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Re: something's wrong here: Qianosuchus phylogeny

Andreas Johansson (andreasj@gmail.com) wrote:

<There is nothing magical with the (morpho-)species level here. Couple of years
ago, SciAm printed a cladogram with _H. erectus_ and _H. sapiens_ as sister
species: very fine, except putting them in as unitary taxa assumes a priori
that the former isn't paraphyletic with regard to the later.>

  While it is likely *H. erectus* (as likely with *H. ergaster*) is
paraphyletic with regards to *H. sapiens*, this doesn't affect what David M.
was talking about, in response to what Dave P. was talking about, which was
individual/specimen verus collective OTU capsulization (i.e., putting a
[hopefully] monophyletic group of taxa into a single operating taxonomic unit).
In these, the chosen OTUs are not tending to be inclusive, but subsidiary. Dave
P. was also confused in what he was regarding as paraphyletic, in the comment
about *Scleromochlus* deriving from Proterochampsidae and other such arguments
(e.g., theropods from ornithischians?). This actually derived from an
inaccurate interpretation of a given phylogeny.

  Closest sister taxa in cladistics are in fact given as the closest known form
to the basal taxa that _could_ have given rise to the more derived sister
taxon, so that, say, *Scleromochlus* represents a descendant of the
paraphyletic group from which also sprang Pterosauria, based on Benton's
phylogeny. Neither *Scleromochlus* nor Pterosauria are given as paraphyletic.
Dave P. argued that using a collective OTU (which can be a species or "genus"
or what-have-you) as a split up into individual specimens is the correct method
of application, which is intelligent, but not wholly wise, as this leads to
using juveniles and mutants of species as potentially taxonomically viable
OTU's. Good for testing at a certain level, but problematic on the whole. David
M. mentions in the post that he is testing on this method, and Mike Keesey
opined that the wisdom on the method of using all specimens is very

  I would argue it should be done case by case, but for the most part, exclude
all juveniles and suspect juveniles, and run trees with them with constricted
outgroups to test for variability in the tree. They also tend to cause
long-branch attraction, something tested for in living species recently, though
I should not be mentioning this without providing a cite (I am not on my own
computer where I keep my reference works, and I am very tired at the moment).


Jaime A. Headden

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)

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