[Taxacom] stem eudicots of NCBI

Kenneth Kinman kennethkinman at webtv.net
Tue Mar 29 21:07:36 CDT 2011

Hi Richard, 
       Well, Angiosperm Phylogeny Group has separated the stem eudicots
from the core eudicots since their first version in 1998 (although they
didn't then use the phrase "stem eudicots" per se, perhaps due in part
to its paraphyletic connotation).  But it continues to be a useful way
to divide eudicots, so I am not worried that NCBI will abandon it.  That
is because such strict cladists seem to recognize the utility of such
taxa, but they generally seem content to use them as long as they are
not formally named.                
      Thus stem taxa like "non-avian dinosaurs" and "stem eudicots" seem
acceptable to them, but if you give such taxa a formal name (like my
classification calling "stem eudicots" the Subclass Ranunculidae), then
they tend to get upset.  Were getting closer, but not quite yet in
agreement. Until Hennigian paraphylophobia (as far as formal taxon names
are concerned)  is eventually abandoned by more and more workers, we can
come close to agreement in such cases (but not quite).      
       Anyway, a division of eudicots into "stem eudicots" and clade
Pentapetalae seems a very good compromise in the meantime, as long as
the strict cladists don't feel pressured into giving the stem taxon a
formal name.  That's fine with me, and botanists seem more reasonable on
this front than vertebrate paleontologist PhyloCoders (who seem intent
on naming every possible clade (even if the evidence that they are
holophyletic is weak to marginal at best).  Anyway, once NCBI adopts the
clade name Pentapetalae, they would be well advised to shift Order
Gunnerales into their "stem eudicots".  It seems advantageous to all
concerned that they do this.  Botanists seem easier to work with than
the hard-core PhyloCoders (very strongly represented in Vertebrate
      As for your restricted usage of the term paraphyletic, I'm afraid
we will have to agree to disagree.  And I don't think most workers who
use the term believe that it is inappropriate for broad diachronic
macroevolution.   One of the broadest examples is a paraphyletic Empire
Prokaryota giving rise to an Empire Eukaryota (as proposed by Ernst
Mayr).  Empire Prokaryota is clearly truncated, most importantly as the
source of the first eukaryote, but also the organelles (such as
mitochondria and plastids) which later became incorporated into various
eukaryotic taxa.  It is not a simple and singular truncation, such as
Class Reptilia giving rise to Class Aves, but it is truncation
           ------------Ken Kinman

Richard Zander wrote:
      Don't send a congratulatory note to NCBI, Ken. They might think
they overlooked something, and "fix" it.             
          One should use the word "paraphyletic" when one is discussing
synchronic (present-day) nesting of exemplars. That's the phylogenetic
dimension. It is inappropriate for diachronic (through-time) theory of
evolution, in which case "macroevolution" or the equivalent is
appropriate. IMO, anyway.           
      How can a clade be truncated if it is just part of a nested set of
exemplars? Where is the truncation in, say, ((((A,B)C)A)D)E,F ? 

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