Kingdom (biology)

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla (singular phylum).

Traditionally, textbooks from Canada and the United States have used a system of six kingdoms (Animalia, Plantae, Fungi, Protista, Archaea/Archaebacteria, and Bacteria or Eubacteria), while textbooks in other parts of the world, such as Bangladesh, Brazil, Greece, India, Pakistan, Spain, and the United Kingdom have used five kingdoms (Animalia, Plantae, Fungi, Protista and Monera).

Some recent classifications based on modern cladistics have explicitly abandoned the term kingdom, noting that some traditional kingdoms are not monophyletic, meaning that they do not consist of all the descendants of a common ancestor. The terms flora (for plants), fauna (for animals), and, in the 21st century, funga (for fungi) are also used for life present in a particular region or time.^[1][2]

When Carl Linnaeus introduced the rank-based system of nomenclature into biology in 1735, the highest rank was given the name "kingdom" and was followed by four other main or principal ranks: class, order, genus and species.^[3] Later two further main ranks were introduced, making the sequence kingdom, phylum or division, class, order, family, genus and species.^[4] In 1990, the rank of domain was introduced above kingdom.^[5]

Prefixes can be added so subkingdom (subregnum) and infrakingdom (also known as infraregnum) 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.^[6]

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.^[7]

Carl 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.

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.

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".^[8]

In 1860 John Hogg proposed the Protoctista, a third kingdom of life composed of "all the lower creatures, or the primary organic beings"; he retained Regnum Lapideum as a fourth kingdom of minerals.^[8] In 1866, Ernst Haeckel also proposed a third kingdom of life, the Protista, for "neutral organisms" or "the kingdom of primitive forms", which were neither animal nor plant; he did not include the Regnum Lapideum in his scheme.^[8] 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).^[8]

The development of microscopy revealed important distinctions between those organisms whose cells do not have a distinct nucleus (prokaryotes) and organisms whose cells do have a distinct nucleus (eukaryotes). In 1937 Édouard Chatton introduced the terms "prokaryote" and "eukaryote" to differentiate these organisms.^[9]

In 1938, Herbert F. Copeland proposed a four-kingdom classification by creating the novel Kingdom Monera of prokaryotic organisms; as a revised phylum Monera of the Protista, it included organisms now classified as Bacteria and Archaea. Ernst Haeckel, in his 1904 book The Wonders of Life, had placed the blue-green algae (or Phycochromacea) in Monera; this would gradually gain acceptance, and the blue-green algae would become classified as bacteria in the phylum Cyanobacteria.^[8][9]

In the 1960s, Roger Stanier and C. B. van Niel promoted and popularized Édouard Chatton's earlier work, particularly in their paper of 1962, "The Concept of a Bacterium"; this created, for the first time, a rank above kingdom—a superkingdom or empire—with the two-empire system of prokaryotes and eukaryotes.^[9] The two-empire system would later be expanded to the three-domain system of Archaea, Bacteria, and Eukaryota.^[10]

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,^[8] but was largely ignored in this separation by scientists of his time. Robert Whittaker recognized an additional kingdom for the Fungi.^[11] 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.^[11] The five kingdom system may be combined with the two empire system. In the Whittaker system, Plantae included some algae. In other systems, such as Lynn Margulis's system of five kingdoms, the plants included just the land plants (Embryophyta), and Protoctista has a broader definition.^{[12][page needed]}

Following publication of Whittaker's system, the five-kingdom model began to be commonly used in high school biology textbooks.^[13] But 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 cyanobacteria), Mycota (fungi and supposed relatives), and Chlorota (algae and land plants).^[14]

Whittaker's five kingdom system (1969)^[11]

Kingdom Monera Branch Myxomonera Phylum Cyanophyta Phylum Myxobacteriae Branch Mastigomonera Phylum Eubacteriae Phylum Actinomycota Phylum Spirochaetae

