Editing Alveolate (section)

==Classification==
Alveolata include around nine major and minor groups. They are diverse in form, and are known to be related by various ultrastructural and genetic similarities:<ref name=Tikhonenkov14>{{cite journal | doi = 10.1371/journal.pone.0095467 | pmid=24740116 | pmc=3989336 | volume=9 | issue=4 | title=Description of ''Colponema vietnamica'' sp.n. and ''Acavomonas peruviana'' n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes | year=2014 | journal=PLOS ONE | pages=e95467 | last1 = Tikhonenkov | first1 = DV | last2 = Janouškovec | first2 = J | last3 = Mylnikov | first3 = AP | last4 = Mikhailov | first4 = KV | last5 = Simdyanov | first5 = TG | last6 = Aleoshin | first6 = VV | last7 = Keeling | first7 = PJ| bibcode=2014PLoSO...995467T | doi-access=free }}</ref>

*[[Ciliate]]s – very common protozoa with many short [[cilium|cilia]] arranged in rows, and two nuclei
*[[Acavomonidia]]<ref name=Tikhonenkov14/>
*[[Colponemidia]]<ref name=Tikhonenkov14/>
*[[Dinoflagellate]]s s.l. – mostly marine [[flagellate]]s many of which have [[chloroplast]]s
*[[Perkinsozoa]]
*[[Chromerida]] – a marine phylum of photosynthetic protozoa
*[[Colpodellida]]
*[[Voromonadida]]
*[[Sporozoa|Apicomplexa]] – parasitic and secondary non-photosynthetic protozoa that lack [[Axoneme|axonemal]] locomotive structures except in [[gamete]]s

The Acavomonidia and Colponemidia were previously grouped together as colponemids, a taxon now split because each has a distinctive organization or [[ultrastructural identity]]. The Acavomonidia are closer to the dinoflagellate/perkinsid group than the Colponemidia are.<ref name=Tikhonenkov14/> As such, the informal term "colponemids", as it stands currently, covers two non-sister groups within Alveolata: the Acavomonidia and the Colponemidia.<ref name=Tikhonenkov14/>

The Apicomplexa and dinoflagellates may be more closely related to each other than to the ciliates.  Both have [[plastid]]s, and most share a bundle or cone of [[microtubule]]s at the top of the cell.  In apicomplexans this forms part of a complex used to enter host cells, while in some colorless dinoflagellates it forms a peduncle used to ingest prey.  Various other genera are closely related to these two groups, mostly flagellates with a similar apical structure.  These include free-living members in ''[[Oxyrrhis]]'' and ''[[Colponema]]'', and parasites in ''[[Perkinsus marinus|Perkinsus]]'',<ref name=Zhang2011>{{cite journal | last1 = Zhang | first1 = H | last2 = Campbell | first2 = DA | last3 = Sturm | first3 = NR | last4 = Dungan | first4 = CF | last5 = Lin | first5 = S | year = 2011 | title = Spliced leader RNAs, mitochondrial gene frameshifts and multi-protein phylogeny expand support for the genus ''Perkinsus'' as a unique group of Alveolates | journal = PLOS ONE | volume = 6 | issue = 5| page = e19933 | doi=10.1371/journal.pone.0019933 | pmid=21629701 | pmc=3101222| bibcode = 2011PLoSO...619933Z | doi-access = free }}</ref> ''[[Parvilucifera]]'', ''[[Rastrimonas]]'' and the [[ellobiopsid]]s.  In 2001, direct amplification of the [[rRNA]] gene in marine [[picoplankton]] samples revealed the presence of two novel alveolate lineages, called group I and II.<ref>{{cite journal |vauthors=López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D |title=Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton |journal=Nature |volume=409 |issue=6820 |pages=603–7 |year=2001 |pmid=11214316 |doi=10.1038/35054537 |bibcode=2001Natur.409..603L |s2cid=11550698 }}</ref><ref>{{cite journal |vauthors=Moon-van der Staay SY, De Wachter R, Vaulot D |title=Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity |journal=Nature |volume=409 |issue=6820 |pages=607–10 |year=2001 |pmid=11214317 |doi=10.1038/35054541 |bibcode=2001Natur.409..607M |s2cid=4362835 }}</ref>  Group I has no cultivated relatives, while group II is related to the dinoflagellate parasite ''[[Amoebophrya]]'', which was classified until now in the [[Syndiniales]] dinoflagellate order.

