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Taxonomy of Protista

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(Redirected from Protista taxonomy) Classification of eukaryotes A modern non-hierarchical interpretation of the phylogeny of eukaryotes, including protists
(the gray unlabeled line next to Sar represents Telonemia)

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; 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". 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).

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

Symbols and abbreviations used:

nom. cons. — Indicates a conserved name, a name which has been chosen for a taxon despite not being the priority name.
ICZN/ICN — Indicates an ambiregnal taxon that is accepted in both the zoological and the botanical codes of nomenclature, regulated by the ICZN and the ICN respectively.
(P) — Indicates a paraphyletic taxon.
† — Indicates an extinct taxon.
? — Indicates a taxon of uncertain taxonomic position, which may be the case for various reasons, including a lack of genetic data.
→ — Indicates a monotypic relationship.

Current classification

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. Other studies are used for some specific groups of protists that have been revised after 2018, such as slime moulds, glaucophyte algae, arcellinid testate amoebae and planktonic foraminifera. The usage of higher-level taxon ranks (phylum and kingdom) is unstable, as it varies from one author to the next; as such, said ranks are generally ommitted.

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.

Eukaryota
Diaphoretickes
TSAR
SAR
Halvaria

Stramenopiles

Alveolata

Rhizaria

Telonemia

Haptista

CAM

Cryptista

Microheliella

Archaeplastida (Kingdom Plantae s.l.)

Provora

Hemimastigophora

Meteora sporadica

Discoba

Jakobea

Tsukubea

Discicristata

Heterolobosea

Euglenozoa

Metamonada

Malawimonada

Ancyromonadida

Podiata

CRuMs

Amorphea

Amoebozoa

Obazoa

Breviatea

Apusomonadida

Opisthokonta
Holomycota

Fungi

Cristidiscoidea

Holozoa

Ichthyosporea

Pluriformea

Tunicaraptor

Filozoa

Filasterea

Choanozoa

Choanoflagellata

Metazoa (Kingdom Animalia)

Choanozoa (P)
sensu Cavalier-SmithExcavates (P)

Amorphea Adl et al. 2012

Obazoa Brown et al. 2013

Breviatea

Apusomonadida

Opisthokonta 
 Nucletmycea 
Fungi 

'True fungi'

Aphelida

Rozellida

Microsporidia

Rotosphaerida

Holozoa
 Ichthyosporea 

Dermocystida

Ichthyophonida

Pluriformea

Corallochytrium

Syssomonas

Filozoa 

Filasterea

Choanozoa 

Choanoflagellata

Metazoa

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

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

Phylum Amoebozoa Lühe 1913, sensu Cavalier-Smith 1998

Tubulinea 

Corycida

Echinamoebida

Elardia 

Leptomyxida

Euamoebida

Arcellinida

 Discosea 
 Centramoebia 

Acanthamoebida

Pellitida

Himatismenida

 Flabellinia 

Dermamoebida

Vannellida

Dactylopodida

Thecamoebida

Stygamoebida

 Evosea 

Cutosea

Conosa 
 Variosea 

Cavosteliida

Fractovitelliida

Profiliida

Archamoebea

Eumycetozoa 

Dictyostelia

Protosporangiida

Myxogastria

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

Class Tubulinea Smirnov et al. 2005

Evosea Kang et al. 2017

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

Diaphoretickes Adl et al. 2012

  • Order Microhelida Cavalier-Smith & Chao in Yabuki et al. 2012 → family Microheliellidae Cavalier-Smith & Chao in Yabuki et al. 2012. Sole genus: Microheliella Cavalier-Smith & Chao in Yabuki et al. 2012.
  • Phylum Telonemia Shalchian-Tabrizi 2006 → class Telonemea Cavalier-Smith 1993 → order Telonemida Cavalier-Smith 1993 → family Telonemidae Cavalier-Smith 1993. Genera: Arpakorses Tikhonenkov & Karpov 2022; Lateronema Cavalier-Smith 2015; Telonema Griessmann 1913.

Archaeplastida Adl et al. 2005

  • Division Glaucophyta Skuja 1954 (=Glaucocystaceae West 1904, Glaucocystophyta Kies and Kremer 1986, Glaucoplantae Marin & Melkonian in Li et al. 2020). Incertae sedis genera: Archaeopsis, Chalarodora, Glaucocystopsis, Peliaina, Strobilomonas.
  • Phylum Picozoa Seenivasan, Sausen, Medlin & Melkonian 2013 (=picobiliphytes Not et al. 2007) → class Picomonadea Seenivasan, Sausen, Medlin & Melkonian 2013 → order Picomonadida Seenivasan, Sausen, Medlin & Melkonian 2013 → family Picomonadidae Seenivasan, Sausen, Medlin & Melkonian 2013. Sole genus: Picomonas Seenivasan, Sausen, Medlin & Melkonian 2013.
  • Phylum Rhodelphidia Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → class Rhodelphidea Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → order Rhodelphida Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → family Rhodelphidae Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019. Sole genus: Rhodelphis Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019.
  • Division Rhodophyta Wettstein 1901 (=Rhodophyceae Thuret 1855, emend. Rabenhorst 1863, Rhodoplantae Saunders and Hommersand 2004 emend. Adl et al. 2005)

Chloroplastida Adl et al. 2006

Stramenopiles Patterson 1989, emend. Adl et al. 2005

  • Class Platysulcea Cavalier-Smith 2018 → order Platysulcida Cavalier-Smith 2018 → family Platysulcidae Shiratori, Nakayama & Ishida 2015. Sole genus: Platysulcus Shiratori, Nakayama & Ishida 2015.
  • Family Kaonashiidae Weston, Eglit & Simpson 2023. Sole genus: Kaonashia Weston, Eglit & Simpson 2023.

Phylum Bigyra Cavalier-Smith 1998 emend. 2006

  • Subphylum Opalozoa Cavalier Smith 1991 emend. 2006
    • Infraphylum Placidozoa Cavalier-Smith 2013
      • Class Placididea Moriya, Nakayama & Inouye 2002 → order Placidida Moriya, Nakayama & Inouye 2002 → family Placididae Moriya, Nakayama & Inouye 2002. Genera: Allegra Rybarski & Arndt 2021; Haloplacidia Rybarski, Nitsche & Arndt 2021; Pendulomonas S.M.Tong 1997; Placidia Moriya, Nakayama & Inouye 2002; Placilonga Rybarski & Arndt 2021; Suigetsumonas Okamura & Kondo 2015; Wobblia Moriya, Nakayama & Inouye 2000.
      • Class Nanomonadea Cavalier-Smith in Cavalier-Smith & Scoble 2013 (=clade MAST-3) → order Uniciliatida Cavalier-Smith in Cavalier-Smith & Scoble 2013
      • Class Opalomonadea Cavalier-Smith 2013 (=clade MAST-12). No described species.
      • Superclass Opalinata Wenyon 1926 emend. Cavalier-Smith 1997
    • Infraphylum Bikosea Cavalier-Smith 2018 (=Bicosoecida Grassé 1926 emend. Karpov 1998) → class Bikosea Cavalier-Smith 1986 as "Bicosoecea" orth. em. 2013. Genera not assigned to families: Bilabrum Schoenle & Arndt in Schoenle et al. 2020; Cafileria Jirsová, Füssy, Richtová, Gruber, & Oborník 2019; Cantina Yubuki et al. 2015.
      • Family Pseudobodonidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Pseudobodo Griessmann 1913.
      • Subclass Rictidia Cavalier-Smith in Cavalier-Smith & Scoble 2013 → order Rictida Cavalier-Smith in Cavalier-Smith & Scoble 2013 → family Rictidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Rictus Yubuki, Leander & Silberman 2010.
      • Subclass Bicosidia/Bicosoecophycidae Cavalier-Smith in Cavalier-Smith & Chao 2006
        • Superorder Borokiae Cavalier-Smith in Cavalier-Smith & Chao 2006 → order Borokida/Borokales Cavalier-Smith in Cavalier-Smith & Chao 2006 → family Borokidae/Borokaceae Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Boroka Cavalier-Smith in Cavalier-Smith & Chao 2006.
        • Superorder Cyathobodoniae Cavalier-Smith 1993 emend. 2006. Incertae sedis genus: Halocafeteria Park, Cho & Simpson 2006.
  • Subphylum Sagenista Cavalier-Smith 1995
    • Class Labyrinthulomycetes Arx 1970 ex Dick 2001 (=Labyrinthulea L.S.Olive 1975 ex Cavalier-Smith 1989, 'phylum' Labyrinthomorpha Page in Levine et al. 1980/Labyrinthulomycota Whittaker 1969)
    • Class Eogyrea Cavalier-Smith 2013 (=clade MAST-6). Genera not assigned to families: Mastreximonas Lax, Cho & Keeling 2024; Vomastromonas Tikhonenkov, Prokina, Cho & Keeling 2024.
      • Order Eogyrida Cavalier-Smith 2018 → family Pseudophyllomitidae/Pseudophyllomitaceae Shiratori et al. 2017. Sole genus: Pseudophyllomitus Lee 2002.

