[Taxacom] Kingdom Protista (minor recoding, but big changes)

[Kenneth Kinman]

Dear All, 
???????Last year I posted on Taxacom some minor recoding
of the Phyla in my classification of Kingdom Protista.  However, I did
not realize (until this weekend) that Cavalier-Smith had proposed a
revised phylogeny in his paper "Kingdoms Protozoa and Chromista and the
eozoan root of the eukaryotic tree" (Biology Letters, 6:342-345).
? ? ? ? 
??????Although he has expanded his separate protist Kingdom
Chromista to match the "SAR" clade, our view of the phylogeny of that
clade is identical, so I see no need whatsoever to change the coding of
that second part of my classification. Our major disagreement remains
that instead of recognizing a single Kingdom Protista (as I do), he
still insists on dividing it into two Kingdoms, a basal Kingdom Protozoa

(paraphyletic) and a derived Kingdom Chromista (which is now much larger

than what he previously included within it). I still believe the single
Kingdom Protista has always been a far more stable taxon and also far
easier for most biologists to wrap their head around (even more so for
non-biologists).  This split seems to have caused more confusion than it

has provided new understanding or clarity.              ?      
????????Anyway, the big change is in the rooting and
early phylogeny of Kingdom Protista. To put it simply, Cavalier-Smith
has now placed the excavates at the base of the protists instead of the
unikonts. You would think that a new rerooting of the eukaryotic tree
would require a radical recoding of my classification, but it does not,
because the major clades are still the same and just need to be slightly

rearranged with relatively minor changes in coding. ?          ? ?

? 
?????????And as far as the content, I have only added
the Phylum Apusozoa (which has now clearly been shown to be distinct
from Rhizaria). So below, I first show my 2010 classification, and below

that is my 2011 recoding (with the addition of Phylum Apusozoa)
following Cavalier-Smith's most recent paper (which makes perfect sense
to me as far as evolution and phylogeny are concerned).  But I still
don't like his splitting of Kingdom Protista into two separate Kingdoms
(which I have always thought just complicates the classification
unnecessarily). I didn't like Chromista sensu stricto, and I don't like
this new Chromista (sensu lato) any better. It's just one of many clades

within Kingdom Protista as far as I am concerned. ? 
????????????????????????---------Ken
Kinman
 
? My 2010 classification: ? ? 

??????????????????KINGDOM PROTISTA 
? 
? ?1 ? Choanozoa%% 
?_a_ ? {{Kingdom EUMYCOTA}} (true fungi) 
?_b_ ? {{Kingdom METAZOA}} 
? ?2 ? Amoebozoa ? 
??3A ? Metamonada (incl. Parabasalia) 
???B ? Loukozoa (jakobids and allies) 
?? C ? Percolozoa 
?? D ? Euglenozoa 
??4A ? Glaucophyta 
?? B ? Rhodophyta 
?? C ? Chlorophyta% 
?_a_ ? {{Kingdom METAPHYTA}} (embryophytes) ? 
??5A ? Cryptophyta 
?? B ? Haptophyta 
???6 ? Rhizaria 
???7 ? Heterokonta (stramenopiles) 
? ?8? Ciliophora 
?? 9 ? Dinozoa (or Dinophyta) 
? 10 ? Sporozoa ? ? ? ? ? ? 
---------------------------------------------- 

Now recoded to reflect Cavalier-Smith's paper: ? 
??????????????????KINGDOM PROTISTA 
? 
???1 ? Euglenozoa 
??2A ? Percolozoa 
???B ? Loukozoa 
???C ? Metamonada 
??3A ? Amoebozoa ? 
???B ? Apusozoa 
?  C? Choanozoa%% 
?_a_ ? {{Kingdom EUMYCOTA}} (true fungi) 
?_b_ ? {{Kingdom METAZOA}} 
??4A ? Glaucophyta 
?? B ? Rhodophyta 
?? C ? Chlorophyta% 
?_a_ ? {{Kingdom METAPHYTA}} (embryophytes) 
??5A ? Cryptophyta 
?? B ? Haptophyta 
???6 ? Rhizaria 
???7 ? Heterokonta (stramenopiles) 
? ?8? Ciliophora 
?? 9 ? Dinozoa (or Dinophyta) 
? 10 ? Sporozoa ? ? ? ? ? ? ? 
----------------------------------------------            
NOTES: Clades 5-10 make up the "SAR" clade (Cavalier-Smith's Chromista
sensu lato). Clades 4-10 form the photokaryote clade. ? Clades 3-10
form Cavalier-Smith's "Neozoa"; Clades 2-10 form Cavalier-Smith's
"neokaryotes". ? Clade 3 is "Unikonta" and Clade 3B (Choanozoa and its

two exgroups) form the Opisthokonta clade of which we are a part).