Kingdom Protista Phylum Euglenophyta Phylum Chrysophyta Phylum Pyrrophyta Phylum Hyphochytridiomycota Phylum Plasmodiophoromycota Phylum Sporozoa Phylum Cnidosporidia Phylum Zoomastigina Phylum Sarcodina Phylum Ciliophora

Kingdom Plantae Subkingdom Rhodophycophyta Phylum Rhodophyta Subkingdom Phaeophycophyta Phylum Phaeophyta Subkingdom Euchlorophyta Branch Chlorophycophyta Phylum Chlorophyta Phylum Charophyta Branch Metaphyta Phylum Bryophyta Phylum Tracheophyta

Kingdom Fungi Subkingdom Gymnomycota Phylum Myxomycota Phylum Acrasiomycota Phylum Labyrinthulomycota Subkingdom Dimastigomycota Phylum Oomycota Subkingdom Eumycota Branch Opisthomastigomycota Phylum Chytridiomycota Branch Amastigomycota Phylum Zygomycota Phylum Ascomycota Phylum Basidiomycota

Kingdom Animalia Subkingdom Agnotozoa Phylum Mesozoa Subkingdom Parazoa Phylum Porifera Phylum Archaeocyatha † Subkingdom Eumetazoa Branch Radiata Phylum Cnidaria Phylum Ctenophora Branch Bilateria Grade Acoelomata Phylum Platyhelminthes Phylum Nemertea or Rhynchocoela Grade Pseudocoelomata Phylum Acanthocephala Phylum Aschelminthes Phylum Entoprocta or Kamptozoa Grade Coelomata Subgrade Schizocoela Phylum Bryozoa or Ectoprocta Phylum Brachiopoda Phylum Phoronida Phylum Mollusca Phylum Sipunculoidea Phylum Echiuroidea Phylum Annelida Phylum Arthropoda Subgrade Enterocoela Phylum Brachiata or Pogonophora Phylum Chaetognatha Phylum Echinodermata Phylum Hemichordata Phylum Chordata

In 1977, Carl Woese and colleagues proposed the fundamental subdivision of the prokaryotes into the Eubacteria (later called the Bacteria) and Archaebacteria (later called the Archaea), based on ribosomal RNA structure;^[15] this would later lead to the proposal of three "domains" of life, of Bacteria, Archaea, and Eukaryota.^[5] Combined with the five-kingdom model, this created a six-kingdom model, where the kingdom Monera is replaced by the kingdoms Bacteria and Archaea.^[16] This six-kingdom model is commonly used in recent US high school biology textbooks, but has received criticism for compromising the current scientific consensus.^[13] But the division of prokaryotes into two kingdoms remains in use with the recent seven kingdoms scheme of Thomas Cavalier-Smith, although it primarily differs in that Protista is replaced by Protozoa and Chromista.^[17]

Thomas Cavalier-Smith supported the consensus at that time, that the difference between Eubacteria and Archaebacteria was so great (particularly considering the genetic distance of ribosomal genes) that the prokaryotes needed to be separated into two different kingdoms. He then divided Eubacteria into two subkingdoms: Negibacteria (Gram-negative bacteria) and Posibacteria (Gram-positive bacteria). Technological advances in electron 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 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.^[18] 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 superkingdom was opposed to the Metakaryota superkingdom, grouping together the five other eukaryotic kingdoms (Animalia, Protozoa, Fungi, Plantae and Chromista). This was known as the Archezoa hypothesis, which has since been abandoned;^[19] later schemes did not include the Archezoa–Metakaryota divide.^[6][17]

‡ No longer recognized by taxonomists.

In 1998, Cavalier-Smith published a six-kingdom model,^[6] which has been revised in subsequent papers. The version published in 2009 is shown below.^[20][a][21] Cavalier-Smith no longer accepted the importance of the fundamental Eubacteria–Archaebacteria divide put forward by Woese and others and supported by recent research.^[22] The kingdom Bacteria (sole kingdom of empire Prokaryota) was subdivided into two sub-kingdoms according to their membrane topologies: Unibacteria and Negibacteria. Unibacteria was divided into phyla Archaebacteria and Posibacteria; the bimembranous-unimembranous transition was 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 paraphyla (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 Cavalier-Smith to realize that all the phyla thought to be archezoans (i.e. primitively amitochondriate eukaryotes) had in fact secondarily lost their mitochondria, typically 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.

