Kingdom (biology)

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Life Domain Kingdom Phylum Class Order Family Genus Species
The hierarchy of biological classification's eight major taxonomic ranks. A domain contains one or more kingdoms. Intermediate minor rankings are not shown.

In biology, kingdom (Latin: regnum, pl. regna) is the second highest taxonomic rank below domain. Kingdoms are divided into smaller groups called phyla. Traditionally, textbooks from the United States used a system of six kingdoms (Animalia, Plantae, Fungi, Protista, Archaea, and Bacteria) while British, Australian and Latin American textbooks used five kingdoms (Animalia, Plantae, Fungi, Protoctista, and Prokaryota/Monera). Some recent classifications based on modern cladistics have explicitly abandoned the term "kingdom", noting that the traditional kingdoms are not monophyletic, i.e., do not consist of all the descendants of a common ancestor.

Definition and associated terms[edit]

When Carl Linnaeus introduced the rank-based system of nomenclature into biology, the highest rank was given the name "kingdom" and was followed by four other main or principal ranks: the class, order, and genus.[1] Later two further main ranks were introduced, making the sequence kingdom, phylum or division, class, order, family, genus and species.[2] In the 1960s a rank was introduced above kingdom, namely domain (or empire), so that kingdom is no longer the highest rank.

Prefixes can be added so subkingdom and infrakingdom are the two ranks immediately below kingdom. Superkingdom may be considered as an equivalent of domain or empire or as an independent rank between kingdom and domain or subdomain. In some classification systems the additional rank branch (Latin: ramus) can be inserted between subkingdom and infrakingdom (e.g. Protostomia and Deuterostomia in the classification of Cavalier-Smith[3]).

Modern view[edit]

The three domains of life[edit]

Bacteria Archaea Eucaryota Aquifex Thermotoga Cytophaga Bacteroides Bacteroides-Cytophaga Planctomyces Cyanobacteria Proteobacteria Spirochetes Gram-positive bacteria Green filantous bacteria Pyrodicticum Thermoproteus Thermococcus celer Methanococcus Methanobacterium Methanosarcina Halophiles Entamoebae Slime mold Animal Fungus Plant Ciliate Flagellate Trichomonad Microsporidia Diplomonad
A phylogenetic tree based on rRNA data showing Woese's three-domain system. All smaller branches can be considered kingdoms.


From around the mid-1970s onwards, there was an increasing emphasis on comparisons of genes on the molecular level (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, thought life could be divided into three large divisions and referred to them as the "three primary kingdom" model or "urkingdom" model.[4] In 1990, the name "domain" was proposed for the highest rank.[5] Woese divided the prokaryotes (previously classified as the Kingdom Monera) into two groups, called Eubacteria and Archaebacteria or Archaea, stressing that there was as much genetic difference between these two groups as between either of them and all eukaryotes.

According to genetic data, although eukaryote groups such as plants, fungi, and animals may look different, they are more closely related to each other than they are to either the Eubacteria or Archaea. It was also found that the eukaryotes are more closely related to the Archaea than they are to the Eubacteria. Although the primacy of the Eubacteria-Archaea divide has been questioned, it has been upheld by subsequent research.[6] There is no consensus on how many kingdoms exist in the classification scheme proposed by Woese.

How many kingdoms are present in the Eukarya?[edit]

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

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 held that only monophyletic groups should be accepted as formal ranks in a classification and that, while this approach had been impractical previously (necessitating "literally dozens of eukaryotic ‘kingdoms’"), it had now become possible to divide the eukaryotes into "just a few major groups that are probably all monophyletic". On this basis, the diagram opposite (redrawn from their article) showed the real 'kingdoms' (their quotation marks) of the eukaryotes.[7] 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".[8] The published classification deliberately did not use formal taxonomic ranks, including that of "kingdom".


life

Domain Bacteria

Bacteria





Domain Archaea

Archaea





Domain Eukarya

Excavata — Various flagellate protozoa



Amoebozoa — most lobose amoeboids and slime moulds



Opisthokontaanimals, fungi, choanoflagellates, etc.



