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Change to Oomycota? (That page exists already but as a redirect)

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Ruggiero et al., 2015 called this phylum "Pseudofungi/Oomycota" however since then, the latter name seems to be preferred (if not exclusively so) in the main fungal databases and overviews including MycoBank (Oomycota), Index Fungorum, and Hyde et al., 2024 "The 2024 Outline of Fungi and fungus-like taxa". Wikispecies (https://species.wikimedia.org/wiki/Oomycota) has Oomycota but also has Phylum: Gyrista Subphylum: Pseudofungi in the hierarchy, which is not correct; as of today IRMNG (my database) has been changed to have Oomycota as an accepted phylum, with Pseudofungi as a synonym. I believe Wikipedia should be updated to reflect current practice in this group, at least between the major players. Thoughts, anyone? Tony 1212 (talk) 06:55, 25 September 2025 (UTC)[reply]

@Tony 1212 The name Oomycota only includes oomycetes in almost all treatments as well as your database, while the name Pseudofungi includes also hyphochytrids. I suspect Ruggiero et al. ignored this; it would not be the only time they made a mistake. It is true, however, that many botanists/mycologists refer to both subgroups of Pseudofungi as phyla: Oomycota and Hyphochytriomycota. But neither is a synonym of Pseudofungi itself. — Snoteleks (talk) 11:01, 25 September 2025 (UTC)[reply]
Also in several instances, Pseudofungi can also include Bigyromonada. — Snoteleks (talk) 15:36, 25 September 2025 (UTC)[reply]
OK, so maybe I was being misled by the equivalence stated in Ruggiero et al. I will read around the subject a bit more and see how best to treat Pseudofungi in my system and also therefore in Wikipedia and Wikispecies (e.g. perhaps retain it as a superphylum; I see this page currently has it as an unranked clade anyway), thanks. Tony 1212 (talk) 18:46, 25 September 2025 (UTC)[reply]
@Tony 1212 It's perfectly understandable, this is a very confusing topic and a subject I internally complain about a lot. There is little agreement (and little effort to reach agreement) between protistologists over which phylum names to use for gyristan stramenopiles, and even the main defender of the Pseudofungi taxon (T. Cavalier-Smith) changed circumscription and/or rank several times. Frankly, the main difficulty lies on bigyromonads, since they are usually a subphylum of two classes (Developea and Pirsonea), never a phylum, and they may or may not be part of Pseudofungi. There have been four different interpretations as far as I've seen:
  1. Treating oomycetes and hyphochytrids as individual phyla (Oomycota and Hyphochytriomycota), and ignoring any existence of the Pseudofungi taxon. This is mainly a botanist-exclusive view, where bigyromonads are not considered.[1][2] This one would be nice and consistent, if only there was at least one source that explicitly treated bigyromonads as a phylum.
  2. Treating both Pseudofungi and Bigyromonada as two separate subphyla of phylum Gyrista (along with the third subphylum Ochrophytina). This interpretation, while taxonomically consistent, fails to account for the fact that nobody wants Ochrophytina; everyone unanimously prefers treating ochrophytes as a full phylum (Ochrophyta or Heterokontophyta),[3] so there is not much consensus. The only defender was T. Cavalier-Smith,[4] until 2021 when he died. Ignoring the Ochrophytina part, Pseudofungi and Bigyromonada are interpreted by Adl et al. (2019) as taxa on the same level, although no ranks are disclosed by them to avoid controversy,[5] meaning that the issue is still unresolved.
