User talk:Snoteleks

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Opisthosporidia

Eumycota as "cladistically included but traditionally excluded taxa" is misinterpretation. Opisthosporidias definition (doi 10.3389/fmicb.2014.00112) was not cladistic, but includes following statements:

superphylum includes three phyla: Microsporidia, Cryptomycota and Aphelida
they are not fungi – it is a group of Opisthokonta, sister to Fungi

It could be transformed into a cladistic definition (≈ a clade that includes Rozella allomycis, Aphelidium deformans, Glugea weissenbergi but not Agaricus campestris) but it would be a not allowed "original research".

The statement Eumycota is cladistically included into Opisthosporidia is also an "original research", changing the definition of the taxon.

Correct statement is, that Opisthosporidia is a paraphyletic group, cladistically it does not exist (Eumycota is not included). Petr Karel (talk) 17:34, 10 October 2024 (UTC)[reply]

The thing is, cladistically Opisthosporidia does form a paraphyletic group toward Eumycota. Aphelida is more closely related to Eumycota, while Cryptomycota and Microsporidia are a separate clade (see: any phylogenetic analysis, including the one present in the Opisthosporidia article).

The template {{Paraphyletic group}} is used correctly in this context. It is intended to be used for paraphyletic groups, where the |includes parameter is what the paraphyletic group actually contains (for example, Crustacea includes all the crustacean classes), and the |excludes parameter is what its monophyletic counterpart contains (for example, Crustacea excludes Hexapoda even though Hexapoda has evolved from crustaceans; the monophyletic counterpart would be Pancrustacea). — Snoteleks (talk) 19:52, 10 October 2024 (UTC)[reply]

I can only agree with all you wrote, but the problem is the text "Cladistically included but traditionally excluded taxa", which is not correct. Is it originated in the template? Is it applied to all paraphyletic groups? There are taxons which are defined cladistically, but later the supposed grouping appear paraphyletic/polyphyletic and the definition is invalid (innerly inconsistent) so such taxon is not existing – in such cases the problematic text is a complete nonsens, if applied.

Possible correct wording (I am not a native English speaker, language correction may be needed) "Taxa to be included to get a clade / to reach monophyly".

Btw. cladistically the taxon including all Microsporidia, Cryptomycota, Aphelida, and Eumycota is not Opisthosporidia but Fungi, see the cladistic (PhyloCode like) definition (doi:10.5598/imafungus.2018.09.02.05):

"Fungi R.T. Moore, Bot. Marina 23: 371 (1980)
Definition: The smallest crown clade containing Rozella allomycis F.K. Faust 1937, Batrachochytrium dendrobatidis Longcore et al. 1999, Allomyces arbusculus E.J. Butler 1911, Entomophthora muscae (Cohn) Fresen.1856, Coemansia reversa Tiegh. & G. Le Monn. 1873, Rhizophagus intraradices (N.C. Schenck & G.S. Sm.) C. Walker & A. Schüßler 2010, Rhizopus oryzae Went & Prins. Geerl. 1895, Saccharomyces cerevisiae Meyen 1838, and Coprinopsis cinerea (Schaeff.) Redhead et al. 2001. This is a minimum-crown-clade definition." --Petr Karel (talk) 07:45, 11 October 2024 (UTC)[reply]

It is indeed something originated by the template itself, and is meant to apply to all paraphyletic groups with said template. I think the best solution is to ask in the template talk that the text be changed to "Cladistically excluded" instead of "Cladistically included but traditionally excluded", since I agree it is very confusing otherwise. — Snoteleks (talk) 18:03, 11 October 2024 (UTC)[reply]

Protist: TSAR

I would be careful with TSAR, at least in formulations ("probable hypothesis" instead of fact). It is the result of analyses of one group of scientists and their citations by the same group (see the refs in SAR supergroup and Telonemia, documenting that TSAR "is widely accepted by the scientific community"). Do you know any analysis of an independent group, confirming this clade? I would appreciate it, but the history of placing many orphan groups into the eukarytic cladogram made me sceptical.

Thank you for your effort in updating and improving the phylogeny, I can only admire it. Petr Karel (talk) 15:42, 13 November 2024 (UTC)[reply]

@Petr Karel Good point. It is true that Telonemia is not often included in analyses. I did see an analysis that recovered TSAR, from a different group of scientists (doi:10.1038/s41586-018-0708-8), but another (albeit not yet peer-reviewed) did not have the same result (doi:10.21203/rs.3.rs-5059906/v1). I am definitely considering moving Telonemia into the orphan section and changing the title of this section to SAR, just to be safe, but maybe it could stay this way until it is disproven by a peer-reviewed analysis. In any case, thanks for bringing this into my attention, and for the feedback in general, much appreciated! — Snoteleks (talk) 16:39, 13 November 2024 (UTC)[reply]

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