Kingdom (biology)

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The various levels of the scientific classification system. Life Domain Kingdom Phylum Class Order Family Genus Species

The hierarchy of biological classification's eight major taxonomic ranks, which is an example of definition by genus and differentia. A domain contains one or more kingdoms. Intermediate minor rankings are not shown.

In biology, kingdom (Latin: regnum, pl. regna) is a taxonomic rank, which is either the highest rank or in the more recent three-domain system, the rank below domain. Kingdoms are divided into smaller groups called phyla (in zoology) or divisions in botany. The complete sequence of ranks is life, domain, kingdom, phylum, class, order, family, genus, and species.

Currently, textbooks from the United States use a system of six kingdoms (Animalia, Plantae, Fungi, Protista, Archaea, Bacteria) while British, Australian and Latin American textbooks may describe five kingdoms (Animalia, Plantae, Fungi, Protista, and Prokaryota or Monera).

Historically, the number of kingdoms in widely accepted classifications has grown from two to six. However, phylogenetic research from about 2000 onwards does not support any of the traditional systems.

Two kingdoms

The classification of living things into animals and plants is an ancient one. Aristotle (384–322 BC) classified animal species in his work the History of Animals, and his pupil Theophrastus (c. 371–c. 287 BC) wrote a parallel work on plants (the History of Plants).[1]

Carolus Linnaeus (1707–1778) laid the foundations for modern biological nomenclature, now regulated by the Nomenclature Codes. He distinguished two kingdoms of living things: Regnum Animale ('animal kingdom') for animals and Regnum Vegetabile ('vegetable kingdom') for plants. (Linnaeus also included minerals, placing them in a third kingdom, Regnum Lapideum.) Linnaeus divided each kingdom into classes, later grouped into phyla for animals and divisions for plants.

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Three kingdoms

In 1674, Antonie van Leeuwenhoek, often called the "father of microscopy", sent the Royal Society of London a copy of his first observations of microscopic single-celled organisms. Until then the existence of such microscopic organisms was entirely unknown. At first these organisms were divided into animals and plants and placed in the appropriate Kingdom. However, by the mid-19th century it had become clear that "the existing dichotomy of the plant and animal kingdoms [had become] rapidly blurred at its boundaries and outmoded".[2] In 1866, following earlier proposals by Richard Owen and John Hogg, Ernst Haeckel proposed a third kingdom of life. Haeckel revised the content of this kingdom a number of times before settling on a division based on whether organisms were unicellular (Protista) or multicellular (animals and plants).[2]

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Four kingdoms

The development of microscopy, and the electron microscope in particular, revealed an important distinction between those unicellular organisms whose cells do not have a distinct nucleus, prokaryotes, and those unicellular and multicellular organisms whose cells do have a distinct nucleus, eukaryotes. In 1938, Herbert F. Copeland proposed a four-kingdom classification, moving the two prokaryotic groups, bacteria and "blue-green algae", into a separate Kingdom Monera.[2]

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It gradually became apparent how important the prokaryote/eukaryote distinction is, and in the 1960s Stanier and van Niel popularized Édouard Chatton's much earlier proposal to recognize this division in a formal classification. This required the creation, for the first time, of a rank above kingdom, a superkingdom or empire, also called a domain.[3]

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Five kingdoms

The differences between fungi and other organisms regarded as plants had long been recognized. For example, at one point Haeckel moved the fungi out of Plantae into Protista, before changing his mind.[2] Robert Whittaker recognized an additional kingdom for the Fungi. The resulting five-kingdom system, proposed in 1969 by Whittaker, has become a popular standard and with some refinement is still used in many works and forms the basis for new multi-kingdom systems. It is based mainly on differences in nutrition; his Plantae were mostly multicellular autotrophs, his Animalia multicellular heterotrophs, and his Fungi multicellular saprotrophs. The remaining two kingdoms, Protista and Monera, included unicellular and simple cellular colonies.[4] The five kingdom system may be combined with the two empire system.

