Talk:Taxonomy of Protista

Protista Top‑importance

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Tree of Life Mid‑importance

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Great modification of this article

Hello, I am slowly but steadily improving this article by updating the outdated taxonomy and correcting mistakes, as well as making things less confusing and overwhelming by adding some bits of explanations, images and, most importantly, adding bibliography, which was almost nonexistent beforehand. If anyone has any questions, doubts or suggestions about this feel free to answer this message! Snoteleks (talk) 11:29, 10 August 2022 (UTC)[reply]

Announcement of March 2023

Hello, for the past weeks I have been remaking this page to be as accurate as possible according to the newest classification by Adl et al. (2019),^[1] which finally rejects traditional paraphyletic taxa in favour of clear-cut cladistic definitions. I finally posted my edit today, which brought 100% of the info on that classification. However, there are still a couple things that need to be taken care of, in order to make this page as complete as possible:

Complete the list of genera for ciliates, ochrophytes, foraminifera and dinoflagellates. The study by Adl et al. does not include all the genera of these big groups, so this needs to be completed independently.
Fix disambiguation links to names of genera. A lot of genera haven't been given their own page yet, and overlap instead with the names of different pages.
Update the page according to studies from 2019 to 2023 and so on. Many new changes to lower classifications have been made, including the revision of some taxa and the creation of others. This should be reflected in the page, as it is meant to be the nexus for all pages that include some level of protist classification.

Any help is useful and welcome, like in any Wikipedia article, but remember, always cite sources for your additions and changes. I cannot stress this enough, because when I began modifying this page it was absolutely sourceless! ☽ Snoteleks ☾ 08:33, 3 March 2023 (UTC) ☽ Snoteleks ☾ 08:33, 3 March 2023 (UTC)[reply]

References

^ Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q (2018). "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes". Journal of Eukaryotic Microbiology. 66: 4–119. doi:10.1111/jeu.12691.

Kingdom Chromista - needs more discussion in the article?

Not sure how this might best be included, but possibly worthy of note that as an alternative to the Adl et al. treatment set out here, Catalogue of Life (CoL), WoRMS, AlgaeBase and elsewhere use kingdoms Protozoa and Chromista in place of Protista at this time, following the treatment of Ruggiero et al., 2015 and later works by Cavalier-Smith in particular. See e.g. https://www.catalogueoflife.org/data/taxon/C and https://www.catalogueoflife.org/data/taxon/Z . I do the same in my own database (IRMNG), principally to maintain congruence with CoL/WoRMS at this time; when or if they change, I shall do the same... Tony 1212 (talk) 23:26, 15 February 2024 (UTC)[reply]

Also noting, kingdom Chromista currently treated as valid in ITIS (https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=630578) and GBIF (https://www.gbif.org/species/4). NCBI taxonomy, by contrast, does not include it (example: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2985 for Ochromonas). A matter of taste perhaps, but its current pervasiveness should possibly be documented here... Tony 1212 (talk) 00:14, 16 February 2024 (UTC)[reply]

PS I currently supply around 5,600 generic names from my database to CoL (see https://www.catalogueoflife.org/data/dataset/2007), mainly in Chromista, Protozoa, and "plant algae", which is a practical reason for my compilation to remain "in step" with their current treatment(s) at any particular time :) Tony 1212 (talk) 00:19, 16 February 2024 (UTC)[reply]

@Tony 1212 I completely agree. I've been meaning to include a section of the traditional classifications that delves deeper into the Protozoa-Chromista configuration. It would be nice for readers to have the complete context. My idea was to make this into a section before the "Current classification" section. I would also like to update the Cavalier-Smith's system of classification page according to his 2017-2018-2022 papers, which seem to be the last peer-reviewed traces of this traditional system. —Snoteleks (Talk) 06:55, 16 February 2024 (UTC)[reply]

Euglenids

Just to remind myself, there is starting to be a phylogenetic taxonomy of euglenids, despite what the note says. I will add that soon, I have already found enough references. —Snoteleks (Talk) 07:37, 16 February 2024 (UTC)[reply]

Ochrophyta: Instability of the position of Eustigmatophyceae

(@User:Snoteleks) Results of phylogenomic analyses from 2024 show the instability of the position of Eustigmatophyceae among ochrophytes. When plastid genes are used, there is evidence for eustigmatophytes being nested within the SII clade, specifically related to Chrysophyceae and Synchromophyceae /Picophagea (e.g. [1] or the preprint [2], to have recent references from 2022). Analyses of nuclear genes however tend to favor eustigmatophytes being a sister lineage of the SI clade (preprint [3]).

After adding new transcriptomes to an existing phylogenomic dataset and updating the dataset to represent 14 out of 17 major ochrophyte classes including Olisthodiscophyceae, Phaeothamniophyceae, Schizocladiophyceae, and Picophagea, a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae (SI clade) was recovered in a study ([4] issued in September 2024) by another group of scientists.

I propose to take the class Eustigmatophyceae out of Limnistia and raise it to the same level as SI and SII clades until the position is finally clarified. (It would be strange to have it in a group named "clade" SII which then may be polyphyletic!) Petr Karel (talk) 15:58, 16 December 2024 (UTC)[reply]

Petr, I made one small edit to this article 6 years ago (fixing a wikilink). Chiswick Chap (talk) 16:04, 16 December 2024 (UTC)[reply]

I am sorry, I wanted to ping the item to User:Snoteleks. Petr Karel (talk) 16:33, 16 December 2024 (UTC)[reply]

@Petr Karel Hi, thank you for pointing that out! Can you link to the analysis? — Snoteleks (talk) 19:46, 16 December 2024 (UTC)[reply]

My bad @Petr Karel, I was reading this talk page from my phone and none of the links showed up. Now on my desktop I'll get to reading. — Snoteleks (talk) 21:35, 16 December 2024 (UTC)[reply]

[Adl_2019-1] Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q (2018). "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes". Journal of Eukaryotic Microbiology. 66: 4–119. doi:10.1111/jeu.12691.

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