I've been away for a few weeks, but came back to find the weird 
new dinosaur Chilesaurus exists.  Just looking at it, any dinosaur 
worker would notice an odd mix of characters, making me curious exactly 
what it's related to.  Novas et al. (2015) used four analyses to 
determine it belonged in non-orionidan Tetanurae.  To use a Peters-ism, 
that's one strange bed fellow.  So let's go in for a closer look.
Their analyses 
The
 first analysis was Nesbitt et al.'s (2009) Tawa analysis (315 
characters), which focused on basal theropods and saurischians.  This 
found Chilesaurus to be a coelurosaur, though so was Ceratosaurus.  The 
authors rightly note the matrix was not designed to test neotheropod 
phylogeny, and the low Bremer supports show this, though I note the 
pairing of Chilesaurus with the only included actual coelurosaur 
Velociraptor is better supported than the other neotheropodan nodes. 15 
more steps were needed to constrain it as sister to Avepoda, 16 more to 
constrain it as a sauropodomorph (ended up sister to Plateosaurus 
instead of Saturnalia or Efraasia), and 14 more as an ornithischian (as 
the basalmost one or a heterodontosaurid).  These sound impressive until
 you realize that the matrix wasn't designed with ornithischian or 
sauropodomorph apomorphies in mind.  Also, I wonder how many more steps 
it took to place as a basal tetanurine where Novas et al. ultimately 
conclude it goes?  And why not use Nesbitt's (2011) larger anlysis which
 expanded on this and has had a major update by Langer and Ferigolo 
(2013), or at least Sues et al.'s (2011) version of Nesbitt et al.'s 
that added Daemonosaurus?  The latter genus also has three premaxillary 
teeth, a short snout, broad posterolateral premaxillary process and 
elongate cervicals with pleurocoels, so might help move Chilesaurus out 
of Avepoda.
The second analysis is a logical follow up,
 coding Chilesaurus in the sauropodomorph-focused matrix of Otero and 
Pol (2013) (with Tawa added; 353 characters), that is itself basically 
Yates' 2007 'prosauropod' matrix.  This finds Chilesaurus in a polytomy 
with Avepoda, Tawa and Chindesaurus, but placing it in Sauropodomorpha 
(as the most basal member) is now only five steps longer.  I'd say 
that's not strong support for Chilesaurus being a theropod, as numerous 
relationships rejected by five steps in one matrix end up being 
supported in other or later matrices.  It now takes 11 more steps to 
place it sister to Ornithischia, but that OTU isn't divided up, making 
the situation more problematic than above.
The third analysis uses a revised version of Smith et al.'s (2007) theropod matrix that is terribly mis/un-coded. 
 Not encouraging, though Novas et al. "deeply rescored" "several taxa" 
"based on new available data" including at least Eoraptor and 
Megaraptor.  They also added Tawa, Aerosteon, Falcarius, 
Jianchangosaurus and Therizinosauridae and 56 new characters (total now 
412 characters).  Here, Chilesaurus emerges as sister to 
Piatnitzkysauridae+Orionides.  However, only TWO steps are needed to 
constrain it as the sister of Avepoda*, and only three are needed to 
place it as the basalmost coelurosaur.  So even if the authors fixed the
 matrix, it only very weakly supports a basal tetanurine position.  
Suspiciously, Plateosaurus was deleted from the matrix "because of the 
morphological gap present between the very early sauropodomorphs present
 in the data set (e.g. Saturnalia) and Plateosaurus."  This is rich when
 they left Velociraptor in Nesbitt et al.'s matrix, which is at least as
 different from Allosaurus.  As the only sauropodomorphs left were the 
incomplete Saturnalia and controversial Eoraptor, and considering 
Chilesaurus emerged sister to Plateosaurus when constrained as a 
sauropodomorph in their first analysis, I can't help but wonder if 
Chilesaurus was sister to Plateosaurus here too until the latter was 
deleted.  Novas et al. never say how many more steps it takes to place 
Chilesaurus in Sauropodomorpha in this matrix, and ornithischians 
weren't included.
* Just looking through their list of 
characters supporting the position, 
astragalar ascending process height is miscoded in Smith et al.'s (it's 
clearly not "higher than the astragalar body, typically covering only 
lateral half of anterior surface of distal tibia"), 
as is "ridge on lateral side of tibia for connection with fibula present
 and clearly separated from proximal articular surface."  So there's the
 two steps we need to move it outside Avepoda. 