Because Cavalier-Smith allows paraphyly, the diagram below is an 'organization chart', not an 'ancestor chart', and does not represent an evolutionary tree.

Cavalier-Smith's six kingdom system (1998)^[6]

Kingdom Bacteria     Subkingdom Negibacteria         Infrakingdom Lipobacteria             Superphylum Eobacteria         Phylum Heliobacteria         Phylum Hadobacteria           Subphylum Chlorobacteria           Subphylum Deinobacteria       Superphylum Endoflagellata         Phylum Spirochaetae           Subphylum Euspirochaetae           Subphylum Leptospirae     Infrakingdom Glycobacteria       Superphylum Pimelobacteria         Phylum Sphingobacteria           Subphylum Chlorobibacteria           Subphylum Flavobacteria         Phylum Eurybacteria           Subphylum Sclenobacteria           Subphylum Fusobacteria           Subphylum Fibrobacteria         Phylum Cyanobacteria           Subphylum Gloeobacteria           Subphylum Phycobacteria         Phylum Proteobacteria           Subphylum Rhodobacteria             Infraphylum Alphabacteria             Infraphylum Chromatibacteria           Subphylum Thiobacteria       Superphylum Planctobacteria         Phylum Planctobacteria   Subkingdom Unibacteria     Infrakingdom Posibacteria       Phylum Posibacteria         Subphylum Teichobacteria           Infraphylum Endobacteria           Infraphylum Actinobacteria         Subphylum Togobacteria     Infrakingdom Archaebacteria       Phylum Mendosicutes         Subphylum Euryarcheota           Infraphylum Halomebacteria           Infraphylum Eurytherma         Subphylum Sulfobacteria

Kingdom Protozoa   Subkingdom Archezoa     Phylum Metamonada       Subphylum Eopharyngia       Subphylum Axostylaria     Phylum Trichozoa       Subphylum Anaeromonada       Subphylum Parabasala   Subkingdom Neozoa     Infrakingdom Sarcomastigota       Phylum Neomonada         Subphylum Apusozoa         Subphylum Isomita         Subphylum Choanozoa       Phylum Cercozoa         Subphylum Phytomyxa         Subphylum Reticulofilosa         Subphylum Monadofilosa       Phylum Foraminifera       Phylum Amoebozoa         Subphylum Lobosa         Subphylum Conosa           Infraphylum Archamoebae           Infraphylum Mycetozoa             Superclass Eumyxa             Superclass Dictyostelia     Infrakingdom Discicristata       Phylum Percolozoa         Subphylum Tetramitia         Subphylum Pseudociliata       Phylum Euglenozoa         Subphylum Plicostoma         Subphylum Saccostoma     Infrakingdom Alveolata       Superphylum Miozoa         Phylum Dinozoa           Subphylum Protalveolata           Subphylum Dinoflagellata         Phylum Sporozoa           Subphylum Gregarinae           Subphylum Coccidiomorpha           Subphylum Manubrispora       Superphylum Heterokaryota         Phylum Ciliophora           Subphylum Tubulicorticata           Subphylum Epiplasmata           Subphylum Filocorticata     Infrakingdom Actinopoda       Phylum Heliozoa       Phylum Radiozoa         Subphylum Spasmaria         Subphylum Radiolaria

