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Using "P" in a Cladistic Engine



--- Mickey Mortimer <Mickey_Mortimer111@msn.com> wrote:

<2. Frontal process of premaxilla extending posteriorly to level of
lacrimal Lu et al. miscoded oviraptorids (p), enantiornithines (p) and
Hesperornis (0) (see above).>

  I just want to jump on this in case anyone's doing it in their matrices:

  Coding "P" as a "polymoprhic" condition in a character state acts _as_ a
character state in the matrix. There is no way in PAUP to use a separate
character aside from that assigned to be missing "?", a gap "-", or a
series of varying states "1, 2," etc.. "P" is included in the last group
and PAUP treats it as a valid state, meaning that any taxon with it will
run a tree where it tries to group with other taxa having the same state
coded as so. I noticed that recently some recent matrices of the Theropod
Working Group Matrix and our own Tom Holtz have resolved to using actual
different states in parentheses, which can include any number of states,
e.g. "(01)" or "(134)" and PAUP treats each occurance of a state in a
different tree. Some may wish to simplify this method by assigning each
variable another character, say x for "(012)" but this, as in "P", gives a
false signal of assignment, and PAUP actuallys runs the tree with "(01)"
as if the same position was occupied by a "0", and then occupied by a "1".

  Variable transformation and distribution of a condition in any taxon is
usually broken down when taxa are also broken down to just their species
or "genera", as has become the preferred method in recent matrices (see
for instance Xu et al., 2002; Hwang et al., 2002; Holtz, 2001, with some
exceptions, and there are others; genetic matrices are always based on
selection from individuals, but these use a slightly different version of
matrix when in PAUP that permit the four states available ["A, C, G," and
"T"] only). It thus seems problematic that assigning a "P" condition,
which is what is being done, will screw up any matrix at least a little,
and the more "P"'s in the matrix, the worse your signal is likely to be.

  Cheers,

=====
Jaime A. Headden

  Little steps are often the hardest to take.  We are too used to making leaps 
in the face of adversity, that a simple skip is so hard to do.  We should all 
learn to walk soft, walk small, see the world around us rather than zoom by it.

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