  3. Treating Pseudofungi as a phylum, in which bigyromonads are lowered to a class Bigyromonadea and its two usual classes (Developea and Pirsonea) are lowered to orders (Developayellales and Pirsoniales). This is doable, since both Developea and Pirsonea are monotypic classes. However, there is only one instance of this being formally supported, in a 2006 article by none other than T. Cavalier-Smith (who, as explained above, supported something else afterwards).[6] So, not very consensed.
  4. Treating Pseudofungi as simply a clade that includes the oomycetes, hyphochytrids, and bigyromonads. This is what occurs in several recent phylogenetic studies.[7][8] The main issue is that the taxonomic rank is not explained, it's all names without ranks. But most papers use the variant name "Bigyromonadea" (class-level suffix), meaning that it implicitly supports the brief 2006 treatment where Pseudofungi are a phylum and Bigyromonadea are a class of phylum Pseudofungi. In Cho et al. (2024), they even write Pirsoniales (order-level suffix) in the cladogram, implicitly supporting lowering the two bigyromonad classes to orders, but they still write Developea (class-level suffix), so their intentions are not yet clear. Other names are inconsistent, like Oomycota, and hyphochytrids are excluded in their analyses.
Due to this mess, a couple of editors (myself included; also Jako96) have agreed to keep Gyrista and Pseudofungi as unranked clades until we decide on a better choice (or until someone publishes a coherently ranked stramenopile taxonomy). Personally I support setting Pseudofungi as phylum and Bigyromonadea as class (so options 3-4), as this is the most harmonious choice. — Snoteleks (talk) 19:49, 26 September 2025 (UTC)[reply]
Adl et al. doesn't use Bigyromonada or Pseudofungi, I support Tony's proposal for using Oomycota. And yes, I do think that we should use the class Bigyromonadea instead of the clade Bigyromonada. Jako96 (talk) 17:13, 28 September 2025 (UTC)[reply]
Wait, now I did some research, yes, researchers often use separate phyla Oomycota and Hyphochytriomycota. I think we should also do that for this group. Jako96 (talk) 17:17, 28 September 2025 (UTC)[reply]
@Snoteleks I found this paper which proposes more genera of Pirsoniaceae and uses the class Bigyromonadea under the phylum Pseudofungi. Finally, I think we should follow this paper since we should try to classify all taxa. Jako96 (talk) 20:11, 8 October 2025 (UTC)[reply]
@Jako96 They still use the name Developea, but I suppose it is perfectly consistent if we ignore it in the taxobox system and use Developayellales instead. After all, this paper is further proof that there is a recent consensus toward using Bigyromonadea (and toward bigyromonads belonging to Pseudofungi). So yes, let's follow it. — Snoteleks (talk) 20:23, 8 October 2025 (UTC)[reply]
Sure, we should use the order's name. Jako96 (talk) 20:41, 8 October 2025 (UTC)[reply]
What do you think, @Tony 1212? Jako96 (talk) 20:25, 12 October 2025 (UTC)[reply]
Sorry, I took a step back on thinking about this one for a while while I do other tasks (hint: https://www.irmng.org/aphia.php?p=sourcedetails&id=232125 - masses of new(ish) prokaryote names being dealt with for my system...). Basically I am happy to follow whatever seems to be current usage but not sure exactly what that is... I think you guys have looked into this more than I at this stage. Perhaps you can precis for me what you feel is the best current solution? Tony 1212 (talk) 19:33, 20 October 2025 (UTC)[reply]
As you see, we agreed with using the phylum Pseudofungi that includes oomycetes, hyphochytriomycetes and bigyromonads per this source which also proposes new genera of bigyromonads. This seems to be the scientific consensus for now. Jako96 (talk) 19:41, 20 October 2025 (UTC)[reply]
Well at the moment WP has this on the Pseudofungi page:
Clade: Pseudofungi

Cavalier-Smith, 1986

Groups

And this on the Oomycete page (redirect from Oomycetes):

