[Taxacom] Kingdom Protista (a preferable third optional coding?)

[Kenneth Kinman]

Dear All, 
         A recent paper (Hampl, et al., 2009; in Proc.
Natl. Acad. Sci.) indicates that the coding for the excavates (Clade 3)
needs a slight modification. Phylum Metamonada now appears to be sister
group to the other three excavate phyla (forming a new clade Discoba).
In other words Loukozoa and Metamonada have switched positions. As for
the problematic Family Malawimonadidae, I prefer to continue leaving it
in Phylum Loukozoa unless another placement can be shown to be more
likely. 
       As for the problematic Phylulm Rhizaria, there is
actually a third alternative placement which now seems to me to be the
most likely, namely as sister group of chromalveolates (rather than
*within* chromalveolates as sister group to Heterokonta). This change is
also reflected in the recoded classification below. However, at this
time, note that I see no reason whatsoever to change the number or
contents of the 16 Phyla which I recognized in 2006. It's just a matter
of recoding.         
       The biggest remaining question (in my mind) is just
another coding question. Does Phylum Amoebozoa form an exclusive
anterokont clade (clades 2-9) as sister group to the bikonts (clades
3-9), as my coding still reflects?  Some molecular analyses show
Unikonta (clades 1-2) as holophyletic (strictly monophyletic), although
bikonts probably evolved from a unikont ancestor. I am still betting
that this unikont ancestor split off between opisthokonts (clade 1) and
Amoebozoa (clade 2), rather than some unknown ancestor of an
Opisthokont-Amoebozoa clade.  Only time and further analyses will tell
(we shall see). Anyway, unless I have overlooked some pertinent
literature, the coding of the classification below will remain my
classification of Kingdom Protista for 2009.        
       ---------Cheers,     
                            Ken
Kinman         
 P.S.  If you want to recognize formal taxa between Kingdom and Phylum,
the best bet would be Subkingdoms Unikonta (clades 1-2) and Bikonta
(clades 3-9), although Unikonta would almost certainly be paraphyletic
at some level.  You could further subdivide Bikonta into Superkingdoms
Excavata, Plantae, and the SAR clade (i.e., Chromalveolata sensu lato?).      

                   KINGDOM
PROTISTA       

   1   Choanozoa%% (= Mesomycetozoa)
 _a_   {{EUMYCOTA}}
 _b_   {{METAZOA}}
   2   Amoebozoa
   3   Metamonada (incl. Parabasalia)
   B   Loukozoa (jakobids and allies)
   C   Percolozoa
   D   Euglenozoa
   4   Glaucophyta
   B   Rhodophyta
   C   Chlorophyta%
 _a_   {{METAPHYTA}}
   5   Rhizaria
   6   Cryptophyta
   B   Haptophyta
   C   Heterokonta (stramenopiles)
   7   Ciliophora
   8   Dinozoa (or Dinophyta)
   9   Sporozoa 
---------------------------------------------- 
NOTES: Clades 6-9 make up the Chromalveolate clade. Clades 5-9 make up 
the recently discovered "SAR" clade. Clades 4-9 is the photokaryote
clade (sensu lato). And of course, clades 3-9 still forms the bikont
clade.