Infrakingdom

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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.

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

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.[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]). Because of its position, branch can be considered as a minor rank of the kingdom group even if it is not etymologically derived from it.

Systems of classification

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.

An initial dichotomy: 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 (Historia Plantarum (The History of Plants)).[4]

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.


life

Regnum plantae



Regnum Animalia




An increasing number of kingdoms

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".[5] In 1866, following earlier proposals by Richard Owen and 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).[5]


life

Kingdom Monera



Kingdom Plantae



Kingdom Animalia




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.[5]


life

Kingdom Monera (prokaryotes, i.e. bacteria and "blue-green algae")



Kingdom Protista (single-celled eukaryotes)



Kingdom Plantae



Kingdom Animalia




The importance of the distinction between prokaryotes and eukaryotes gradually became apparent. 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.[6]

  life 
Empire Prokaryota

Kingdom Monera



Empire Eukaryota

Kingdom Protista



Kingdom Plantae



Kingdom Animalia




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.[5] 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.[7] 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).

Recent developments: six kingdoms or more?

The three domains of life

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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 divided the prokaryotes (hitherto classified as the 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. Similarly, though eukaryote groups such as plants, fungi and animals may look different, they are more closely related to each other from a genetic standpoint 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 been upheld by subsequent research.[8]

Woese attempted to establish a "three primary kingdom" or "urkingdom" system.[9] In 1990, the name "domain" was proposed for the highest rank.[10] 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.



life

Domain Bacteria

Kingdom Bacteria





Domain Archaea

Kingdom Archaea





Domain Eukarya

Kingdom Protoctista or Protista



Kingdom Plantae



Kingdom Fungi



Kingdom Animalia






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 system

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.[12]

Eight kingdoms

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. 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

In 1998, he published a six-kingdom model,[3] which has been revised in subsequent papers. The version published in 2009 is shown below.[13] (Compared to the version he published in 2004,[14] 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.[8] 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






International Society of Protistologists Classification (2005)


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 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.[15] 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".[16] 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 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.[16]

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,[17] and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.[18]

As of 2010, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup,[19] so that Rhizaria is not one of the main eukaryote groups.[13][20][21][22][23] 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."[24] 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.[20][21][25]

Summary

The sequence from the two-kingdom system up to Cavalier-Smith's six-kingdom system can be summarized in the table below. 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.

The kingdom-level classification of life is still widely employed as a useful way of grouping organisms, notwithstanding some problems with this approach:

  • Kingdoms such as Bacteria represent grades rather than clades, and so are rejected by phylogenetic classification systems.
  • The most recent research does not support the classification of the eukaryotes into any of the standard systems. As of April 2010, no set of kingdoms is sufficiently supported by research to attain widespread acceptance. 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."[26]

Viruses

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.[27] [28] A principal reason for inclusion comes from the discovery of unusually large and complex viruses, such as Mimivirus, that possess typical cellular genes.[29]

See also

References

External links

  • The five kingdom concept
  • Whittaker's classification

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