Re: Notarium question

["David Marjanovic" <david.marjanovic@gmx.at>]

----- Original Message ----- 
From: "David Peters" <davidpeters@att.net>
Sent: Friday, February 13, 2009 12:44 PM

> > (But wouldn't notarium fusion by very ontogenetically dependent
> > anyway?)
>
> Only if pterosaurs were archosaurs. [...]
>
> Maisano 2004 reports that you can throw out the old rules if
> pterosaurs are not archosaurs.

I don't understand what you mean. Basic vertebrate ontogeny doesn't depend 
on whether you're a pterosaur.

----- Original Message ----- 
From: "evelyn sobielski" <koreke77@yahoo.de>
Sent: Friday, February 13, 2009 12:45 PM

> In the case of the notarium, its presence was used to argue for the 
> monophyly of "Metaves" - which, as it seems now, are almost certainly a 
> pseudoclade.

Why do you think so?

> For a similar error, consider the fallacy "everything with feathery 
> integument is a member of Aves".

How is that similar? Everything with feathers does indeed form a clade -- it 
just happens not to make subjective sense to call it Aves.

> You can usually get around this by de-emphasizing the trait as a whole and 
> concentrating on particular sub-traits - by considering the *structure* of 
> a feature rather than its *existence*.

Still, make them a single multistate character (as explained in my last 
e-mail), and not lots of binary characters. Atomizing characters the latter 
way risks producing lots of correlated characters (which are in reality a 
single character with higher weight). If it's impossible to have one state 
and another at the same time, these states belong to a single character.

> In determining character choice & scoring, it helps that we have robust 
> grounds to suspect a particular overall polarity: notarium fusion is 
> apomorphic vs vertebral nonfusion, as far as can be told.

This is completely irrelevant. Don't polarize characters yourself. That's 
what the outgroup is for!

PAUP* generates _unrooted_ trees, because an apomorphy (a change from a 
character state to another) in one direction is also an apomorphy in the 
other. When it's done, it puts the root on wherever the outgroup is. If you 
haven't told it what the outgroup is, it arbitrarily chooses the first taxon 
in the list.

It does, therefore, not matter whether you call the most plesiomorphic state 
of each (or any) character "0" or not. People often try to do it, but that's 
just for their own convenience, and then it still often turns out that the 
outgroup has a state other than 0.

> This need not yield "better" results (i.e. better-supported and less 
> polytomies). But uncertainty that is correct is preferrable to certainty 
> that is wrong, and in some cases - when the potentially misleading traits 
> carry much weight in the scope of your analysis - this may be the only way 
> to get results that are not outright wrong.

Quite so. "Beautiful" and "correct" aren't the same thing.