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



----- Original Message -----
From: "David Peters" <davidpeters@att.net>
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?

Sure.

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 present (2).


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.

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.

Yep.

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 prevail.

Fine, but I don't see how this... correlates to the problem of correlated characters. :-)


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.