Finally,
 the fourth analysis used Carrano et al.'s (2012) basal 
tetanurine-focused analysis (351 characters).  Now Chilesaurus emerges 
in a polytomy with Monolophosaurus, Chuandongocoelurus, Megalosauroidea 
(including piatnitzkysaurids) and Avetheropoda.  Again, only two more 
steps are necessary to place it in Megalosauroidea, so its precise 
position here is very poorly supported.  Seven more steps are needed to 
place it in Coelurosauria (emerges sister to Compsognathus), but only 
three coelurosaurs are included in the matrix and they're heavily 
miscoded.  I added a lot of basal coelurosaurs to it when testing 
Bahariasaurus and found e.g. Compsognathus has 112 miscodings
 (of 351 characters).  That these include at least 7 that are actually 
more similar to Chilesaurus seems likely, though of course they probably
 also include at least 7 less similar to it, with the conclusion that 
the original matrix can't tell us how Chilesaurus compares to 
coelurosaurs.  As no maniraptoriforms were included, it can't tell us if
 Chilesaurus might belong there either.  No sauropodomorphs except the 
controversial Eoraptor were included, and no ornithischians.  Though 
like above matrix, this one wasn't made to test such basal nodes.
Given
 these results, Novas et al.'s conclusion seems to be stated far more 
strongly than their evidence indicates.  They say "the four independent 
phylogenetic data matrix [sic] favours a position as a neotheropod 
[avepod in my terminology], and particularly as a basal tetanuran", "The
 results of the four analyses are detailed below, but all of them agree 
in the position of Chilesaurus as a tetanuran theropod", and 
"Remarkably, all these analyses placed Chilesaurus as a member of 
Theropoda, near the origin of tetanurans."  Only the first two matrices have 
the needed basal taxa to test whether Chilesaurus is in Avepoda, and the
 second doesn't place it any closer to avepods than Tawa or Chindesaurus
 and supports Sauropodomorpha as a highly plausible alternative.  
Further, the first places it as a ceratosaur not a tetanurine, the 
second doesn't even split Avepoda into multiple OTUs so can't weigh in, 
and the third is basically ambiguous whether Chilesaurus is actually 
sister to Avepoda or a coelurosaur.  Only the fourth analysis may 
strongly support placing Chilesaurus as a monolophosaur-piatnitzkysaur 
grade tetanurine, though we don't know how easy it is to place outside 
Avepoda in that one.
I'd say that even if we trusted 
these matrices accuracy 100%, they only tell us it's quite possible 
Chilesaurus is the basalmost sauropodomorph or coelurosaur and is about 
equally likely to be sister to Avepoda, a non-orionidan tetanurine or a 
basal megalosauroid.  Not actually much agreement there.
My analyses
Will come next... 
References- Smith, Makovicky, Hammer and Currie, 2007. Osteology of Cryolophosaurus ellioti 
  (Dinosauria: Theropoda) from the Early Jurassic of Antarctica and implications 
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Yates, 2007. The first complete skull of the Triassic dinosaur Melanorosaurus Haughton (Sauropodomorpha, Anchisauria). Special Papers in Palaeontology. 77, 9-55.
Nesbitt, Smith, Irmis, Turner, Downs and Norell, 2009. A 
  complete skeleton of a Late Triassic saurischian and the early evolution of 
  dinosaurs. Science. 326, 1530-1533.
Nesbitt, 2011. The early evolution of archosaurs: Relationships and the origin of major clades. Bulletin of the American Museum of Natural History. 352, 292 pp.
Sues, Nesbitt, Berman and Henrici, 2011. A late-surviving basal theropod 
  dinosaur from the latest Triassic of North America. Proceedings of the Royal 
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Carrano, Benson and Sampson, 2012. The phylogeny of Tetanurae (Dinosauria: Theropoda). 
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Langer and Ferigolo, 2013. The Late Triassic dinosauromorph Sacisaurus agudoensis (Caturrita Formation; Rio Grande do Sul, Brazil): Anatomy and affinities. Geological Society, London, Special Publications. 379(1), 353-392.
Otero and Pol, 2013. Postcranial anatomy and phylogenetic relationships of Mussaurus patagonicus (Dinosauria, Sauropodomorpha). Journal of Vertebrate Paleontology. 33(5), 1138-1168.
Novas, Salgado, Suarez, Agnolın, Ezcurra, Chimento, Cruz, Isasi, Vargas and Rubilar-Rogers, 2015. An enigmatic plant-eating theropod from the Late Jurassic period of Chile. Nature. doi:10.1038/nature14307