Phylum Gyrista Cavalier-Smith 1998

Alveolata Cavalier-Smith 1991

Myzozoa

Apicomplexa

Colpodellida

Squirmida

Perkinsozoa

Dinoflagellata

Neocolponema

Palustrimonas

Ciliophora

Acavomonas

Colponema

Loeffela

Cladogram of Alveolata, based on a SSU rDNA phylogeny of basal alveolates and a 203-gene phylogeny of apicomplexans and their relatives published in 2023.
  • Colponemida Cavalier-Smith 1993 emend. Adl et al. 2019 (=Protalveolata Cavalier-Smith 1991 emend. 2017. Genera not assigned to families: Neocolponema Gigeroff et al. 2023; Loeffela Gigeroff et al. 2023
    • Phylum Colponemidia Tikhonenkov et al. 2014 → class Colponemea Cavalier-Smith 1993 → order Colponemida Cavalier-Smith 1993 → family Colponemidae Cavalier-Smith & Chao 2004. Sole genus: Colponema Stein 1878.
    • Phylum Acavomonidia Tikhonenkov et al. 2014 → class Acavomonea Tikhonenkov et al. 2014 → order Acavomonida Tikhonenkov et al. 2014 → family Acavomonidae Tikhonenkov et al. 2014. Acavomonas Tikhonenkov et al. 2014.
    • Order Palustrimonadida Cavalier-Smith 2017 → family Palustrimonadidae Cavalier-Smith 2017. Sole genus: Palustrimonas Patterson & Simpson 1996.

Myzozoa Cavalier-Smith & Chao 2004

Phylum Ciliophora Doflein 1901

Rhizaria Cavalier-Smith 2002

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

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

Retaria Cavalier-Smith 2002

Haptista Cavalier-Smith 2003

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

Excavates

Malawimonadida Cavalier-Smith 2003

Metamonada Grassé 1952, emend. Cavalier-Smith 1987

Discoba Simpson in Hampl et al. 2009

Jakobida Cavalier-Smith 1993

Tsukubamonadida Yabuki et al. 2011

Heterolobosea Page & Blanton 1985

Euglenozoa Cavalier-Smith 1981, emend. Simpson 1997

Orphan groups

Ancyromonadida Cavalier-Smith 1998

CRuMs Brown et al. 2018

Hemimastigophora Foissner et al. 1988

Provora Tikhonenkov et al. 2022

Genera of uncertain affiliation

Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol, Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium, 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, Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Labyrinthomyxa Dubosq 1921, Lagenidiopsis, Liegeosia, Luffisphaera, Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Meringosphaera, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Parakaryon, 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, Thaulirens, Topsentella, Toshiba, Trichonema, Urbanella.

