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Taxonomy of Protista

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A protist (/ˈproʊtɪst/) is any eukaryotic organism (one with cells containing a nucleus) that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor;[a] but, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues".[1][b] In the 21st century, the classification shifted toward a two-kingdom system of protists: Chromista (containing the chromalveolate, rhizarian and hacrobian groups) and Protozoa (containing excavates and all protists more closely related to animals and fungi).[2]

A modern non-hierarchical interpretation of the phylogeny of eukaryotes, including protists

The following groups contain protists. The clade Opisthokonta also contains the animals and the fungi, and the kingdom Archaeplastida also contains algae and plants.

Key to symbols used:

(P) = Paraphyletic group.
† = Extinct group.
? = Group of uncertain taxonomic position.
* = Group lacking molecular data.
[ ] = Synonyms and alternative names.

Current classification

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This article largely follows the efforts of the scientific community and the International Society of Protistologists to revise the taxonomy of protists in a manner that reflects their phylogeny and evolution, striving away from the use of historical paraphyletic taxa and relying exclusively on clades as the basis of the classification. The reference used for the general arrangement of groups is the publication Revisions to the Classification, Nomenclature and Diversity of Eukaryotes, published in 2019 by researcher Sina Adl and coauthors.[3] Other studies are used for some specific groups of protists that have been revised after 2018, such as slime moulds,[4] glaucophyte algae,[5] arcellinid testate amoebae[6] and planktonic foraminifera.[7]

The following cladogram shows the relationships between the major groups of protists, as well as the kingdoms of animals, plants and fungi, according to the most recent phylogenetic analyses.[8][9][10][11][12]

Eukaryota
Choanozoa (P)
sensu Cavalier-Smith

Amorphea Adl et al. 2012

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Obazoa Brown et al. 2013

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Cladogram of Obazoa based on several analyses.[11][13] It includes the earliest diverging 'fungi' (microsporidians, aphelids and rozellids), which are only sometimes considered protists under the name of Opisthosporidia.[14]

Opisthokonta Cavalier-Smith 1987, emend. Adl et al. 2005

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Amoebozoa Lühe 1913, sensu Cavalier-Smith 1998

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Cladogram of Amoebozoa based on an 824-gene phylogenetic analysis published in 2022.[22]

Incertae sedis Amoebozoa: Belonocystis, Boveella, Biomyxa, Corallomyxa, Gibbodiscus, Hartmannia, Malamoeba, Malpighamoeba, Microglomus, Oscillosignum, Pseudothecamoeba, Rhabdamoeba, Schoutedamoeba, Stereomyxa, Subulamoeba, Thecochaos, Triaenamoeba, Unda.[3]

Tubulinea Smirnov et al. 2005

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Evosea Kang et al. 2017

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Discosea Cavalier-Smith et al. 2004 sensu Smirnov et al. 2011

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Diaphoretickes Adl et al. 2012

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Archaeplastida Adl et al. 2005

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Stramenopiles Patterson 1989, emend. Adl et al. 2005

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Stramenopiles incertae sedis:

Bigyra Cavalier-Smith 1998, emend. 2006

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Gyrista Cavalier-Smith 1998

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Alveolata Cavalier-Smith 1991

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Cladogram of Alveolata, based on a SSU rDNA phylogeny of basal alveolates[57] and a 203-gene phylogeny of apicomplexans and their relatives[58] published in 2023.

Myzozoa Cavalier-Smith & Chao 2004

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Ciliophora Doflein 1901

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Rhizaria Cavalier-Smith 2002

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Rhizaria incertae sedis: Gymnosphaerida Poche 1913, emend. Mikrjukov 2000. Actinocoryne, Cienkowskya, Gymnosphaera, Hedraiophrys [possible synonym of Cienkowskya], Wagnerella.

Cercozoa Cavalier-Smith 1998, emend. Adl et al. 2005; emend. Cavalier-Smith 2018

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Endomyxa Cavalier-Smith 2002, emend. Bass & Berney in Adl et al. 2019

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Retaria Cavalier-Smith 2002

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Haptista Cavalier-Smith 2003

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Cryptista Cavalier-Smith 1989, 2018, emend. Adl et al. 2019

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Excavates

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Malawimonadida Cavalier-Smith 2003

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Metamonada Grassé 1952, emend. Cavalier-Smith 1987

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Discoba Simpson in Hampl et al. 2009

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Jakobida Cavalier-Smith 1993

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Tsukubamonadida Yabuki et al. 2011

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Heterolobosea Page & Blanton 1985

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Euglenozoa Cavalier-Smith 1981, emend. Simpson 1997

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Orphan groups

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Hemimastigophora Foissner et al. 1988

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CRuMs Brown et al. 2018

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Ancyromonadida Cavalier-Smith 1998