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Six kingdoms

From around the mid-1970s onwards, there was an increasing emphasis on molecular level comparisons of genes (initially ribosomal RNA genes) as the primary factor in classification; genetic similarity was stressed over outward appearances and behavior. Taxonomic ranks, including kingdoms, were to be groups of organisms with a common ancestor, whether monophyletic (all descendants of a common ancestor) or paraphyletic (only some descendants of a common ancestor). Based on such RNA studies, Carl Woese divided the prokaryotes (Kingdom Monera) into two groups, called Eubacteria and Archaebacteria, stressing that there was as much genetic difference between these two groups as between either of them and all eukaryotes. Eukaryote groups, such as plants, fungi and animals may look different, but are more similar to each other in their genetic makeup at the molecular level than they are to either the Eubacteria or Archaebacteria. (It was also found that the eukaryotes are more closely related, genetically, to the Archaebacteria than they are to the Eubacteria.) Although the primacy of the eubacteria-archaebacteria divide has been questioned, it has also been upheld by subsequent research.[5]

Woese attempted to establish a "three primary kingdom" or "urkingdom" system.[6] In 1990, the name "domain" was proposed for the highest rank.[7] The six-kingdom system shown below represents a blending of the classic five-kingdom system and Woese's three-domain system. Such six-kingdom systems have become standard in many works.

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Woese also recognized that the kingdom Protista was not a monophyletic group and might be further divided at the level of kingdom.

Cavalier-Smith's six kingdoms

Thomas Cavalier-Smith has published extensively on the evolution and classification of life, particularly protists. His views have been influential but controversial, and not always widely accepted.[8] In 1998, he published a six-kingdom model,[9] which has been revised in subsequent papers. The version published in 2009 is shown below.[10] (Compared to the version he published in 2004,[11] the alveolates and the rhizarians have been moved from Kingdom Protozoa to Kingdom Chromista.) Cavalier-Smith does not accept the importance of the fundamental eubacteria–archaebacteria divide put forward by Woese and others and supported by recent research.[5] His Kingdom Bacteria includes the Archaebacteria as part of a subkingdom along with a group of eubacteria (Posibacteria). Nor does he accept the requirement for groups to be monophyletic. His Kingdom Protozoa includes the ancestors of Animalia and Fungi. Thus the diagram below does not represent an evolutionary tree.

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International Society of Protistologists Classification 2005

One hypothesis of eukaryotic relationships, modified from Simpson and Roger (2004).

The "classic" six-kingdom system is still recognizably a modification of the original two-kingdom system: Animalia remains; the original category of plants has been split into Plantae and Fungi; and single-celled organisms have been introduced and split into Bacteria, Archaea and Protista.

Research published in the 21st century has produced a rather different picture. In 2004, a review article by Simpson and Roger noted that the Protista were "a grab-bag for all eukaryotes that are not animals, plants or fungi". They argued that only monophyletic groups–an ancestor and all of its descendents — should be accepted as formal ranks in a classification. On this basis, the diagram opposite (redrawn from their article) showed the real 'kingdoms' (their quotation marks) of the eukaryotes.[12] A classification which followed this approach was produced in 2005 for the International Society of Protistologists, by a committee which "worked in collaboration with specialists from many societies". It divided the eukaryotes into the same six "supergroups".[13] Although the published classification deliberately did not use formal taxonomic ranks, other sources[cn] have treated each of the six as a separate kingdom.

