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Re: Query on so-called "correlated" characters, reply
----- Original Message -----
From: "David Peters" <firstname.lastname@example.org>
Sent: Saturday, May 23, 2009 12:08 AM
On the same subject, is scapula size correlated to humerus size?
I'd rather say the size of certain muscle attachment areas is correlated
between the two.
Now think about Effigia.
Don't know it by heart and won't look it up now, but *Scleromochlus* has
long humeri and very small scapulae.
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.
ARGH! Sorry! I misread that one.
Not correlated. All four possibilities occur.
I'm simply showing that two bones widely separated can be correlated.
Which AFAIK nobody has ever denied.
Given this, does vertebral count also correlate with loss of limbs?
And if so, which character gets the boot?
Don't boot one, merge them.
Do you see how it becomes very unworkable and crazy-making
if you allow yourself to make correlation after correlation?
YES!!! And this is my POINT and has been for YEARS!!!
Phylogenetics really IS hard work.
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
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
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.
Straightforward? Not if you consider skull size versus neck length.
All four combinations occur (rauisuchians, azhdarchids, sauropods, caseids).
Pubis orientation versus tooth shape and predentary presence.
That one's tricky. All of these are adaptations to herbivory, but don't need
to appear in the same order.
It gets crazy real fast.
My point is that you can't simply pretend it's not crazy and code as if it
weren't crazy. It is crazy, and you can't escape it. You just can't.
Point is: I've had experience separating legless squamates from one
another even though the various characters for leglessness were left in.
There remains enough phylogenetic data to separate them according to
their leggy sisters. Parsimony wins every time, even though it would seem
the odds would be stacked against it. I say, throw a ton of characters
and scores at a taxon and see how it comes out. The sister are going to,
more or less, have the same situation. Parsimony has weight and should
Fine, but I don't see how this... correlates to the problem of correlated
IF it doesn't (and I'm just trying to see all sides of this argument),
can you reply with an example of how deleting correlated characters and
scores brings greater resolution and insight to a cladogram?
_Greater_ resolution? No, but I can give you two examples of equal ( = full
or almost full) resolution resulting, in part, from the fusion of correlated
characters. That is, I could, if they were published or even just in a state
where they could be submitted. Stay tuned.
A mild example, where two characters were correlated, we fused them, and the
result changed, is my paper to which I recently posted the link. But there
we changed so many other things in the matrix (including splitting
characters which are actually independent, but had been coded as the same
character!) that I can't possibly say how much of an effect the merger had.
Actually, you might be able to try it yourself. You know the tetrapod matrix
by Ruta & Coates (2007)? It is chock full of correlated characters. Maybe
you should try playing with it. Speaking from experience, it doesn't take
much to tip the topology over.