Thursday, December 16, 2010

Adventures in Not Coding- Marasuchus by Smith et al.

I've complained about the recent trend to not code taxa for characters in phylogenetic analyses here before.  Today I thought I'd show you an example.

The paper is Smith et al.'s (2007) influential basal theropod analysis in the Cryolophosaurus monograph.  Holtz said on the DML that it was "truly good stuff, and I strongly suspect that they have better captured the actual phylogeny of basal theropods than most previous studies."  The paper includes Makovicky and Currie as coauthors- two people who know their stuff and have access to specimens.  There's no excuse to make obvious mistakes.

The taxon is Marasuchus, the outgroup of the analysis.  This basal dinosauriform includes the more complete specimens once referred to Lagosuchus and has been described by Bonaparte (1975) and Sereno and Arcucci (1994) in addition to the briefer original descriptions by Romer (e.g. 1972).  This is a classic OTU for dinosaur analyses, used in papers by Rauhut, Ezcurra, Novas and others.  So there's plenty of information on the taxon available in easily accessed journals like JVP.

What follows are Smith et al.'s codings compared to my codings, divided by anatomical section.  Note somebody with access to the specimens themselves would be able to code even more than I could. 

Cranial
Smith et al.- ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ???0???00? 00??-???00 ?0???????? ?????????? ?????????? ?
Me- ?0???????? ?????????? ?0?????00- ?0??10???? ?????????? ?????????? ?????????? ?????????? 0????????0 0??????00? 0000-?1?01 ?0???????? ?????????? ?????????? ?

Cranially, Marasuchus is known from a maxilla and braincase.  Note the first section of coded characters in my row pertains to the maxilla, which went completely uncoded by Smith et al..  The second section pertains to the braincase, and here I was also able to code more.  Altogether Smith et al. coded 9 characters, while I coded 22.

Axial
Smith et al.- ?00?????- ??0?0??0?0 0?00????0? ?????????0 0???-??0?? ?0??????0? ?????
Me- 0110?0--- 0-0?10000- 01000??010 -?00010?00 100?1010?0 0p00000000 00???

Axially, Smith et al.'s laziness really shows.  Marasuchus preserves an almost complete vertebral column, yet Smith et al. only coded a few of the characters.  What's confusing too is that it's not the obvious characters which were coded.  Things like axis, cervical and dorsal pleurocoels absent, and amphicoelous cervical centra should be second nature to code for anyone even vaguely familiar with the taxon, but then there are characters like "cervical prespinal fossa narrow" which WERE coded.  Now having a wide prespinal fossa is an abelisaurid character, so nobody describes the state in something like Marasuchus, and Marasuchus' vertebrae have only been illustrated laterally as far as I know (not anteriorly, as you'd need to see the prespinal fossa).  It's not that I doubt Marasuchus would have a narrow fossa if examined, but since almost every non-coelurosaur with preserved cervicals is coded for this obscure character, and the matrix certainly doesn't show signs of rigorous coding in general, I'm suspicious.  Another issue is that some of the uncoded characters are important to code in Marasuchus, like the absence of hyposphenes or the presence of only two sacrals.  Again these are things anyone with even a passing interest in dinosaur origins would be aware of, as they are classic characters excluding it from Saurischia and Dinosauria respectively.  Without coding Marasuchus, the state "2 sacrals" is useless, as all other taxa have more (even the miscoded Saturnalia).  In the axial area, 17 characters were coded by Smith et al., but 54 could be coded by me.

The two integumentary characters cannot be coded, of course.

Pectoral
Smith et al.- ??? ?????????
Me- ??? 10010?000

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.  So 0 coded by them, and 8 by me.

Forelimb
Smith et al.- ? ????????0? ?????????? ?????????? ?
Me- 0 00p?000?0? ?????????? ?????????? ?

In the forelimb, Marasuchus preserves a humerus, radius and ulna.  Smith et al. bothered to code one character- radius over half humeral length.  At least it's an obvious character this time.  That's 1 coded by them, and 8 by me.

Pelvic
Smith et al.- ????????? 0??0??1p00 00-00??0?? ?00?00???? ?
Me- 0000010?1 00020p0100 ---00p?000 --00?0?00? 0

Marasuchus preserves an essentially complete pelvis.  This situation is rather like the axial skeleton.  Again, obvious characters are left uncoded- propubic pelvis, short preacetabular process, no post-obturator notch.  And again, some are important.  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.  Of pelvic characters, Smith et al. code 16 and I code 35.

Hindlimb
Smith et al.- ??0000000 0000001?0? 0?0????000 00000000?0 0000???0?0 00r????
Me- 001000000 000000100- 0000010000 0101000000 0000001100 001?0??

Finally, a decently coded area.  There are certainly some absences, like the obvious anteromedially oriented femoral head and absent fibular crest of the tibia, and none of the fibular characters are coded.  But overall it looks like someone actually tried in this area.  Smith et al. code 38 and I code 53.


In all, Smith et al. coded 81 characters while I coded 180.  That leaves 91 characters uncoded. So they only coded 45% of what was possible using the literature, and an even smaller percentage of what's possible with the specimens in hand.  You might not think it's important to code the outgroups, but you'd be wrong.  The major conclusion of this paper was that Crylophosaurus and other dilophosaurs were closer to neotheropods than coelophysoids, but this depends on having the polarity for characters in basal Avepoda correct.  I can tell you now that even though I haven't worked my way through most of the matrix yet, just adding the codings for Marasuchus, Silesaurus and some for Herrerasaurus has changed the results to give a huge polytomy in basal Avepoda between coelophysoids, Zupaysaurus, dilophosaurids and neotheropods.  Who knows how that will change though, as I note that "Dilophosaurus" sinensis wasn't coded at all postcranially, for instance. 

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.

Reference- Smith, Makovicky, Hammer and Currie, 2007. Osteology of Cryolophosaurus ellioti (Dinosauria: Theropoda) from the Early Jurassic of Antarctica and implications for early theropod evolution. Zoological Journal of the Linnean Society. 151, 377-421.

2 comments:

  1. I sincerely hope David Marjanovic follows up on his 'threats' of getting your critiques published. Why this stuff should not be a part of the scientific literature is beyond me.

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  2. Where can I access this supplementary matrix? The URL given in the paper is http://www.blackwell-synergy.com/doi/abs/10.1111/j.1096-3642.2007.00325.x, which redirects me to http://onlinelibrary.wiley.com/doi/10.1111/j.1096-3642.2007.00325.x/abstract, where I find no mention of supplementary appendixes, even when I am logged in through my university (I was able to download the .PDF of the main paper with no problem at all).

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