Re: Smith et al.'s (2007) Cryolophosaurus analysis is untrustworthy due to a lack of coding

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

>  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 
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.