RhizariaForaminifera, Radiolaria, and various other amoeboid protozoa



ChromalveolataStramenopiles (or Heterokonta), Haptophyta, Cryptophyta (or cryptomonads), and Alveolata



Archaeplastida (or Primoplantae) — Land plants, green algae, red algae, and glaucophytes






In this system the multicellular animals (Metazoa) are descended from the same ancestor as the unicellular choanoflagellates and the fungi which form the Opisthokonta. [8] Plants are thought to be more distantly related to animals and fungi.

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,[9] and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.[10]

As of 2010, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup,[11] so that Rhizaria is not one of the main eukaryote groups.[12][13][14][15][16] 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."[17] 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.[13][14][18]

Historical development[edit]

The classification of living things into animals and plants is an ancient one. Aristotle (384–322 BC) classified animal species in his History of Animals, while his pupil Theophrastus (c. 371–c. 287 BC) wrote a parallel work, the Historia Plantarum, on plants.[19]

Carolus Linnaeus (1707–1778) laid the foundations for modern biological nomenclature, now regulated by the Nomenclature Codes, in 1735. He distinguished two kingdoms of living things: Regnum Animale ('animal kingdom') and Regnum Vegetabile ('vegetable kingdom', for plants). Linnaeus also included minerals in his classification system, placing them in a third kingdom, Regnum Lapideum.


life

Regnum Plantae



Regnum Animalia




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. Despite this, Linnaeus did not include any microscopic creatures in his original taxonomy.

Haeckel's original (1866) conception of the three kingdoms of life, including the new kingdom Protista. Notice the inclusion of the cyanobacterium Nostoc with plants.

At first, microscopic organisms were classified within the animal and plant kingdoms. However, by the mid-19th century, it had become clear to many that "the existing dichotomy of the plant and animal kingdoms [had become] rapidly blurred at its boundaries and outmoded".[20] In 1866, Ernst Haeckel proposed a third kingdom of life, the Protista, for "neutral organisms" which were neither animal nor plant. 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).[20]


life

Kingdom Plantae



Kingdom Protista



Kingdom Animalia




The development of the electron microscope revealed important distinctions 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, elevating the protist classes of bacteria (Monera) and blue-green algae (Phycochromacea) to phyla in the novel Kingdom Monera.[20]

The importance of the distinction between prokaryotes and eukaryotes gradually became apparent. In the 1960s, Stanier and van Niel popularised Édouard Chatton's much earlier proposal to recognise this division in a formal classification. This required the creation, for the first time, of a rank above kingdom, a superkingdom or empire, later called a domain.[21]

  life 
Empire Prokaryota

Kingdom Monera



Empire Eukaryota

Kingdom Protista



Kingdom Plantae



Kingdom Animalia




The differences between fungi and other organisms regarded as plants had long been recognised by some; Haeckel had moved the fungi out of Plantae into Protista after his original classification,[20] but was largely ignored in this separation by scientists of his time. 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 upon 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.[22] The five kingdom system may be combined with the two empire system:


life

Empire Prokaryota

Kingdom Monera





Empire Eukaryota

Kingdom Fungi



Kingdom Protista



Kingdom Plantae



Kingdom Animalia






In the Whittaker system, Plantae included some algae. In other systems (e.g., Margulis system), Plantae included just the land plants (Embryophyta).

Despite the development from two kingdoms to five among most scientists, some authors as late as 1975 continued to employ a traditional two-kingdom system of animals and plants, dividing the plant kingdom into Subkingdoms Prokaryota (bacteria and cyanophytes), Mycota (fungi and supposed relatives), and Chlorota (algae and land plants).[23]

Other proposed systems[edit]

Eight kingdoms[edit]

Thomas Cavalier-Smith thought at first, as it was nearly consensually admitted at that time, that the difference between eubacteria and archaebacteria was so great (particularly considering the genetic distance of ribosomal genes) that they needed to be separated in two different kingdoms, hence splitting the empire Bacteria into two kingdoms. Eubacteria was divided into two subkingdoms: Negibacteria (Gram negative bacteria) and Posibacteria (Gram positive bacteria).

Technological advances in electronical microscopy allowed the separation of the Chromista from the Plantae kingdom. Indeed, the chloroplast of the chromists is located in the lumen of the endoplasmic reticulum instead of in the cytosol. Moreover, only chromists do contain chlorophyll c. Since then, many non-photosynthetic phyla of protists, thought to have secondarily lost their chloroplasts, were integrated into the kingdom Chromista.

Finally, some protists lacking mitochondria were discovered[citation needed]. As mitochondria were known to be the result of the endosymbiosis of a proteobacterium, it was thought that these amitochondriate eukaryotes were primitively so, marking an important step in eukaryogenesis. As a result, these amitochondriate protists were separated from the protist kingdom, giving rise to the, at the same time, superkingdom and kingdom Archezoa. This was known as the Archezoa hypothesis. This superkingdom was opposed to the Metakaryota superkingdom, grouping together the five other eukaryotic kingdoms (Animalia, Protozoa, Fungi, Plantae and Chromista).

Six kingdoms[edit]

In 1998, Cavlier-Smith published a six-kingdom model,[3] which has been revised in subsequent papers. The version published in 2009 is shown below.[12] (Compared to the version he published in 2004,[24] the alveolates and the rhizarians have been moved from Kingdom Protozoa to Kingdom Chromista.) Cavalier-Smith no longer accepts the importance of the fundamental eubacteria–archaebacteria divide put forward by Woese and others and supported by recent research.[6] His Kingdom Bacteria includes Archaebacteria as a phylum of the subkingdom Unibacteria which comprises only one other phylum: the Posibacteria. The two subkingdoms Unibacteria and Negibacteria of kingdom Bacteria (sole kingdom of empire Prokaryota) are opposed according to their membrane topologies. The bimembranous-unimembranous transition is thought to be far more fundamental than the long branch of genetic distance of Archaebacteria, viewed as having no particular biological significance. Cavalier-Smith does not accept the requirement for taxa to be monophyletic ("holophyletic" in his terminology) to be valid. He defines Prokaryota, Bacteria, Negibacteria, Unibacteria and Posibacteria as valid paraphyletic (therefore "monophyletic" in the sense he uses this term) taxa, marking important innovations of biological significance (in regard of the concept of biological niche).

In the same way, his paraphyletic kingdom Protozoa includes the ancestors of Animalia, Fungi, Plantae and Chromista. The advances of phylogenetic studies allowed to realize that all the phyla thought to be archezoans (i.e. primitively amitochondriate eukaryotes) had in fact secondarily lost their mitochondria, most of the time by transforming them into new organelles: hydrogenosomes. This means that all living eukaryotes are in fact metakaryotes, according to the significance of the term given by Cavalier-Smith. Some of the members of the defunct kingdom Archezoa, like the phylum Microsporidia, were reclassified into kingdom Fungi. Others were reclassified in kingdom Protozoa like Metamonada which is now part of infrakingdom Excavata.

The diagram below does not represent an evolutionary tree.


life

Empire Prokaryota

Kingdom Bacteria — includes Archaebacteria as part of a subkingdom





Empire Eukaryota

Kingdom Protozoa — e.g. Amoebozoa, Choanozoa, Excavata



Kingdom Chromista — e.g. Alveolata, cryptophytes, Heterokonta (stramenopiles), Haptophyta, Rhizaria



Kingdom Plantae — e.g. glaucophytes, red and green algae, land plants



Kingdom Fungi



Kingdom Animalia






Viruses[edit]

There is ongoing debate as to whether viruses, obligate intracellular parasites that are not capable of replication outside of a host, can be included in the tree of life.[25][26] A principal reason for inclusion comes from the discovery of unusually large and complex viruses, such as Mimivirus, that possess typical cellular genes.[27]

Summary[edit]

A summary of the different kinds of proposed classification schemes presented in this article is summarized in the table below.

