Paraphyly and names

[Ken Kinman]

Dear All,
     I will get to Richard Pyle's more complicated scenario in a second
e-mail later today (time permitting).  But first I'm going to respond to the
Zdenek Skala and Thomas Pape debate, since it has a relatively simple
pectinate cladogram, with E splitting off first, then D, then C, then B & A
(one short-hand way of representing this is with parentheses, and two
"swiggles" for the big gaps):

           (E~~(D(C~~(B(A)))))

      Zdenek's arguments make complete sense to me, and it's too bad the
strict cladists aren't paying closer attention to his arguments (especially
how plesiomorphies should NOT be treated as "worthless" negative evidence).
Anyway, I will classify this theoretical example, and then show how it
relates to the concrete example of Amphibia and Amniota.
     Since E (call it genus E-us) splits off first, it will come first in my
classification.  In the scenario being discussed, a bunch of synapomorphies
separate E-us from group ABCD (and another bunch of synapomorphies separate
AB from CD).  The Kinman System can classify it as three distinctive
families (with a paraphyletic "i.e. truncated" Family CD-idae):

  1   E-idae
  2   CD-idae
          1  D-us
          2  C-us
          3  {{AB-idae}}
_a_  AB-idae
          1  B-us
          2  A-us

     Relating this to the Amphibia example, the "truncated/paraphyletic"
CD-idae is like Amphibia, and the holophyletic AB-idae is like Amniota (and
E-idae would be the sarcopterygian family Panderichthyidae).  Not a perfect
analogy, but I think it works well enough so you get the idea.
     Please note, that although we define Amniota on the basis of "the
amniotic egg",  this is really an extremely complex series of numerous
synapomorphies (which fossils will probably never document).  And there are
undoubtedly many other synapomorphies that evolved just before, just after,
and also during that "amniotic" series of events for which we have no
transitional fossils (and may never have, especially if they involve soft
tissues or genes).
     The above classification (and the Amphibia-Amniota parallel situation)
can reflect and document this kind of relatively long series of anagenetic
events (which combine to form a big knowledge "gap") which everyone agrees
is a good place to mark a "boundary" between major taxa.
     Eclecticists (like Zdenek and myself) are not only using this large
"amniotic" character gap to mark the beginning of Amniota, but also as a
termination of Amphibia.  The lack of the amniotic character-complex
distinguishes Amphibia from its descendants (in the exgroup Amniota), so
this is still positive information (certainly not of zero value just because
it is plesiomorphic).  Likewise Amphibia began with a boundary around the
stegocephaly-tetrapody character-complex, which is a large gap that
separates amphibians from Family Panderichthyidae and other sarcopterygians
(and their ancestors).  It is no accident that such big gaps have been used
to mark the boundaries of major taxa.
     Finally, I could certainly reduce the ABCDE example to a simple
cladistic (branching only) classification as follows (but in this case you
would be losing a lot of valuable information, and if you are wrong about
the branching order, it could be very destabilizing in the future,
especially if you have formally named these nodes instead of just coding
them):

  ABCDE-idae
       1  E-us
       2  D-us
       3  C-us
       4  B-us
       5  A-us

I use such strict cladifications fairly often, but only when all the gaps
are in the same "ballpark" of size.  But here we really have tiny gaps and
huge gaps mixed together, so we would have lost lots of information and also
set ourselves up for future instability and confusion (especially when more
taxa are added).  Ignoring anagenetic information and plesiomorphic
information is often a very costly mistake (in both the short term and even
more so in the long term).
             -------  Ken Kinman
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