Clade: Pseudofungi
Phylum: Oomycota
Class: Oomycetes

Winter, 1880

So you (we) need to decide whether Oomycota is a phylum (per WP hierarchy just above, and most current fungal texts) with Pseudofungi above it, or Pseudofungi is a phylum with Oomycota beneath it (rank??)... Just saying they cannot both be at phylum level :) Tony 1212 (talk) 01:02, 21 October 2025 (UTC)[reply]
The authors follow the Cavalier-Smith & Chao, 2006 treatment, so we would use the classes Oomycetes, Hyphochytrea and Bigyromonadea under the phylum Pseudofungi. Jako96 (talk) 15:00, 21 October 2025 (UTC)[reply]
Hmm. I recently adjusted IRMNG to follow Hyde et al, 2024, "The 2024 Outline of Fungi and fungus-like taxa" which has phylum Oomycota containing classes Oomycetes, Peronosporomycetes, Saprolegniomycetes as well as "Oomycota orders incertae sedis" (Anisolpidiales, Eurychasmales, Haliphthorales, Haptoglossales, Miraculales, Olpidiopsidales, Pontismatales and Rozellopsidales; in IRMNG these latter orders are presently under class Oomycetes per Ruggiero et al., but my plan would be to change their parent per Hyde et al.). I am not 100% convinced (yet) that reverting to (in effect) a 2006 treatment from Cavalier-Smith & Chao (which diverges from the latest treatment by fungal workers at least) is necessarily a good move, but am certainly happy to look at all options (but favouring those most recent and/or widely accepted...) I am not saying that Hyde et al., 2024 is necessarily correct in all respects, but that paper is recent, is authored by over 300 individuals, and should carry "weight" as it were (the author list alone, with their affiliations, occupies the first 16 pages...) Tony 1212 (talk) 17:50, 21 October 2025 (UTC)[reply]
For what it's worth, MycoBank (which does not always follow Hyde et al. verbatim) also has phylum Oomycota, class Oomycetes, see https://www.mycobank.org/details/708/92382 . They treat e.g. Anisolpidiales as an order of oomycetes, though, at least at present (hierarchy for the latter is Chromista > Oomycota > Oomycetes > Anisolpidiales). Tony 1212 (talk) 18:27, 21 October 2025 (UTC)[reply]
@Tony 1212 I read the Hyde paper and it seems like the inclusion of a class Oomycetes (not in the sense of all Oomycota, but in the sense or one order, Ducellieriales) was an error. It lacks authority, and the clarifying footnote points to an article that treats Oomycetes as all Oomycota, not just one order; this article also does not "support" the division of oomycetes into various classes. I don't think this should be counted as explicit disagreement, since "Oomycetes" is how many scientists know this taxon; the authors simply do not take sides by only showing orders.
However, if we look past this, the proposal of two classes (Saprolegniomycetes and Peronosporomycetes) plus several class-less orders mirrors the treatment of the 2017 Handbook of protists chapter. I agree that it seems to be the consensus, with both the main experts (mainly Beakes and Thines) and secondary sources (such as this one) adopting this system. — Snoteleks (talk) 19:56, 21 October 2025 (UTC)[reply]
MycoBank (https://www.mycobank.org/details/708/92382) has (class) Oomycetes G. Winter, Rabenhorst's Kryptogamen-Flora, Pilze - Schizomyceten, Saccharomyceten und Basidiomyceten 1(1): 32 (1880). Here is their classification within Oomycota more generally:
  • Chromista, Oomycota, Oomycetes: Anisolpidiales, Ducellieriales, Haliphthoraceae, Miraculales, Myzocytiopsidales, Olpidiopsidales, Peronosporales, Pythiales, Rhipidiales
  • Chromista, Oomycota, Peronosporomycetes: Albuginales, Combresomycetales, Peronosporales
  • Chromista, Oomycota, Saprolegniomycetes: Leptomitales, Saprolegniales
  • Chromista, Oomycota (unallocated): Haptoglossales, Lagenaceae, Lagenismatales, Pontismatales, Rozellopsidales
Tony 1212 (talk) 04:50, 22 October 2025 (UTC)[reply]
@Tony 1212 The issue with this is that there are two incompatible systems at place: one that recognizes a single class Oomycetes, and one that recognizes two classes, Peronosporomycetes and Saprolegniomycetes. IRMNG, and the Hyde paper, both make the mistake of assuming that articles supporting the 1st view are recognizing a third class, when in fact they are recognizing no additional classes. — Snoteleks (talk) 16:39, 22 October 2025 (UTC)[reply]
@Snoteleks@Jako96Aha, now that makes sense! I just read the full text of Beakes and Thines, 2017 (Handbook of the Protists Ch. 13) and while they use the term "Oomycetes" 71 times, it is always in an informal sense, and seems to be equivalent to the formal phylum Oomycota (no "Oomycetes" in their classification, as you say, just basal Oomycota, then 2 "major (class level) clades, the Saprolegniomycetes and Peronosporomycetes"); thus Oomycetes incertae sedis (or similar) in Hyde et al./MycoBank should logically be Oomycota incertae sedis. I would be happy to implement this in my system i.e. IRMNG; what best to do at higher ranks i.e. phylum level is then still to be determined, perhaps? Also IRMNG and Wikipedia/Wikispecies do not have to conform, but it is preferred if they do... Tony 1212 (talk) 17:36, 22 October 2025 (UTC)[reply]
@Tony 1212 I believe we are down to two possible solutions. I will make a more open discussion at WT:TOL to decide. — Snoteleks (talk) 20:34, 27 October 2025 (UTC)[reply]
Surprisingly, I did find a source that treats bigyromonads as a phylum (https://www.cell.com/current-biology/abstract/S0960-9822(25)00551-2) but they use the name Bigyromonadea. I don't think we should use that source, though. Jako96 (talk) 19:34, 20 October 2025 (UTC)[reply]
@Jako96 I don't like that they use Oomycota to include hyphochytrids, that makes no sense. However, given how widespread the phylum-level name Oomycota is, perhaps it would make sense for us to use Bigyromonadea as a phylum too. I will wait and see the response of other editors based on the comments above about the Hyde paper. — Snoteleks (talk) 21:08, 21 October 2025 (UTC)[reply]