Linnaeus
1735[1]
Haeckel
1866[28]
Chatton
1925[29][30]
Copeland
1938[31][32]
Whittaker
1969[22]
Woese et al.
1977[4][33]
Woese et al.
1990[34]
Cavalier-Smith
1993[35][36][37]
Cavalier-Smith
1998[38][24][39]
2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 6 kingdoms 3 domains 8 kingdoms 6 kingdoms
(not treated) Protista Prokaryota Monera Monera Eubacteria Bacteria Eubacteria Bacteria
Archaebacteria Archaea Archaebacteria
Eukaryota Protoctista Protista Protista Eucarya Archezoa Protozoa
Protozoa
Chromista Chromista
Vegetabilia Plantae Plantae Plantae Plantae Plantae Plantae
Fungi Fungi Fungi Fungi
Animalia Animalia Animalia Animalia Animalia Animalia Animalia


The kingdom-level classification of life is still widely employed as a useful way of grouping organisms.[citation needed]

  • There is no current consensus on how many kingdoms are present in the Eukarya. In 2009, Andrew Roger and Alastair Simpson emphasized the need for diligence in analyzing new discoveries: "With the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution."[40]

See also[edit]

References[edit]

  1. ^ a b Linnaeus, C. (1735). Systemae Naturae, sive regna tria naturae, systematics proposita per classes, ordines, genera & species. 
  2. ^ See e.g. McNeill, J.; Barrie, F. R.; Burdet, H. M. et al., eds. (2006), International Code of Botanical Nomenclature (Vienna Code) Adopted by the Seventeenth International Botanical Congress, Vienna, Austria, July 2005 (electronic ed.), Vienna: International Association for Plant Taxonomy, retrieved 2011-02-20  , article 3.1
  3. ^ a b Cavalier-Smith, T. (1998), "A revised six-kingdom system of life", Biological Reviews 73 (3): 203–66, doi:10.1111/j.1469-185X.1998.tb00030.x, PMID 9809012 
  4. ^ a b 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 
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  7. ^ 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 
  8. ^ a b 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 
  9. ^ 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 
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  14. ^ a b 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. 
  15. ^ 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: 231–8, doi:10.1093/gbe/evp022, PMC 2817417, PMID 20333193 
  16. ^ 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 
  17. ^ 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: 99–113, doi:10.1093/gbe/evp011, PMC 2817406, PMID 20333181 
  18. ^ Kim, E.; Graham, L.E. & Redfield, Rosemary Jeanne (2008), "EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata", in Redfield, Rosemary Jeanne, PLoS ONE 3 (7): e2621, Bibcode:2008PLoSO...3.2621K, doi:10.1371/journal.pone.0002621, PMC 2440802, PMID 18612431 
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  27. ^ Raoult, Didier; Stéphane Audic, Catherine Robert, Chantal Abergel, Patricia Renesto, Hiroyuki Ogata, Bernard La Scola, Marie Suzan, Jean-Michel Claverie (2004). "The 1.2-Megabase Genome Sequence of Mimivirus". Science 306 (5700): 1344–1350. Bibcode:2004Sci...306.1344R. doi:10.1126/science.1101485. PMID 15486256. 
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  29. ^ Chatton, É. (1925). "Pansporella perplexa. Réflexions sur la biologie et la phylogénie des protozoaires". Annales des Sciences Naturelles - Zoologie et Biologie Animale. 10-VII: 1–84. 
  30. ^ Chatton, É. (1937). Titres et Travaux Scientifiques (1906–1937). Sette, Sottano, Italy. 
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  33. ^ Woese, C. R.; Fox, G. E. (November 1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744. 
  34. ^ Woese, C.; Kandler, O.; Wheelis, M. (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.". Proceedings of the National Academy of Sciences of the United States of America 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744. 
  35. ^ Cavalier-Smith, T. (1981). "Eukaryote kingdoms: seven or nine?". Bio Systems 14 (3–4): 461–481. doi:10.1016/0303-2647(81)90050-2. PMID 7337818.  edit
  36. ^ Cavalier-Smith, T. (1992). "Origins of secondary metabolism". Ciba Foundation symposium 171: 64–80; discussion 80–7. PMID 1302186.  edit
  37. ^ Cavalier-Smith, T. (1993). "Kingdom protozoa and its 18 phyla". Microbiological reviews 57 (4): 953–994. PMC 372943. PMID 8302218.  edit
  38. ^ 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 
  39. ^ Cavalier-Smith T (June 2010). "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree". Biol. Lett. 6 (3): 342–5. doi:10.1098/rsbl.2009.0948. PMC 2880060. PMID 20031978. 
  40. ^ 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 

External links[edit]