[Taxacom] An experiment for NCBI's taxonomy?

Kenneth Kinman kennethkinman at webtv.net
Thu Dec 16 13:24:15 CST 2010

Dear All, 
        I would like to propose an experiment. The
taxonomy used by NCBI has attempted to eliminate paraphyletic taxa. I
wonder what would happen if they put back in just one major paraphyletic
group (with simple annotation to explicitly state this and to identify
the exgroup)? Would most users find it more useful and with taxon names
that are more familiar?        
         If go to their Amniota page (the weblink
below takes you to their taxonomy browser and then just type in
Amniota), you will see that it is divided into Mammalia and Sauropsida.
No mention there of either Reptilia or Aves (instead they have Sauria
and Testudines). And if you just wanted to browse the hierarchy to Aves,
it goes through a whole series of nested subclades, Sauria, Archosauria,
Dinosauria, Saurischia, Theropoda, Coelurosauria, and finally Aves.
YIKES, no wonder they had to eliminate rank names too.                 
          Wouldn't it be much simpler and
user-friendly if they just divided Sauropsida into two familiar taxa: 
          Aves (birds)
          Reptilia % (paraphyletic WRT: Aves)      

        And on a new Reptilia page, they could 
divide them into familiar groups, plus {{Aves}} (exgroup marker for
      {{Aves}} (exgroup of Dinosauria)
     Dinosauria % (paraphyletic WRT: Aves)

         By the way, I normally would list the
paraphyletic group first, followed by the exgroup, but NCBI alphabetizes
its subgroups (which seems to suit their purposes and can be useful when
there are lots of subgroups listed). Anyway, if NCBI were to try this
experiment, the PhyloCoders might scream foul, but I bet a lot of other
people would find it more familiar and user-friendly. Some PhyloCoders
might even come to realize that their classifications won't come
crashing down if they include some paraphyletic taxa (and that they are
actually useful if properly annotated).  Well, I can at least hope that
some of them might.        
        It would be an interesting experiment. And NCBI
is going to have to change its classification of Sauropsida anyway if
Testudines (turtles) are actually diapsids that are secondarily anapsid
(and thus a part of Sauria, not its sister group at all). That would
mean that their Sauria is a paraphyletic taxon (and not a very useful
                  --------Ken Kinman                     


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