User:Faendalimas/Protists

In an effort to help with the Protists I asked on Taxacom for advice below are the responses.

Scott Thomson via Taxacom

Tue, Feb 8, 6:17 PM (7 days ago)

to taxacom I am thinking this will be a pain but I have to figure out how to deal with everything that was or is or may be in Protista as I currently have 191 non-standard and 526 disputed taxa many of which were a part of this group. I am not sure what to do with them.

Can someone recommend a Checklist or other publication that is the most recent assessment of all things this group please.

Thanks in advance

Cheers Scott

-- Scott Thomson

Kenneth Kinman

Hi Scott,
       Most of them would be classified in Kingdom Protozoa (and some in Kingdom Chromista?) in "A Higher Level Classification of All Living Organisms" (published in 2015).  Here's a weblink: [1]

Tony Rees

Hi Scott,

Basically you have to appreciate that there are 2 (if not more) current "world views" as to what to do with former Protista. According to the Cavalier-Smith world view, presently adopted in the 2015 paper by Ruggiero et al (which includes C-S among its authors), they split into 2 kingdoms, Protozoa and Chromista. However there is alternative view, that of Adl et al. (the latest iteration being at [2]) that does not include either of these names, or indeed any kingdoms outside of Embryophyta; their "Sar" clade (unranked, but higher than phylum) is roughly equivalent to C-S's Chromista, but excludes a few key groups... Also noting that, since the 2015 Ruggiero et al. summary, C-S has continued to publish on a number of protistan/chromistan groups, updating those areas of the classification, however without those updates being incorporated back into any larger summary treatment.

I went through this exercise for IRMNG starting around 4 years back, and decided to implement the Ruggiero et al. classification scheme so far as was practicable, updated as necessary, but departing in a few areas where "accepted practice" seemed to differ - for example treating Rozellids and Microsporidia as Fungi rather than Protozoa as per recent "fungal" treatments, and a few other things. If this approach coincides with what you might wish to do, you will find my current treatment of Protozoa at [3], and Chromista at [4] . All/most names are accompanied by relevant documentation e.g. from where I got the name, and according to which source is it presently considered either a current name or a synonym, sometimes with additional editorial notes as well.

Of course you can always search for a name at any rank via the IRMNG search interface at [5] ; just remember to uncheck the "limit to ... genera" box if you are searching for a name at a higher rank. I cannot guarantee that I have all suprageneric names entered (in fact I am sure I do not), however you may find this helpful for some percentage of the names you are desiring to check.

Likewise I cannot guarantee to have verified and/or updated every name entry in IRMNG at this time, however by viewing the "sources" presented for each, you will get some insight as to the currency of the information held for that name.

Hoping the above may be of some value,

Regards - Tony

Alastair Simpson

Adl et al. 2019 has a few oddities, but generally will closer reflect higher taxonomy of eukaryotes as accepted by protistologists writ large than will Ruggerio et al, 2015.

For example, approximately no evolutionary/systematic protistologists active today* use "Protozoa" as a taxon. One reason amongst many is that Opisthokonta is so widely accepted and is mutually incompatible with treating Protozoa (or Protista!) as taxa.

It also turns out that the evidence that Chromista is polyphyletic has strengthened markedly in the last couple of years.

Cheers Alastair (Simpson)

• Cavalier-Smith himself passed away last year

Alastair Simpson

Me *personally*, I would not use Protista, and accept that there will be a bit of Taxonomic structure under 'Eukarya / Eukaryota' before one got down to Metazoa, Plantae and Fungi.

If you use 'Protista', it means leaving out taxa that people actually use quite a bit (and that appear in first year textbooks), like Opisthokonta, Archaeplastida, Streptophytina, and so on.

