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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.


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 parsimony-uninformative.

(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.