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Re: Query on so-called "correlated" characters, reply

2009/5/22 David Marjanovic <david.marjanovic@gmx.at>:
> ----- Original Message -----
> From: "David Peters" <davidpeters@att.net>
> Sent: Saturday, May 23, 2009 12:08 AM
>>>> 2. Quadratojugal process of jugal present or absent.
>>>> Quadratojugal present or absent.
>>> The first must be scored as unknown (which, for PAUP*, is the same  as
>>> "inapplicable") in all taxa that lack a quadratojugal.

This seems correct. I have heard of the argument of making the
character additive, with states quadratojugal absent (0),
quadratojugal present, without process (1), quadratojugal present,
with process, (2), as if you were progressively adding things. I think
this is likely not certain in this case because the presence of the
process is likely a by-product of the formation of the infratemporal
fenestra (by delay in ossification, I think to remember). Being more
general, if there is any other process in which we observe variation,
which cannot be hierarchically correlated with the process already
assessed, we should codify with the same logic both processes, and
would not consider both additive in the same sense cited above because
we would repeat the change from presence to absence. So, I think the
best option is doing what David (Marjanovic) indicated.

>> And there's the opposite case:
>> Antorbital fenestra with or without a maxillary fossa. 'Without a  fossa'
>> appears on chroniosuchids, pterosaurs and Proterosuchus, which  are not
>> related. The fossa is not necessarily correlated to the  presence of a
>> fenestra. It either is present, or it is not.
> I'd say they're simply correlated the other way around: the fossa is only
> present if the fenestra is present, never otherwise. One ordered multistate
> character: both absent (0), fenestra present and fossa absent (1), both
> present (2).
Well, in this case I think that we can alternatively consider both as
not correlated (except hierarchically), for the multistate character
you proposed is operationally the same of two binary characters being
one presence/absence of the fossa and presence/absence of the
fenestra. I think the currently known distributions implies the the
character of David (M) is not wrong, as do the fact that according to
Witmer (1997, MSVP) the fossa forms by a sac necessarily transversing
the fenestra to reach the fossa from the nasal cavity. But I think
making two independent characters may better accomodate, without harm,
the possibility of a specimen without antorbital fenestra, but which
presents a fossa similar in location and depth to the antorbital

>>>> 4. Naris larger/smaller than antorbital fenestra.    Antorbital
>>>> fenestra present or absent.
>>> The first must be scored as unknown in all taxa that lack an  antorbital
>>> fenestra.
>> >>
>> Yet, if no antorbital fenestra is present, isn't the naris, by  default,
>> larger than the antorbital fenestra? Why not score it that  way? How does an
>> antorbital fenestra phylogenetically begin? I've  seen foramina that might
>> be the start of an antorbital fenestra. Do  you ignore those?
> That needs to be demonstrated first. It needs to be shown that the
> antorbital fenestra starts small and then becomes larger. As long as that
> isn't established, it's safer to score the relation character as unknown
> when the fenestra isn't there.
> Why should foramina and fenestrae be homologous? Foramina contain nerves
> and/or blood vessels; fenestrae can, but only by accident.

Well, here I think we can see foramina and fenestrae as part of a
continuum. There are foramens which can enlarge to make fenestrae
within which a nerve is located, as with the obturator fenestra of
mammals. The suborbital fenestra of diapsids seems to present a great
variation in area. Their difference is in area, and there are nerve
foramina of different areas, and the same applies for fenestrae. I
think we should not deal at this point with which is the origin of the
fenestra; as far as we can we should only observe the similarities and
dissimilarities (which is not always easy).

In my view, an argument for seeing the foramen closer to the absent
condition than the fenestra, and so including the absent into a
continuum, is that if we define the size as area, we should say that 1
cm x cm (suppose this means foramen, the character should be defined
better in a ratio with other feature) is closer than 0 cm x cm than
(absent condition) than a fenestra of say, 30 cm x cm.