Cheers Alastair

Kenneth Kinman

Hi All,

       I haven't worked on my Kingdom Protista classification for a while.  But what I used to call Phylum Choanozoa (sensu lato) would probably best be called Archaeopisthokonta since it gave rise to the two major kingdoms of opisthokonts (Animalia and Eumycota/Fungi).  It is marked %% since it is doubly paraphyletic.  Phylum Chlorophyta% is singly paraphyletic (giving rise to one Kingdom Metaphyta (Embryophyta).  Everything else in the classification below is cladistic (coded with the numbers and letters to the left).  Although I am heavily influenced by Cavalier-Smith's research (and his producing classifications with limited paraphyly), I prefer to mark paraphyletic groups with a % symbol rather than a simple *, since a paraphyletic group is just a basal percentage of a larger clade.

               KINGDOM PROTISTA
  1   Euglenozoa
 2A   Percolozoa
  B    Loukozoa
  C   Metamonada
 3A   Amoebozoa

  B   Breviatea
  C   Apusozoa
  D   "Archeopisthokonta" (Choanazoa sensu lato)
_a_   {{Kingdom EUMYCOTA}} (true fungi)
_b_   {{Kingdom METAZOA, aka ANIMALIA}}
 4A   Glaucophyta
  B   Rhodophyta
  C   Chlorophyta%
_a_   {{Kingdom METAPHYTA}} (embryophytes)
 5A   Cryptista (cryptophytes)
  B   Haptista (haptophytes)
  6   Rhizaria
  7   Heterokonta (stramenopiles)
  8   Ciliophora
  9   Dinozoa (or Dinophyta)
 10  Sporozoa

---

NOTES:

Clade 3D is Opisthokonta.

Clade 3 is Unikonta,

Clade 4 is Archaeplastida,

Clade 5 is Hacrobia.

Clades 6-10 make up the "SAR" clade.

Clades 5-10 might be called Chromista "sensu lato".

Clades 4-10 form the Bikonta (aka Photokaryota or Diaphoretickes) clade.

Clades 3-10 form Cavalier-Smith's "Neozoa";

Clades 2-10 form Cavalier-Smith's "neokaryotes".

Tony Rees

Ken's treatment as "Kingdom Protista" more-or-less coincides with what I was using prior to moving to the "Protozoa, Chromista" approach of Ruggiero et al, 2015, based on the involvement of Cavalier-Smith I presume. I wonder, given that Tom Cavalier-Smith is no longer on the scene, whether an upgrade of the Ruggiero et al. treatment (designed for use at Catalogue of Life and therefore GBIF, etc.) might appear in which Kingdom Chromista is no longer supported... in which case I will change back!

The only problem I see with "Protista" is that it is traditionally associated with single celled organisms, and some groups such as brown algae (Chromista according to Cavalier-Smith) depart from that concept fairly spectacularly... However I am prepared to treat them as "honorary protists" (Margulis et al. would call them all "Protoctists" anyway) if that is required.

As you can see I am not averse to a spot of paraphyly when expedient. After all we are all fishes, aren't we, and fishes are all amoebas (or maybe choanoflagellates, or something)...

Regards - Tony

Scott Thomson

Thanks everyone for all the responses,

yes it is the overarching higher orders that are the major headache and is probably going to require a complete overhaul of the templates for this group. We are lucky to have about 270 editors at present but to my knowledge none of them specialise in this group, including me so it's been a difficulty for a really long time. If no one minds I may copy the responses here over to the wiki so editors can look through and we can plan it out.

Cheers Scott -- Scott Thomson

Alastair Simpson

Well, Adl et al 2019 has a couple of things I dont agree with, but fundamentally it is a good place to start....

...Which is what is happening here. [6]

 The guy who is overseeing this is fundamentally sensible and an evolutionary protistologist.  He really is trying to capture the field's collective understanding (which is mostly what Adl et al. is trying to do), rather than do his own taxonomising and evolutionary hypothesising (in the Cavalier-Smith mould).   

It is slightly 'messier' than you want because it includes major groups of environmental sequences in addition to formally described taxa.