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In this system, the traditional kingdoms have vanished. For example, research shows that the multicellular animals (Metazoa) are descended from the same ancestor as the unicellular choanoflagellates and the fungi. A classification system which places these three groups into different kingdoms (with multicellular animals forming Animalia, choanoflagellates part of Protista and Fungi a separate kingdom) is not monophyletic. The monophyletic group is the Opisthokonta, made up of all those organisms believed to have descended from a common ancestor, some of which are unicellular (choanoflagellates), some of which are multicellular but not closely related to animals (some fungi), and others of which are traditional multicellular animals.[13]

However, in the same year as the International Society of Protistologists' classification was published (2005), doubts were being expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata,[14] and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.[15]

As of 2010, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup,[16] so that Rhizara is not one of the main eukaryote groups.[10][17][18][19][20] Beyond this, there does not appear to be a consensus. Rogozin et al. in 2009 noted that "The deep phylogeny of eukaryotes is an extremely difficult and controversial problem."[21] As of December 2010, there appears to be a consensus that the 2005 six supergroup model does not reflect the true phylogeny of the eukaryotes and hence how they should be classified, although there is no agreement as to the model which should replace it.[17][18][22]

Summary

The sequence from the two-kingdom system up to Cavalier-Smith's six-kingdom system can be summarized in the table below. Template:Biological systems Note that the equivalences in this table are not perfect. For example, Haeckel placed the red algae (his Florideae, modern Florideophyceae) and blue-green algae (his Archephyta, modern Cyanobacteria) in his Plantae.

One or other of the kingdom-level classifications of life is still widely employed as a useful way of grouping organisms, notwithstanding the problems with this approach:

  • Kingdoms such as Bacteria represent grades rather than clades, and so are rejected by phylogenetic classification systems.
  • Research in the 21st century does not support the classification of the eukaryotes into any of the standard systems. As of April 2010, the situation appears to be that there is no set of kingdoms sufficiently supported by current research to gain widespread acceptance; as Roger & Simpson say: "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution."[23]