Kingdom Fungi   Subkingdom Eomycota     Phylum Archemycota       Subphylum Dictyomycotina         Class Chytridiomycetes           Subclass Rumpomycetidae           Subclass Spizomycetidae         Class Enteromycetes       Subphylum Melanomycotina         Infraphylum Allomycotina           Class Allomycetes         Infraphylum Zygomycotina           Superclass Eozygomycetia             Class Bolomycetes             Class Glomomycetes           Superclass Neozygomycetia             Class Zygomycetes               Subclass Mucoromycetidae               Subclass Meromycetidae             Class Zoomycetes               Subclass Entomycetidae               Subclass Pedomycetidae                 Superorder Trichomycetalia                 Superorder Pyxomycetalia     Phylum Microsporidia       Class Minisporea       Class Microsporea         Subclass Pleistophorea         Subclas Disporea   Subkingdom Neomycota     Phylum Ascomycota       Subphylum Hemiascomycotina         Class Taphrinomycetes         Class Geomycetes         Class Endomycetes           Subclass Dipomycetidae           Subclass Saccharomycetidae       Subphylum Euascomycotina         Class Discomycetes           Subclass Calycomycetidae           Subclass Lecomycetidae           Subclass Pezomycetidae         Class Pyrenomycetes           Subclass Verrucomycetidae           Subclass Ostiomycetidae         Class Loculomycetes           Subclass Dendromycetidae           Subclass Loculoascomycetidae         Class Plectomycetes     Phylum Basidiomycota       Subphylum Septomycotina         Class Septomycetes           Subclass Sporidiomycetidae           Subclass Uredomycetidae       Subphylum Orthomycotina         Superclass Hemibasidiomycetia           Class Ustomycetes         Superclass Hymenomycetia           Class Gelimycetes             Subclass Tremellomycetidae             Subclass Dacrymycetidae             Subclass Auromycetidae           Class Homobasidiomycetes             Subclass Clavomycetidae             Subclass Pileomycetidae

Kingdom Animalia   Subkingdom Radiata     Infrakingdom Spongiaria       Phylum Porifera         Subphylum Hyalospongiae         Subphylum Calcispongiae         Subphylum Archaeocyatha †     Infrakingdom Coelenterata       Phylum Cnidaria         Subphylum Anthozoa         Subphylum Medusozoa     Infrakingdom Placozoa       Phylum Placozoa   Subkingdom Myxozoa     Phylum Myxosporidia   Subkingdom Bilateria     Branch Protostomia       Infrakingdom Lophozoa         Superphylum Polyzoa           Phylum Bryozoa             Subphylum Gymnolaemata             Subphylum Lophopoda           Phylum Kamptozoa             Subphylum Entoprocta             Subphylum Cycliophora         Superphylum Conchozoa           Phylum Mollusca             Subphylum Bivalvia             Subphylum Glossophora               Infraphylum Univalvia               Infraphylum Spiculata               Infraphylum Cephalopoda           Phylum Brachiozoa             Subphylum Brachiopoda             Subphylum Phoronida         Superphylum Sipuncula           Phylum Sipuncula         Superphylum Vermizoa           Phylum Annelida             Subphylum Polychaeta               Infraphylum Operculata               Infraphylum Pharyngata             Subphylum Clitellata             Subphylum Echiura             Subphylum Pogonophora           Phylum Nemertina       Infrakingdom Chaetognathi         Phylum Chaetognatha       Infrakingdom Ecdysozoa         Superphylum Haemopoda           Phylum Arthropoda             Subphylum Cheliceromorpha               Infraphylum Pycnogonida               Infraphylum Chelicerata             Subphylum Trilobitomorpha †             Subphylum Mandibulata               Infraphylum Crustacea               Infraphylum Myriapoda               Infraphylum Insecta           Phylum Lobopoda             Subphylum Onychophora             Subphylum Tardigrada         Superphylum Nemathelminthes           Phylum Nemathelminthes             Subphylum Scalidorhyncha               Infraphylum Priapozoa               Infraphylum Kinorhyncha             Subphylum Nematoida               Infraphylum Nematoda               Infraphylum Nematomorpha       Infrakingdom Platyzoa         Phylum Acanthognatha           Subphylum Trochata             Infraphylum Rotifera             Infraphylum Acanthocephala           Subphylum Monokonta         Phylum Platyhelminthes           Subphylum Turbellaria             Infraphylum Mucorhabda             Infraphylum Rhabditophora           Subphylum Neodermata             Infraphylum Trematoda             Infraphylum Cercomeromorpha     Branch Deuterostomia       Infrakingdom Coelomopora         Phylum Hemichordata           Subphylum Pterobranchia           Subphylum Enteropneusta         Phylum Echinodermata           Subphylum Homalozoa           Subphylum Pelmatozoa             Infraphylum Blastozoa             Infraphylum Crinozoa           Subphylum Eleutherozoa             Infraphylum Asterozoa             Infraphylum Echinozoa       Infrakingdom Chordonia         Phylum Urochorda           Subphylum Tunicata             Infraphylum Ascidiae             Infraphylum Thaliae           Subphylum Appendicularia         Phylum Chordata           Subphylum Acraniata             Infraphylum Cephalochordata             Infraphylum Conodonta †           Subphylum Vertebrata             Infraphylum Agnatha             Infraphylum Gnathostomata   Subkingdom Mesozoa     Phylum Mesozoa