Cheers Alastair

Discussion continued (Wikispecies specific)

Tony Rees

My thoughts are that there are 2 fundamental decisions to be made here:

• 1, whether to use Cavalier-Smith's kingdom Chromista (containing groups that other workers are calling Sar, plus Cryptophytes and Haptophytes (and possibly more) in C-S's later incarnations), or not (just segment these groups out as SAR, not at kingdom level, see e.g. Ken Kinman's treatment above), and
• 2, if Chromists are not favoured (with other protists in kingdom Protozoa as per C-S etc.), whether the combined set of groups (excluding animals, fungi and "Plantae"/Viridaeplantae/Archaeplastida) are termed Protozoa, Protista, or nothing in particular (just "other Eukaryotes").

RE (1), the 2015 treatment of Ruggiero et al. "A Higher Level Classification of All Living Organisms", developed for Catalogue of Life, recognises 2 kingdoms, Protozoa and Chromista, according to the C-S view of the world (he was one of the authors on that work); the same is also implemented in e.g. GBIF, AlgaeBase, Species Fungorum and elsewhere. According to this "critical mass" I decided to go with the same system (with a few adjustments) for my own compilation "IRMNG", from 2017 onwards. However some more recent works e.g. "Handbook of the Protists" (Archibald et al., 2017) and Adl et al., 2019 "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes" do NOT recognise Chromista as a kingdom, and instead go with Sar (which I would have thought should correctly be rendered SAR, since it stands for Stramenopiles+Alveolata+Rhizaria). Regarding (2), Archibald et al. call everything "Protists" by implication, while Adl et al. do not use that term; groups just live under "Eukaryotes".

If I were re-working IRMNG in 2022, would I continue with "Chromista" as a kingdom? Probably yes, but if CoL/GBIF were to change everything back to Protista at some future date. I would do the same.

Wikispecies owes less "allegiance" to CoL and GBIF so is free to do as it pleases. If I were an advisor to Wikispecies, I *might* say, go with SAR instead of Chromista, and base a higher classification on that given in the relevant chapter in Archibald et al., 2017 (as it happens, authored by Alastair Simpson + 2 other persons), which is available at doi:10.1007/978-3-319-28149-0_45 if interested (you can probably guess how to obtain a copy to read, or you can request one from either Alastair or myself). Summarising that classification rather crudely (their Fig. 1), we have, in clockwise order:

• some small groups (1) e.g. Malawimonadidae, Ancyromonadida, others (not in major groups)
• Amorphea:
  • Obazoa (which contains kingdoms Fungi and Animalia)
  • Amoebozoa
• Metamonada
• Discicristata (referred to in text as Discoba, with addition of Jakoba)
• Sar:
  • Stramenopiles
  • Alveolata
  • Rhizaria
• some more small groups (2) e.g. Haptophyta, Cryptophyta, others (not in major groups)
• Archaeplastida (green plants and relatives)
• some more small groups (3) e.g. Gymnosphaerida, Heliomondida (not in major groups)

Each group is broken down further in additional figs. and in the chapter text.

Much of this is likely replicated in the Adl et al. paper from 2019, although I have not checked for differences, if any...

So the above represents one possible starting point, and is in the form of a dignificant printed work, being the initial chapter of the 2017 "Handbook of the Protists" entitled "Protist Diversity and Eukaryote Phylogeny", by A.G.B Simpson, C.H. Slamovits & J.M. Archibald. Whether it requires any further amendment I will leave maybe to Alastair to comment further... Regards Tony Tony 1212 (talk) 04:40, 18 February 2022 (UTC)

OK, I checked the above (slightly adjusted as of just now for correctness and readability) against Adl et al. 2019, and spotted the following differences:

• [Adl et al.:] "Eukaryotes now form two Domains called Amorphea and Diaphoretickes, with several additional clades that do not group into a third Domain." Comment: Diaphoretickes does not appear in Simpson et al., 2017. Also noting in passing, neither Amorphea or Diaphoretickes appear in Adl et al.'s "overview" diagram (their Fig. 1), although they do appear in the text.
• [Adl et al.:] "a sister clade to the Amorphea comprising several genera was recently described as CRuMs (Brown et al. 2018)." [ref. is Brown, Matthew W; Heiss, Aaron A; Kamikawa, Ryoma; Inagaki, Yuji; Yabuki, Akinori; Tice, Alexander K; Shiratori, Takashi; Ishida, Ken-Ichiro; Hashimoto, Tetsuo (2018-01-19). "Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group". Genome Biology and Evolution. 10 (2): 427–433. doi:10.1093/gbe/evy014] Comment: CRuMS stands for "i) collodictyonids also known as diphylleids, ii) rigifilids and iii) mantamonadids". It therefore supersedes most of Simpson et al.'s first group of unallocated taxa, with the exception of Ancyromonadida and Malawimonadidae. The latter 2 groups, plus Hemimastigophora, are listed alongside CRuMs but in an unallocated position, in Adl et al.
• Adl et al.'s Fig. 1 (main groupings) includes Discoba, cf. Discicristata in Simpson et al.; the latter is possibly an oversight, since Discoba (= Discicristata + Jakoba) is used in Simpson et al.'s text
• Adl et al. recognise 2 clades, Cryptista and Haptista, that include most/all of Simpson et al.'s second "unallocated" group (these terms do not appear in Simpson et al.). From Adl et al.: "The clade Cryptista comprising the cryptomonads, kathablepharids and Palpitomonas is well recognized and robust, although placement of its node within the Diaphoretickes remains problematic. ... The new robust support for the Cryptista clade is accompanied by a similarly robust support for a clade comprising the Centroplasthelida and Haptophyta as the Haptista within the Diaphoretickes."
• Simpson et al.'s Archaeplastidata (the clade containing green plants and their relatives) does not appear in Adl et al.'s Fig. 1 (where it is replaced by its constituent parts) but is in their text in the relevant position, so presumably is accepted there also, using the same name and definition.

There may be some other anomalies that I have not spotted, time being limited for such comparisons, also (for now at least) neither of these systems are in use in my own compilation :)

Cheers - Tony

---

Hi Tony,

        I (Ken Kinman) would prefer to regard Chromista as a Subkingdom.  Below are the four Subkingdoms that could be recognized (and their Phyla).  I am still not sure where to place Phylum Hemimastigophora.  It could possibly be a distinct Subkingdom splitting off between Unikonta and Archaeplastida).  

                                  KINGDOM PROTISTA
 Subkingdom Eozoa (excavates)  
         Phyla Euglenozoa, Percolozoa, Metamonada, Loukozoa   
 Subkingdom Unikonta/Amorphea (ancestral to Kingdoms Fungi and Animalia/Metazoa)  
         Phyla Varisulca (incl. CRuMs?), Amoebozoa, Breviatea, Apusozoa, Choanozoa (opisthokont ancestors)  
 Subkingdom Archaeplastida (ancestral to Kingdom Plantae/Metaphyta)  
         Phyla Glaucophyta, Rhodophyta, Chlorophyta  
 Subkingdom Chromista (Hacrobia + SAR clade + Telonemia)  
         Phyla Cryptista, Haptista, Telonemia, Rhizaria, Heterokonta (stramenopiles), and 2 or more Alveolate phyla

---

     NOTES:       Two Subkingdoms Archaeplastida + Chromista = Corticata/Bikonta (a.k.a. Diaphoretickes)   
        Three Subkingdoms Unikonta + Archaeplastida + Chromista = Neozoa
        Ruggiero et al.'s Excavata excludes Euglenozoa (even though they are excavates), so I prefer their name Eozoa (ancestors of Neozoa).

---

Reply from Tony Rees: Thanks Ken, the only issue being that Wikispecies (I believe) needs to follow a "published" classification (i.e. citable source), which (as far as I know) would exclude comments on a "Talk" page or similar, see https://species.wikimedia.org/wiki/Wikispecies:No_original_research. So your "preference" as stated above (which may be fine) would only be useable if it refers to, or synthesizes, something already available (anything else comprises Original Research, also known as OR). Suggestions? Regards - Tony Tony 1212 (talk) 18:42, 26 February 2022 (UTC)