PROTISTA - let's move on

[Ken Kinman]

David,
      Yes, let's definitely move on, but NOT with your conservative splitting scheme (which doesn't seem to have advanced much since 1999).  At least Cavalier-Smith keeps his classifications very up-to-date, and he doesn't have huge, uninformative polytomies (which are made even less informative by alphabetizing them).

     First of all, you did a lot of nit-picking about my Clade 4 (excavates sensu lato).  According to the recent paper by Simpson, Inagaki & Roger, 2006 (Molecular Biology and Evolution, 23:615-625), your excavate grouping is actually *quadruply* paraphyletic, since you removed four exgroups:  Parabasalia, Oxymonadida, Euglenozoa, and Percolozoa (the latter being Heterolobosea sensu lato).  They show that jakobids (of Loukozoa) are actually closer to Percolozoa and Euglenozoa, which only requires me to put Loukozoa after Metamonada (instead of before it):

   4  Metamonada (incl. Oxymonadida too!!)
   B  Loukozoa
   C  Percolozoa (heteroloboseans and allies)
   D  Euglenozoa

      Oh, I just realized that you also separated Stephanopogonids from both your heteroloboseans and excavates.  That makes your excavates actually 5 times paraphyletic (not just four).  Yikes!!!  I also don't understand why you separate Mesomycetozoa and Nucleariids from the opisthokont clade.  This seems to make your opisthokonts doubly paraphyletic.   Excessive splitting in order to avoid polyphyly often means strict cladists inadvertently create a lot of paraphyletic taxa (which they profess to despise as obsolete and/or unnatural).  Anyway, I will take your advice, and change "Choanozoa (= Mesomycetozoa)" to "Choanozoa (incl. Mesomycetozoa)".  Sorry about that little slip-up.

   ----Ken Kinman