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

David Marjanovic screamed er... wrote-

> 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).

Er... great!  We might want to adjust the language though, which is fun for an 
editorial or blog post, but not so great for a professional paper. ;)
Also turns out the narrow prespinal fossa might have been taken from Tykoski's 
(2005) matrix, though he only used Sereno and Arcucci's (1994) paper to code 
Marasuchus from, which does not describe or illustrate that character...

> 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).

Thanks for the attempted cite!

> > 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.)

There are six outgroups (Marasuchus, Silesaurus, Herrerasaurus, Saturnalia, 
Plateosaurus and Eoraptor) and multiple states to the sacral number character.  
Thus the character wouldn't be useless, as there are multiple taxa coded as 
having 3 sacrals, 4-5 sacrals, etc..  The authors don't state whether they 
specified all of these as outgroups in PAUP, or whether they just let PAUP 
default Marasuchus as the real outgroup since it's listed first.

> > 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.

Well, the extreme condition in Marasuchus is autapomorphic, but the generally 
broad blade is plesiomorphic and found in plenty of other included taxa.

> > 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.*.

It wouldn't be useless if Confuciusornis were coded correctly.

> > 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.


Mickey Mortimer