Kingdom Plantae   Subkingdom Biliphyta     Infrakingdom Glaucophyta       Phylum Glaucophyta     Infrakingdom Rhodophyta       Phylum Rhodophyta         Subphylum Rhodellophytina         Subphylum Macrorhodophytina   Subkingdom Viridiplantae     Infrakingdom Chlorophyta       Phylum Chlorophyta         Subphylum Chlorophytina           Infraphylum Prasinophytae           Infraphylum Tetraphytae         Subphylum Phragmophytina           Infraphylum Charophytae           Infraphylum Rudophytae     Infrakingdom Cormophyta       Phylum Bryophyta         Subphylum Hepaticae         Subphylum Anthocerotae         Subphylum Musci           Infraphylum Sphagneae           Infraphylum Bryatae       Phylum Tracheophyta         Subphylum Pteridophytina           Infraphylum Psilophytae           Infraphylum Lycophytae           Infraphylum Sphenophytae           Infraphylum Filices         Subphylum Spermatophytina           Infraphylum Gymnospermae           Infraphylum Angiospermae

Kingdom Chromista   Subkingdom Cryptista     Phylum Cryptophyta   Subkingdom Chromobiota     Infrakingdom Heterokonta       Superphylum Sagenista         Phylum Sagenista           Subphylum Bicoecia           Subphylum Labyrinthista         Phylum Ochrophyta           Subphylum Phaeista             Infraphylum Hypogyrista             Infraphylum Chrysista           Subphylum Diatomeae         Phylum Bigyra           Subphylum Bigyromonada           Subphylum Pseudofungi           Subphylum Opalinata     Infrakingdom Haptophyta       Phylum Haptophyta

Cavalier-Smith and his collaborators revised their classification in 2015. In this scheme they introduced two superkingdoms of Prokaryota and Eukaryota and seven kingdoms. Prokaryota have two kingdoms: Bacteria and Archaea. (This was based on the consensus in the Taxonomic Outline of Bacteria and Archaea, and the Catalogue of Life). The Eukaryota have five kingdoms: Protozoa, Chromista, Plantae, Fungi, and Animalia. In this classification a protist is any of the eukaryotic unicellular organisms.^[17]

