[Taxacom] Protists and the ICBN [was: Kingdom Protista (minor recoding)]

[Kenneth Kinman]

Dear All,             
       I have had difficulty accessing all of the "Supplementary Data"
in Cavalier-Smith's paper.  He apparently states that only certain
group(s) of phyla should be under the jurisdiction of the International
Code of Botanical Nomenclature, and that all other protist phyla are
under the jurisdiction of the International Code of Zoological
Nomenclature.   
      I assume most taxacomers have better access to the Supplementary
Data in his paper than I do, and I am interested if any botanists (in
particular) have an opinion on which phyla he regards as being under the

jurisdiction of the ICBN, and more importantly which protist phyla he
regards as under the jurisdiction of the ICZN (even though some of their

taxa have acquired plastids).  For example, I assume he still regards
Phylum Euglenozoa as being under the jurisdiction of the ICZN, but what
about Dinozoa/Dinophyta (now part of his Chromista)?               
                  ----------Ken                            
-------------------------------------------------------
I wrote:            
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).