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Genera of uncertain affiliation

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Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol,[125] Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium[u], Copromonas, Cyanomastix, Cyclomonas, Cytamoeba, Dallingeria, Dictyomyxa, Dimastigamoeba, Dinemula, Dinoasteromonas, Diplocalium, Diplomita, Diplophysalis, Diploselmis, Dobellina, Ducelleria, Ectobiella, Elaeorhanis, Embryocola, Endamoeba, Endemosarca, Endobiella, Endomonas, Endospora, Enteromyxa, Eperythrocytozoon, Errera, Fromentella, Gweamonas,[126] Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Lagenidiopsis, Liegeosia, Luffisphaera[v], Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Meringosphaera, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Parakaryon[w], Paraluffisphaera, Paramonas, Paraplasma, Parastasia, Parastasiella, Peliainia, Peltomonas, Petasaria, Phagodinium, Phanerobia, Phloxamoeba, Phyllomitus, Phyllomonas, Physcosporidium, Pleuophrys, Pleuromastix, Protenterospora, Protomonas, Pseudoactiniscus, Pseudosporopsis, Rhizomonas, Rhynchodinium, Rigidomastix, Schewiakoffia, Sergentella, Serpentoplasma, Sphaerasuctans, Spongastericus, Spongocyclia, Stephanomonas, Strobilomonas, Tetradimorpha, Tetragonidium, Thaulirens, Topsentella, Toshiba, Trichonema, Urbanella.[3]

See also

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Notes

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  1. ^ The first eukaryotes were “neither plants, animals, nor fungi”, hence as defined, the Protista would include the earliest common ancestor of all eukaryotes.
  2. ^ In the original 4-kingdom model proposed in 1959, Protista included all unicellular microorganisms such as bacteria.
  3. ^ a b This taxon belongs to the paraphyletic phylum Apusozoa Cavalier-Smith 1997 emend. 2013.[15]
  4. ^ a b c There are two competing phylogenetic hypotheses: Teretosporea (Corallochytrium + Ichthyosporea) and Pluriformea (Corallochytrium + Syssomonas).[3] This article follows the latter hypothesis, because it is strongly supported by the most recent phylogenetic studies.[11]
  5. ^ The term "Choanozoa" has been used since 1991 by Cavalier-Smith as a paraphyletic assemblage of opisthokont protists, and the terms "Apoikozoa" and "choanimal" were proposed as names for the clade Metazoa+Choanoflagellata. However, these terms have not been formally described or adopted, and were rejected in favour of a renamed Choanozoa to fit the clade Metazoa+Choanoflagellata.[3]
  6. ^ The position of the genera Microcorycia, Parmulina, Penardochlamys and Zonomyxa, which were listed in 2002 under family Microcoryciidae, is not clear. They are placed here by morphological characters but this needs to be supported by molecular data.[3]
  7. ^ The latest revision by Adl et al. (2019) ignores the grouping of some variosean genera into higher rank clades that was made in older studies because of the weakly supported SSU phylogenetic analyses, except for Fractovitellida, which is fully supported by phylogenomic analyses from 2017.[3]
  8. ^ a b c d e f g This order was initially divided into families, but phylogenetic analyses haven't supported the monophyly of each family. For this reason, in recent classifications there is no family rank division within it.[23][3]
  9. ^ This genus groups with Dermamoebidae in a phylogenetic anaysis that uses a limited number of taxa.[31] In the recent taxonomy it is listed as a separate clade until its position is better resolved.[3]
  10. ^ This genus could be a synonym of Vannella.[3]
  11. ^ Both genera group together in some phylogenetic analyses, but usually appear separated. They are considered a potential branch of Discosea, unless proven otherwise in the future with better taxon sampling.[3]
  12. ^ Latest analyses show that Microheliella is the sister group to Cryptista.[12]
  13. ^ Telonemia is the sister group to the SAR clade.[9]
  14. ^ The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.[37]
  15. ^ Cavalier-Smith and Scoble (2013) show a sister relationship between raphidophytes and Actinophryida.[50]
  16. ^ Apart from morphological descriptions, no molecular analysis has solidly affiliated Rastrimonas with the Perkinsozoa.[62]
  17. ^ Highly divergent 18S rRNA.[3]
  18. ^ This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.[3]
  19. ^ There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.[3]
  20. ^ According to Nakamura & Suzuki, the only extant (i.e. not extinct) orders of Polycystinea are Spumellaria, Nassellaria, Collodaria and Orodaria. Therefore, Entactinaria is considered an exclusively fossil group.[99]
  21. ^ Probably a synonym of the zygomycete fungus Nephridiophaga.[3]
  22. ^ May be the same genus as Belonocystis.[3]
  23. ^ It is not yet known whether this organism is an eukaryote or a prokaryote.[127]

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