Taxonomy of Protista: Difference between revisions

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===[[SAR supergroup|SAR]] {{au|Burki et al. 2008, emend. Adl et al. 2012}}===
===[[SAR supergroup|SAR]] {{au|Burki et al. 2008, emend. Adl et al. 2012}}===
====[[Stramenopiles]] {{au|Patterson 1989, emend. Adl et al. 2005}}====
====[[Stramenopiles]] {{au|Patterson 1989, emend. Adl et al. 2005}}====
*?Environmental clades MAST-21, MAST-25 {{au|Massana et al. 2014}}
*? Environmental clades MAST-21, MAST-25 {{au|Massana et al. 2014}}
*?''[[Platysulcus tardus]]'' {{au|Shiratori, Nakayama & Ishida 2015}}
*? ''[[Platysulcus tardus]]'' {{au|Shiratori, Nakayama & Ishida 2015}}
*? ''[[Kaonashia insperata]]'' {{au|Weston, Eglit & Simpson 2023}}<ref>{{cite journal|vauthors=Weston EJ, Eglit Y, ((Simpson AGB))|date=2023|title=Kaonashia insperata gen. et sp. nov., a eukaryotrophic flagellate, represents a novel major lineage of heterotrophic stramenopiles|journal=Journal of Eukaryotic Microbiology|volume=00|pages=e13003|doi=10.1111/jeu.13003|doi-access=free}}</ref>
*'''[[Bigyra]]''' {{au|Cavalier-Smith 1998, emend. 2006}}
*'''[[Bigyra]]''' {{au|Cavalier-Smith 1998, emend. 2006}}
**[[Opalozoa]] {{au|Cavalier Smith 1991, emend. 2006}}. ''Incertae sedis'': ''[[Cantina]]'', ''[[Rictus (bicosoecid)|Rictus]]'', environmental clades MAST-16, MAST-22 and MAST-24 {{au|Massana et al. 2014}}.
**[[Opalozoa]] {{au|Cavalier Smith 1991, emend. 2006}}. ''Incertae sedis'': ''[[Cantina]]'', ''[[Rictus (bicosoecid)|Rictus]]'', environmental clades MAST-16, MAST-22 and MAST-24 {{au|Massana et al. 2014}}.

Revision as of 19:59, 30 December 2023

A modern non-hierarchical interpretation of the phylogeny of protists

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]

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.

Overview

This article 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 by Adl et al. (2019).[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

Obazoa Brown et al. 2013

Incertae sedis Obazoa:

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

Amoebozoa Lühe 1913, sensu Cavalier-Smith 1998

Phylogeny of Amoebozoa[18]

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

Tubulinea Smirnov et al. 2005

Evosea Kang et al. 2017

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

Diaphoretickes Adl et al. 2012

Incertae sedis Diaphoretickes:

Archaeplastida Adl et al. 2005

SAR Burki et al. 2008, emend. Adl et al. 2012

Stramenopiles Patterson 1989, emend. Adl et al. 2005

Alveolata Cavalier-Smith 1991

Rhizaria Cavalier-Smith 2002

Haptista Cavalier-Smith 2003

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

Incertae sedis Eukarya

Hemimastigophora Foissner et al. 1988

Excavates (P)

Malawimonadida Cavalier-Smith 2003

Metamonada Grassé 1952, emend. Cavalier-Smith 1987

Discoba Simpson in Hampl et al. 2009

Clades basal to Amorphea

Genera of uncertain affiliation

Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Anaeramoeba, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol,[76] Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium[t], 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,[77] Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Lagenidiopsis, Liegeosia, Luffisphaera[u], Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Meringosphaera, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Parakaryon[v], Paraluffisphaera, Paramonas, Paraplasma, Parastasia, Parastasiella, Peliainia, Peltomonas, Petasaria, Phagodinium, Phanerobia, Phloxamoeba, Phyllomitus, Phyllomonas, Physcosporidium, Piridium, 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

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. ^ 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]
  4. ^ 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]
  5. ^ 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]
  6. ^ 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]
  7. ^ 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.[19][3]
  8. ^ This genus groups with Dermamoebidae in a phylogenetic anaysis that uses a limited number of taxa.[24] In the recent taxonomy it is listed as a separate clade until its position is better resolved.[3]
  9. ^ This genus could be a synonym of Vannella.[3]
  10. ^ 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]
  11. ^ Latest analyses show that Microheliella is the sister group to Cryptista.[12]
  12. ^ Telonemia is the sister group to the SAR clade.[9]
  13. ^ The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.[29]
  14. ^ Cavalier-Smith and Scoble (2013) show a sister relationship between raphidophytes and Actinophryida.[40]
  15. ^ Highly divergent 18S rRNA.[3]
  16. ^ This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.[3]
  17. ^ a b Initially, Cercozoa contained the clades Filosa and Endomyxa; however it has recently been synonymized with Filosa after a study found Endomyxa more closely related to Retaria.[46] The current classification places Endomyxa either as the sister clade of Retaria or as part of Retaria, even though more recent studies support the monophyly of Cercozoa as Filosa+Endomyxa again.[47]
  18. ^ There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.[3]
  19. ^ There is no phylogenetic taxonomy for phagotrophic euglenids. Some possibly monophyletic taxa have been proposed that cover restricted subgroups of the phagotrophic euglenids, such as Ploeotiida (Ploeotia, Entosiphon, Lentomonas, and presumably Keelungia) and Petalomonadida (Petalomonas, Notosolenus and Calycimonas, and presumably also taxa such as Sphenomonas). There is a limited taxon sampling for molecular data, and many traditional genera are probably paraphyletic.[3]
  20. ^ Probably a synonym of the zygomycete fungus Nephridiophaga.[3]
  21. ^ May be the same genus as Belonocystis.[3]
  22. ^ It is not yet known whether this organism is an eukaryote or a prokaryote.[78]

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