See also

References

  1. Singer, Charles J. (1931), A short history of biology, a general introduction to the study of living things, Oxford: Clarendon Press, OCLC 1197036 
  2. 2.0 2.1 2.2 2.3 Scamardella, Joseph M. (1999), "Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista", International Microbiology 2 (4): 207–16, PMID 10943416 
  3. Stanier, R.Y. & Van Neil, C.B. (1962), "The concept of a bacterium", Archiv Für Mikrobiologie 42 (1): 17–35, doi:10.1007/BF00425185, PMID 13916221 
  4. Whittaker, R.H. (January 1969), "New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms", Science 163 (3863): 150–60, Bibcode 1969Sci...163..150W, doi:10.1126/science.163.3863.150, PMID 5762760, http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=5762760 
  5. 5.0 5.1 Dagan, T.; Roettger, M.; Bryant & Martin, W. (2010), "Genome Networks Root the Tree of Life between Prokaryotic Domains", Genome Biology and Evolution 2: (0): 379–92, doi:10.1093/gbe/evq025 
  6. Balch, W.E.; Magrum, L.J.; Fox, G.E.; Wolfe, C.R.; & Woese, C.R. (August 1977), "An ancient divergence among the bacteria", J. Mol. Evol. 9 (4): 305–11, doi:10.1007/BF01796092, PMID 408502 
  7. Woese, C.R.; Kandler, O. & Wheelis, M. (1990), "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya", Proc Natl Acad Sci U S A 87 (12): 4576–9, Bibcode 1990PNAS...87.4576W, doi:10.1073/pnas.87.12.4576, PMC 54159, PMID 2112744 
  8. Palaeos.com, Origins of the Eukarya, archived from the original on 2010-04-29, http://www.webcitation.org/5pLfYf6U7, retrieved 2010-04-29 
  9. Cavalier-Smith, T. (1998), "A revised six-kingdom system of life", Biological Reviews 73 (03): 203–66, doi:10.1111/j.1469-185X.1998.tb00030.x, PMID 9809012, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=685 
  10. 10.0 10.1 Cavalier-Smith, Thomas (2009), "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree", Biology Letters 6 (3): 342–5, doi:10.1098/rsbl.2009.0948, PMC 2880060, PMID 20031978 
  11. Cavalier-Smith, T. (2004), "Only six kingdoms of life", Proc. R. Soc. Lond. B 271 (1545): 1251–62, doi:10.1098/rspb.2004.2705, PMC 1691724, PMID 15306349, http://www.cladocera.de/protozoa/cavalier-smith_2004_prs.pdf, retrieved 2010-04-29 
  12. Simpson, Alastair G.B. & Roger, Andrew J. (2004), "The real ‘kingdoms’ of eukaryotes", Current Biology 14 (17): R693–6, doi:10.1016/j.cub.2004.08.038, PMID 15341755 
  13. 13.0 13.1 Adl, Sina M.; et al. (2005), "The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists", Journal of Eukaryotic Microbiology 52 (5): 399, doi:10.1111/j.1550-7408.2005.00053.x, PMID 16248873, http://www.blackwell-synergy.com/doi/abs/10.1111/j.1550-7408.2005.00053.x 
  14. Harper, J.T.; Waanders, E. & Keeling, P. J. (2005), "On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes", Nt. J. System. Evol. Microbiol. 55 (Pt 1): 487–496, doi:10.1099/ijs.0.63216-0, PMID 15653923, http://www.botany.ubc.ca/keeling/PDF/05chromalvJSEM.pdf 
  15. Parfrey, Laura W.; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya, Debashish; Patterson, David J. & Katz, Laura A. (2006), "Evaluating Support for the Current Classification of Eukaryotic Diversity", PLoS Genet. 2 (12): e220, doi:10.1371/journal.pgen.0020220, PMC 1713255, PMID 17194223 
  16. Burki et al. 2007, p. 4
  17. 17.0 17.1 Burki, Fabien; Shalchian-Tabrizi, Kamran; Minge, Marianne; Skjæveland, Åsmund; Nikolaev, Sergey I.; Jakobsen, Kjetill S. & Pawlowski, Jan (2007), Butler, Geraldine, ed., "Phylogenomics Reshuffles the Eukaryotic Supergroups", PLoS ONE 2 (8): e790, Bibcode 2007PLoSO...2..790B, doi:10.1371/journal.pone.0000790, PMC 1949142, PMID 17726520, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000790 
  18. 18.0 18.1 Burki, Fabien; Shalchian-Tabrizi, Kamran & Pawlowski, Jan (2008), "Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes", Biology Letters 4 (4): 366–369, doi:10.1098/rsbl.2008.0224, PMC 2610160, PMID 18522922. 
  19. Burki, F. et al.; Inagaki, Y.; Brate, J.; Archibald, J. M.; Keeling, P. J.; Cavalier-Smith, T.; Sakaguchi, M.; Hashimoto, T. et al. (2009), "Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates", Genome Biology and Evolution 1 (0): 231–8, doi:10.1093/gbe/evp022, PMC 2817417, PMID 20333193 
  20. Hackett, J.D.; Yoon, H.S.; Li, S.; Reyes-Prieto, A.; Rummele, S.E. & Bhattacharya, D. (2007), "Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of Rhizaria with chromalveolates", Mol. Biol. Evol. 24 (8): 1702–13, doi:10.1093/molbev/msm089, PMID 17488740 
  21. Rogozin, I.B.; Basu, M.K.; Csürös, M. & Koonin, E.V. (2009), "Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes", Genome Biology and Evolution 1 (0): 99–113, doi:10.1093/gbe/evp011, PMC 2817406, PMID 20333181 
  22. Kim, E.; Graham, L.E. & Redfield, Rosemary Jeanne (2008), Redfield, Rosemary Jeanne, ed., "EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata", PLoS ONE 3 (7): e2621, Bibcode 2008PLoSO...3.2621K, doi:10.1371/journal.pone.0002621, PMC 2440802, PMID 18612431 
  23. Roger, A.J. & Simpson, A.G.B. (2009), "Evolution: Revisiting the Root of the Eukaryote Tree", Current Biology 19 (4): R165–7, doi:10.1016/j.cub.2008.12.032, PMID 19243692 

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