. Retrieved 1 December 2022.
- ^ 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.
- ^ 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. S2CID 1615592.
- ^ Luketa S. (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237. Archived from the original (PDF) on 2 April 2015. Retrieved 4 October 2016.
- ^ Luketa, Stefan (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237.
- ^ Mayr, E. (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.
- ^ 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.
- ^ 13.0 13.1 Lake, J.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.
- ^ 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.
- ^ 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. S2CID 4461775.
External links
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