See also

Notes

  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. ^ This taxon belongs to the paraphyletic phylum Apusozoa Cavalier-Smith 1997 emend. 2013.
  4. ^ There are two competing phylogenetic hypotheses: Teretosporea (Corallochytrium + Ichthyosporea) and Pluriformea (Corallochytrium + Syssomonas). This article follows the latter hypothesis, because it is strongly supported by the most recent phylogenetic studies.
  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.
  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.
  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.
  8. ^ 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.
  9. This genus grouped with Dermamoebidae in a phylogenetic anaysis that used a limited number of taxa. In the recent taxonomy it was listed as a separate clade until its position is better resolved. A 2023 analysis placed it, once again, related to Dermamoebida in a clade with Microglomus.
  10. Both genera group together in some phylogenetic analyses, but usually appear separated. They were considered only a potential branch of Discosea, unless proven otherwise. A 2023 analysis places both genera in Flabellinia, closely related to Thecamoebida.
  11. This genus could be a synonym of Vannella.
  12. Latest analyses show that Microheliella is the sister group to Cryptista.
  13. Telonemia is the sister group to the SAR clade.
  14. The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.
  15. Within the order Anoecida, the four families Anoecaceae, Caecitellaceae, Cafeteriaceae and Symbiomonadaceae were included by T. Cavalier-Smith in 2006. In a 2013 revision, he simplified the classification by transferring Symbiomonadaceae and Anoecaceae to Cafeteriaceae. However, both of those families remain accepted by the scientific community as independent from Cafeteriaceae as of 2020.
  16. ^ Cavalier-Smith hypothesized in 2013 a sister relationship between actinophryids and raphidophytes, with both groups placed under the taxon Raphidomonadea. The molecularly uncharacterized genus Commation was classified as part of this taxon. However, the placement of actinophryids among ochrophytes is still unstable and uncertain, and Commation has never been included in classifications since.
  17. O'Kelly placed the genera Antarctosaccion, Chrysomeris, Chrysonephos, Nematochrysis/Chrysowaernella, Phaeosaccion and Rhamnochrysis in the order Chrysomeridales nomen nudum in 1989, and Cavalier-Smith placed it inside the class Chrysomeridophyceae (spelt originally as Chrysomerophycea) in 1995. However, the class was proven to be polyphyletic. As a result, some of its genera (Nematochrysis/Chrysowaerella) were transferred to the class Chrysoparadoxophyceae, while others (Antarctosaccion and Phaeosaccion) were transferred to the class Phaeosacciophyceae. Due to a lack of molecular data, the placement of Chrysomeris, Chrysonephos and Rhamnochrysis remains unknown.
  18. The position of Eustigmatophyceae is still unstable, with different phylogenetic methodologies showing affinities to either of the SI and SII clades.
  19. ^ The taxonomic ranks above class level (phylum, subphylum, infraphylum, etc.) are unstable within the Alveolata, due to the many different existing classifications. For example, the phylum-level rank has been traditionally assigned to Perkinsozoa, Dinoflagellata, Chromerida and Apicomplexa, all of which have been classified as phylum Myzozoa, which in turn has been classified inside phylum Miozoa. Treating the four myzozoan groups as separate phyla is generally accepted among phycologists, while at the same time the rejection of higher taxonomic ranks due to being superfluous is prevalent among protistologists.
  20. Apart from morphological descriptions, no molecular analysis has solidly affiliated Rastrimonas with the Perkinsozoa.
  21. The genera Parallobiopsis, Ellobiocystis and Rhizellobiopsis are only provisionally placed among ellobiopsids.
  22. Highly divergent 18S rRNA.
  23. This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.
  24. There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.
  25. 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.
  26. The genus Tetragonidium is known only from one written diagnosis and some illustrations, and its affinities with Cryptophyceae are very uncertain.
  27. Probably a synonym of the zygomycete fungus Nephridiophaga.
  28. Labyrinthomyxa, a genus of putative labyrinthulomycetes, is placed incertae sedis because of limited data.
  29. May be the same genus as Belonocystis.
  30. It is not yet known whether this organism is an eukaryote or a prokaryote.

References

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