References

  1. ^ Beakes, Gordon W.; Honda, Daiske; Thines, Marco (2014). "Systematics of the Straminipila: Labyrinthulomycota, Hyphochytriomycota, and Oomycota". In McLaughlin, David J.; Spatafora, Joseph W. (eds.). Systematics and Evolution. Part A. The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research. Vol. 7 (2nd ed.). Berlin, Heidelberg: Springer. doi:10.1007/978-3-642-55318-9_3.
  2. ^ Beakes, Gordon W.; Thines, Marco (2017). "Hyphochytriomycota and Oomycota". In Archibald, John M.; Simpson, Alastair G.B.; Slamovits, Claudio H. (eds.). Handbook of the Protists (PDF). Vol. 1 (2nd ed.). Cham: Springer International Publishing. pp. 435–505. doi:10.1007/978-3-319-28149-0_26. ISBN 978-3-319-28149-0. LCCN 2017945328.
  3. ^ See Ochrophyte article.
  4. ^ Cavalier-Smith, Thomas (5 September 2017). "Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences". Protoplasma. 255 (1): 297–357. doi:10.1007/s00709-017-1147-3. PMC 5756292. PMID 28875267.
  5. ^ Adl, Sina M.; Bass, David; Lane, Christopher E.; Lukeš, Julius; Schoch, Conrad L.; et al. (26 September 2018). "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes". The Journal of Eukaryotic Microbiology. 66 (1): 4–119. doi:10.1111/JEU.12691. PMC 6492006. PMID 30257078.
  6. ^ Cavalier-Smith, Thomas; Chao, Ema E-Y. (2006). "Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista)". Journal of Molecular Evolution. 62 (4): 388–420. doi:10.1007/s00239-004-0353-8. ISSN 0022-2844.
  7. ^ Cho, Anna; Tikhonenkov, Denis V.; Hehenberger, Elisabeth; Karnkowska, Anna; Mylnikov, Alexander P.; Keeling, Patrick J. (2022). "Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles" (PDF). Molecular Phylogenetics and Evolution. 171 (107468): 107468. doi:10.1016/j.ympev.2022.107468. ISSN 1055-7903. PMID 35358688. S2CID 247815732.{{cite journal}}: CS1 maint: article number as page number (link)
  8. ^ Cho, Anna; Tikhonenkov, Denis V.; Lax, Gordon; Prokina, Kristina I.; Keeling, Patrick J. (2024). "Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean". Molecular Phylogenetics and Evolution. 190: 107964. doi:10.1016/j.ympev.2023.107964.{{cite journal}}: CS1 maint: article number as page number (link)
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