Linnaeus 1735[23]	Haeckel 1866[24]	Chatton 1925[25][26]	Copeland 1938[27][28]	Whittaker 1969[29]	Woese et al. 1977[30][31]	Woese et al. 1990[32]	Cavalier-Smith 1993[33][34][35]	Cavalier-Smith 1998[36][37][38]	Ruggiero et al. 2015[39]
—	—	2 empires	2 empires	2 empires	2 empires	3 domains	3 superkingdoms	2 empires	2 superkingdoms
2 kingdoms	3 kingdoms	—	4 kingdoms	5 kingdoms	6 kingdoms	—	8 kingdoms	6 kingdoms	7 kingdoms
—	Protista	Prokaryota	Monera	Monera	Eubacteria	Bacteria	Eubacteria	Bacteria	Bacteria
					Archaebacteria	Archaea	Archaebacteria		Archaea
		Eukaryota	Protista	Protista	Protista	Eucarya	Archezoa	Protozoa	Protozoa
							Protozoa
							Chromista	Chromista	Chromista
Vegetabilia	Plantae		Plantae	Plantae	Plantae		Plantae	Plantae	Plantae
				Fungi	Fungi		Fungi	Fungi	Fungi
Animalia	Animalia		Animalia	Animalia	Animalia		Animalia	Animalia	Animalia

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 Protozoa 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^[update], 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."^[40]

While the concept of kingdoms continues to be used by some taxonomists, there has been a movement away from traditional kingdoms, as they are no longer seen as providing a cladistic classification, where there is emphasis in arranging organisms into natural groups.^[41]

Based on 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.^[15]

In 1990, the name "domain" was proposed for the highest rank.^[5] This term represents a synonym for the category of dominion (lat. dominium), introduced by Moore in 1974.^[42] Unlike Moore, Woese et al. (1990) did not suggest a Latin term for this category, which represents a further argument supporting the accurately introduced term dominion.^[43]

Woese divided the prokaryotes (previously 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.

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.^[22] There is no consensus on how many kingdoms exist in the classification scheme proposed by Woese.

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".^[41]

On this basis, the diagram opposite (redrawn from their article) showed the real "kingdoms" (their quotation marks) of the eukaryotes.^[41] 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".^[44] The published classification deliberately did not use formal taxonomic ranks, including that of "kingdom".

In this system the multicellular animals (Metazoa) are descended from the same ancestor as both the unicellular choanoflagellates and the fungi which form the Opisthokonta.^[44] 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,^[45] and a review in 2006 noted the lack of evidence for several of the six proposed supergroups.^[46]

As of 2010^[update], there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup,^[47] so that Rhizaria is not one of the main eukaryote groups.^{[20][48][49][50][51]} 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."^[52] As of December 2010^[update], there appears to be a consensus that the six supergroup model proposed in 2005 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.^[48][49][53]

Some authors have added non-cellular life to their classifications. This can create a "superdomain" called "Acytota", also called "Aphanobionta", of non-cellular life; with the other superdomain being "cytota" or cellular life.^[54][55] The eocyte hypothesis proposes that the eukaryotes emerged from a phylum within the archaea called the Thermoproteota (formerly known as eocytes or Crenarchaeota).^[56][57]

Taxonomical root node	Two superdomains (controversial)	Two empires	Three domains	Five Dominiums[58]	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

The International Committee on Taxonomy of Viruses uses the taxonomic rank "kingdom" in the classification of viruses (with the suffix -virae); but this is beneath the top level classifications of realm and subrealm.^[59]

There is ongoing debate as to whether viruses can be included in the tree of life. The arguments against include the fact that they are obligate intracellular parasites that lack metabolism and are not capable of replication outside of a host cell.^[60][61] Another argument is that their placement in the tree would be problematic, since it is suspected that viruses have various evolutionary origins,^[60] and they have a penchant for harvesting nucleotide sequences from their hosts.

On the other hand, there are arguments in favor of their inclusion.^[62] One of these comes from the discovery of unusually large and complex viruses, such as Mimivirus, that possess typical cellular genes.^[63]

• Cladistics
• Phylogenetics
• Systematics
• Taxonomy

• Pelentier, B. (2007-2015). Empire Biota: a comprehensive taxonomy, [1]. [Historical overview.]
• Peter H. Raven and Helena Curtis (1970), Biology of Plants, New York: Worth Publishers. [Early presentation of five-kingdom system.]

• A Brief History of the Kingdoms of Life at Earthling Nature
• The five kingdom concept Archived 2021-11-07 at the Wayback Machine
• Whittaker's classification