Taxacom: Kingdom Protista and gene-tree studies

[Kenneth Kinman]

Hi All,
       Some gene-tree studies have continued to challenge the holophyly of a Chromista clade. Although some researchers believe Chromista to be polyphyletic (with Phylum Cryptista instead related to Archaeplastida phyla), I believe Chromista is a clade (preferably recognized at a Subkingdom level, not a Kingdom).  Chromista is an accepted taxon in GBIF but says "It is a polyphyletic group" (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.gbif.org%2Fspecies%2F144093376&data=04%7C01%7Ctaxacom%40lists.ku.edu%7C5568b0c5a9bb4e6b780408d9f7de67f8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637813357871254077%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9llzBVNH5GE7IXPg5oBso%2BWUruLZ%2BTWbTNd2Z6R7nMM%3D&reserved=0).  Wikipedia says the same thing about it being polyphyletic, but oddly cites a very old paper (Cavalier-Smith et al., 1994) as its source for that statement.

      Much more recently, Cavalier-Smith, et al. (December 2015) noted distortion problems with many gene-tree studies:
"Because of suspicions that corticate multigene phylogenies may be seriously distorted by the dual evolutionary origin of chromists, ancestrally a eukaryote–eukaryote cellular chimaera with an internally enslaved red alga, we analysed a series of different taxon samples to investigate this in detail. We found some evidence of taxon-sample dependent reciprocal distortion of chromist and plant multigene trees by attraction between red algae (Plantae) and undetected nuclear gene paralogues of red algal origin in chromists, so undetected paralogues might partly explain why the basal branching order of Plantae and Chromista is often contradictory. However, we conclude that long-branch artefacts, the extremely rapid early radiation of corticate eukaryotes leading to misleadingly high support for contradictory branching patterns on Bayesian trees because of the star-tree paradox, and still insufficient data from some key lineages, are probably also important factors."   https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1055790315002080%3Fvia%253Dihub%23b0235&data=04%7C01%7Ctaxacom%40lists.ku.edu%7C5568b0c5a9bb4e6b780408d9f7de67f8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637813357871254077%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9%2FlUZSTNDiaOfMqEl0KweFlNgCR7pIaPsZFnvTd9abQ%3D&reserved=0

Anyway, in trying to update my classification of Kingdom Protista a bit, I have now omitted a Phylum Loukozoa, and instead added Tsukubea and Jakobea.  However, I have decided not to recognize a Phylum Telonemia as a sister group to the SAR clade, since that placement (as TSAR) could also be a result of the problems noted above by Cavalier-Smith et al., 2015.   Telonemia and Picozoa instead seem rather likely to belong together in a Superclass Corbistoma (perhaps within Phylum Cryptista).  They are sister groups in many gene trees, and morphologically they share a unique asymmetric microfilamentous cytopharyngeal basket.  I am therefore skeptical of a 2021 study entitled "Picozoa are archaeplastids without plastid" (they don't cite any papers by Cavalier-Smith, so were perhaps unaware of the above-mentioned quote from Cavalier-Smith, et al., 2015).

                 KINGDOM PROTISTA%%%

   1   Tsukubea
  2A  Euglenozoa
   B   Percolozoa
   3   Jakobea
   4   Metamonada

  5A  Varisulca (incl. CRuMs, etc.)
   B   Amoebozoa

   C   Breviatea
   D   Apusozoa
   E   "Archeopisthokonta"%%
 _a_   {{Kingdom EUMYCOTA}} (true fungi)
 _b_   {{Kingdom METAZOA, aka ANIMALIA}}
  6A   Glaucophyta
   B    Rhodophyta
   C   Chlorophyta%
 _a_   {{Kingdom METAPHYTA}} (embryophytes)
  7A   Cryptista (cryptophytes)
   B   Haptista (haptophytes)
   8   Rhizaria
   9   Heterokonta (stramenopiles)
  10  Ciliophora
  11  Myzozoa (incl. Dinozoa and Apicomplexa)


----------------------------------------------
NOTES:

Clade 5 is Podiata.

Clade 6 is Archaeplastida,

Clade 7 is Hacrobia.

Clades 8-11 make up the "SAR" clade.

Clades 7-11 is Chromista

Clades 6-11 form the Corticata (aka Bikonta, Photokaryota or Diaphoretickes) clade.

Clades 1-3 form the Discoba (probably paraphyletic).

Clades 1-4 form the Excavata of some authors (probably paraphyletic).