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Re: Smith et al.'s (2007) Cryolophosaurus analysis is untrustworthy due to a lack of coding
I've complained before about the recent trend of not coding included
taxa in theropod matrices (as in the Limusaurus and Haplocheirus
analyses), but here's a explicit and quantified example. I post it
here since I think this is an important issue in our field that needs
to be confronted and addressed.
THEN PUBLISH IT INSTEAD!!!
Yes, I am screaming. What, really, are you waiting for?
You know what? As soon as I get the next 1 or 2 tasks done (maybe
Sunday), I'll turn your e-mail into a paper. I'll add things like an
introduction (after all, I have some published experience with
questionable codings in data matrices, and I know a few references to
more examples). Then I'll slap our names on it (yours obviously as the
first author), send it to you for approval, and then I'll submit it to
the JVP as a Brief Communication. Or to the JSP or the ZJLS if you like
(if they take short papers).
This kind of information needs to get _out there_. Way too few people
read blogs or mailing list archives, and, well, there are entire
generations of people out there who simply don't get the idea that
anything on the Internet could possibly deserve to be taken seriously.
Just recently a reviewer found it _utterly preposterous_ that I dared
cite a mailing-list message (your 2006 DML message which showed the
authors of the description of *Juravenator* shouldn't have dropped taxa
from their analysis to increase resolution, eerily foreshadowing the JVP
paper by Butler & Upchurch 2007 which said the same and which I also cited).
Without coding Marasuchus, the state "2 sacrals" is useless, as all
other taxa have more (even the miscoded Saturnalia).
Is *M.* the only outgroup OTU? If so, the character is useless _anyway_.
A character that has one state in one OTU and the other in all others is
(Yes, even when that one OTU is the outgroup. That's because the ingroup
is already assumed to be monophyletic; trying to sustain this assumption
by characters is a category error.)
In the pectoral girdle, Marasuchus preserves a scapulocoracoid.
Smith et al. didn't bother coding it at all. Even obvious characters
like the broad scapular blade, which was explicitly noted by Sereno
and Arcucci to be an autapomorphy of the taxon.
If it really is an autapomorphy, there's no point in coding it.
If Marasuchus isn't coded as lacking a brevis fossa, why even have
the character? Everything else in the matrix has one (except
Confuciusornis, which is nonsensically coded as inapplicable), so
without coding Marasuchus the character's useless.
Again, it's useless either way.
Ask Smith et al. why they scored it as inapplicable in *C.*.
I'd honestly like to know how this happens. This isn't some obscure
foreign paper by ignorant beginners, it's a landmark paper in a high
tier journal by experts in the field. Yet what I've described here
is unacceptable. If you're publishing a phylogenetic analysis,
please code your taxa. If you're reviewing/editing a paper, please
check a taxon or two in the matrix. And if you find uncoded taxa,
send the paper back. Because coding only half the available data
makes the resulting cladogram worthless.
I think most reviewers simply don't read supplementary information or
even appendices intended for print, and those that do still don't read
tables full of (kind of) raw data.