Some studies suggested the [[Ascetosporea|haplosporid]]s, mostly parasites of marine invertebrates, might belong here, but they lack alveoli and are now placed among the [[Cercozoa]].

The ellobiopsids are of uncertain relation within the alveolates. Silberman et al 2004 establish that the ''[[Thalassomyces]]'' genus of ellobiopsids are alveolates using [[phylogenetic]] analysis, however {{as of|2016|lc=yes}} no more certainty exists on their place.<ref name="Hoppenrath-2016">{{cite journal | last=Hoppenrath | first=Mona | title=Dinoflagellate taxonomy — a review and proposal of a revised classification | journal=[[Marine Biodiversity]] | publisher=[[Senckenberg Institute]] ([[Springer Science+Business Media|Springer]]) | volume=47 | issue=2 | date=2016-04-29 | issn=1867-1616 | doi=10.1007/s12526-016-0471-8 | pages=381–403| s2cid=42100119 }}</ref><ref name="Taylor-2004">{{cite journal | last=Taylor | first=F. J. R. "Max" | title=Illumination or confusion? Dinoflagellate molecular phylogenetic data viewed from a primarily morphological standpoint | journal=[[Phycological Research]] | publisher=[[Japanese Society of Phycology]] ([[Wiley Publishing|Wiley]]) | volume=52 | issue=4 | year=2004 | issn=1322-0829 | doi=10.1111/j.1440-183.2004.00360.x | pages=308–324| s2cid=86797666 }}</ref>

===Phylogeny===

In 2017, [[Thomas Cavalier-Smith]] described the phylogeny of the Alveolata as follows:<ref name="Cavalier-Smith 2017">{{Cite journal |last=Cavalier-Smith |first=Thomas |date=5 September 2017 |title=Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences |journal=Protoplasma |pages=297–357 |doi=10.1007/s00709-017-1147-3 |pmid=28875267 |pmc=5756292 |volume=255 |issue=1}}</ref>

{{clade| style=font-size:100%;line-height:100%
|label1=[[Alveolata]]
|1={{clade
  |label1=[[Ciliophora]]
  |1={{clade
    |label1=[[Intramacronucleata]]
    |1={{clade
      |1=[[Heterotrichea]]
      |2=[[Karyorelictea]]
       }}
    |label2=[[Postciliodesmatophora]]
    |2={{clade
       |1=[[Desmata]]
       |2=[[Spirotrichia]]
       }}
     }}
  |label2=[[Miozoa]]
  |2={{clade
    |1=[[Colponemea]]<!--T C-S marks the visibly paraphyletic "Protalveoalata" for this and the Acavomonadea-->
    |2={{clade
      |label1=Acavomonadia
      |1=[[Acavomonadea]]
      |label2=[[Myzozoa]]
      |2={{clade
        |label1=[[Apicomplexa]]
        |1={{clade
           |1=[[Apicomonada]]
           |2=[[Sporozoa]]
           }}
        |label2=[[Dinozoa]]
        |2={{clade
           |1=[[Dinoflagellata]]
           |2=[[Perkinsea]]
           }}
         }}
       }}
     }}
   }}
}}

===Taxonomy===
'''Alveolata''' <small>Cavalier-Smith 1991</small> [Alveolatobiontes]
* Phylum [[Ciliophora]] <small>Doflein 1901 stat. n. Copeland 1956</small> [Ciliata <small>Perty 1852</small>; Infusoria <small>Bütschli 1887</small>; Ciliae, Ciliozoa, Cytoidea, Eozoa, Heterocaryota, Heterokaryota]
** Subphylum [[Postciliodesmatophora]] <small>Gerassimova & Seravin 1976</small>
*** Class [[Heterotrichea]] <small>Stein 1859</small>
*** Class [[Karyorelictea]] <small>Corliss 1974</small>
** Subphylum [[Intramacronucleata]] <small>Lynn 1996</small>
*** Class ?[[Mesodiniea]] <small>Chen et al. 2015</small>
*** Infraphylum Lamellicorticata
**** Class [[Litostomatea]] <small>Small & Lynn 1981</small>
**** Class [[Armophorea]] <small>Lynn 2004</small>
**** Class [[Cariacotrichea]] <small>Orsi et al. 2011</small>
**** Class [[Spirotrichea]] <small>Bütschli 1889</small>
**** Infraphylum Ventrata <small>Cavalier-Smith 2004</small> [Conthreep <small>Lynn 2012</small>]
**** Order ?[[Discotrichida]] <small>Chen et al. 2015</small>
**** Class [[Protocruziea]] <small>Chen et al. 2015</small> [Protocruziidia <small>de Puytorac, Grain & Mignot 1987</small>]
**** Class [[Colpodea]] <small>Small & Lynn 1981</small>
**** Class [[Nassophorea]] <small>Small & Lynn 1981</small>
**** Class [[Phyllopharyngea]] <small>de Puytorac et al. 1974</small>
**** Class [[Prostomatea]] <small>Schewiakoff 1896</small>
**** Class [[Plagiopylea]] <small>Small & Lynn 1985 sensu Lynn 2008</small>
**** Class [[Oligohymenophorea]] <small>de Puytorac et al. 1974</small>
* Phylum [[Miozoa]] <small>Cavalier-Smith 1987</small>
** Subphylum Colponemidia <small>Tikhonenkov, Mylnikov & Keeling 2013</small>
*** Class [[Colponemea]] <small>Cavalier-Smith 1993</small>
** Subphylum Acavomonadia <small>Tikhonenkov et al. 2014</small>
*** Class [[Acavomonadea]] <small>Tikhonenkov et al. 2014</small>
** Subphylum [[Myzozoa]] <small>Cavalier-Smith 2004</small>
*** Infraphylum [[Apicomplexa]] <small>Levine 1970 emend. Adl et al. 2005</small>
**** Order ?[[Vitrellida]] <small>Cavalier-Smith 2017</small>
**** Class ?[[Myzomonadea]] <small>Cavalier-Smith & Chao 2004 sensu Ruggiero et al. 2015</small>
**** Class [[Chromerida|Chromerea]]
**** Order [[Colpodellida]] <small>Patterson & Zölffel 1991</small> [Spiromonadida <small>Krylov & Mylnikov 1986</small>]
**** Superclass [[Sporozoa]] <small>Leuckart 1879 stat. nov. Cavalier-Smith 2013</small>  [Gamontozoa]
***** Class [[Blastogregarinida]] <small>Chatton & Villeneuve 1936</small> [Blastogregarinina; Blastogregarinorina <small>Chatton & Villeneuve 1936</small>]
***** Class [[Paragregarea]] <small>Cavalier-Smith 2014</small>
***** Class [[Gregarinomorphea]] <small>Grassé 1953</small>
***** Class [[Coccidiomorphea]] <small>Doflein 1901</small>
*** Infraphylum [[Dinozoa]] <small>Cavalier-Smith 1981 emend. 2003</small>
**** Order ?[[Acrocoelida]] <small>Cavalier-Smith & Chao 2004</small>
**** Order ?[[Rastromonadida]] <small>Cavalier-Smith & Chao 2004</small>
**** Class [[Squirmidea]] <small>Norén 1999 stat. nov. Cavalier-Smith 2014</small>
**** Superclass [[Perkinsozoa]] <small>Norén et al. 1999 s.s.</small>
***** Class [[Perkinsea]] <small>Levine 1978</small> [Perkinsasida <small>Levine 1978</small>]
**** Superclass [[Dinoflagellata]] <small>Butschli 1885 stat. nov. Cavalier-Smith 1999 sensu Cavalier-Smith 2013</small> [Dinozoa <small>Cavalier-Smith 1981</small>]
***** Class [[Pronoctilucea]]
***** Class [[Ellobiopsea]] <small>Cavalier-Smith 1993</small> [Ellobiophyceae <small>Loeblich III 1970</small>; Ellobiopsida <small>Whisler 1990</small>]
***** Class [[Myzodinea]] <small>Cavalier-Smith 2017</small>
***** Class [[Oxyrrhea]] <small>Cavalier-Smith 1987</small>
***** Class [[Syndinea]] <small>Chatton 1920 s.l.</small> [Syndiniophyceae <small>Loeblich III 1970 s.s.</small>; Syndina <small>Cavalier-Smith</small>]
***** Class [[Endodinea]] <small>Cavalier-Smith 2017</small>
***** Class [[Noctilucales|Noctiluciphyceae]] <small>Fensome et al. 1993</small> [Noctilucae <small>Haeckel 1866</small>; Noctilucea <small>Haeckel 1866 stat. nov.</small>; Cystoflagellata <small>Haeckel 1873 stat. nov. Butschli 1887</small>]
***** Class [[Dinophyceae]] <small>Pascher 1914</small> [Peridinea <small>Ehrenberg 1830 stat. nov. Wettstein</small>]