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AW: Notarium question
> If you score them differently on the assumption that they
> are separate
> apomorphies, then you're assuming what you're
> setting out to prove.
On the other hand, if you score simply "notarium present (y/n)?", you may not
be able to show they are separate apomorphies *even if they were* because your
scoring assumes that the notarium is a monolithic entity - which any cladistic
analysis will try to optimize towards a single origin.
(This is the mistake that led Cracraft to "prove" that Hesperornithes, loons
and grebes are a clade to the exclusion of all other birds living and extinct.
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. For
a similar error, consider the fallacy "everything with feathery integument is a
member of 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*. 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 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.
There are some more ways to avoid this problem; Kevin McCracken et al did a
nice study of the issue some years ago: