First, recall I questioned the authors' method of constraining Saurischia- "They tested this in an IMO un-ideal way, by constraining all 42 saurischians to be in an exclusive clade. Would have been better to just use a backbone of e.g. (Euparkeria, Lesothosaurus (Plateosaurus, Coelophysis), in case e.g. herrerasaurids aren't dinosaurs." So I did the latter (replacing Euparkeria with Postosuchus due to how TNT works) and found Saurischia is actually only 15 steps longer, not 20. Herrerasaurids are still sauropodomorphs, and Saltopus and silesaurids are still in a trichotomy with Dinosauria. I also wondered how many steps were needed to move Eoraptor to Sauropodomorpha. The answer is 22(!). Hmm. And ornithischian silesaurids? 28 more steps, which results in Saurischia.
But one aspect I didn't initially notice is that Daemonosaurus is missing from Baron et al.'s analysis. This genus has a skull which is rather odd for a supposed basal theropod- short-snouted with pronounced heterodonty. It also didn't include weird theropod-ornithischian cross Chilesaurus or theropod-like supposed basal sauropodomorph Buriolestes. So I added these three taxa to Baron et al.'s matrix.
|Phylogeny of the Baron et al. 2017 dataset after adding Buriolestes, Daemonosaurus and Chilesaurus (highlighted).|
What happens? Ornithoscelida is still a thing, but herrerasaurids move to outside Dinosauria. Buriolestes is the most basal sauropodomorph and Daemonosaurus is a theropod sister to Tawa, which are normal placements for these taxa. Chilesaurus is an ornithischian sister to Pisanosaurus at the base of the clade, which is interesting. Both are South American... Though note Chilesaurus' proposed avepod relatives (basal tetanurines) aren't in the matrix.
This makes Saurischia only ten steps longer than Ornithoscelida, with Buriolestes as the basalmost theropod and herrerasaurids still basal sauropodomorphs in that case. A sauropodomorph Eoraptor is now 16 steps longer. 21 more steps are needed for ornithischian silesaurids, with Buriolestes again a theropod and Chilesaurus remaining sister to Pisanosaurus.
Unfortunately, coding these taxa exposed a ton of problems with Baron et al.'s matrix. First it doesn't really have 458 characters. Weirdly enough, 6 characters are coded the same for every taxon and another 47(!) are only coded as different in one taxon. Which makes them useless for resolving relationships, or "parsimony uninformative" in the technical jargon. Taking into account the fake character zero that's only there because of how TNT works, the matrix actually only has 404 characters that are doing anything. Still big, but not so much bigger than Nesbitt et al.'s 315.
Also, some of the characters are badly formed at a Petersian level.
Check out 167- "Dentition: 0, homodont; 1, slightly heterodont, with small observable changes across tooth rows; 2, markedly heterodont, clearly distinct types of teeth present (modified from Parrish, 1993; Nesbitt, 2011). ORDERED." This ignores the fact that heterodonty can exist in numerous ways that aren't necessarily homologous at all. The anterior peg teeth, big canines and crushing cheek teeth of heterodontosaurids (coded 2) aren't just a further development of Eoraptor's (coded 1) anterior leaf shaped teeth which grade into posterior generalized carnivorous teeth, for instance. The direction of gradation to herbivorous teeth is even different there.
Or how about character 139- "Foramen located on the dorsal (and sometimes lateral) face of the surangular (surangular foramen): 0, present; 1, absent. NEW." This codes for whether an anterior or a posterior surangular foramen (or both) are present, with the next character coding for which one (or both) exist- "Surangular foramen: 0, both foramen (anterior, dorsally positioned and posterior, laterally positioned) remain open; 1 only the foramen on the dorsal surface of the surangular, anterior to or at the point of maximum mandibular depth remains open; 2, only the foramen located laterally, posterior to the point of maximum mandibular depth remains open. NEW." But the very fact both foramina can exist in the same element shows they are not homologous with each other, so a taxon with only a posterior foramen shouldn't be counted as having the same state in character 139 as a taxon with only an anterior foramen (e.g. Coelophysis and Eocursor in the matrix), but they are.
Or character 274- "Metacarpals I and V: 0, both substantially shorter in length than metacarpal III; 1, only metacarpal I longer than or subequal to metacarpal III; 2, only metacarpal V longer than or subequal to metacarpal III; 3, both are longer than or subequal to metacarpal III (modified from Butler et al., 2008)." This just provides all the permutations of mcI and mcV length relative to mcIII. But the fact you need all four permutations shows mcI and mcV length don't covary, so shouldn't be covered by the same character in the first place. This kind of coding also hides homology, since e.g. the metacarpal V reduction in states 0 and 1 won't be counted as more similar to each other by TNT. If you're wondering which dinosauromorphs have only mcV longer or subequal to mcIII, the matrix says it's Dilophosaurus. Which is untrue, as Dilophosaurus' mcV is a tiny nub. Character 434 does the same thing, but for shaft widths of mtI and mtV.
|Metacarpus of Dilophosaurus wetherilli (UCMP 37303?) showing metacarpal V (outlined and arrowed). I wouldn't assign that the state "only metacarpal V longer than or subequal to metacarpal III"... (after Xu et al., 2009).|
There are also a lot of correlated characters- 2 and 3; 7, 9 and 10; 21 and 24; 139 and 140; 147 and 149; 167 vs. 168, 171 and 180; 215, 221, 222 and 225; 244 and 245 (but nothing is coded 0 for 245 though Postosuchus should be...); 252 and 253; 260 and 261; 279 and 278; 292, 306 and 308; 293, 294, 296, 307 and 326; 295 and 297; 314 and 316; 328 vs. 323 and 324; 344 and 345; 378 and 380; 411 and 412; 435, 436 and 446. These seem to happen when the authors took characters from different sources but didn't realize they cover the same ground. So for example, 215 codes for sacral number (from Butler et al.), 221 codes for a vertebra inserted between ancestral sacrals 1 and 2 (from Nesbitt et al.), 222 codes for the number of dorsosacrals (from Gauthier) and 225 for the number of caudosacrals (supposedly new). And now sacral number is weighted more than it should be in the matrix.
Similarly, while Baron et al. did order a number of characters, many more should have been- 10, 11, 52, 58, 80, 92, 107, 129, 151, 154, 155, 179, 194, 306, 320, 324, 329, 336, 341, 354, 358 and 403. They also ordered 333 in the wrong way- "Shaft of pubis (postpubis), shape in cross-section: 0, blade-shaped; 1, rod-like; 2, rod-like, but with a tapering medial margin (tear-drop shaped) (modified from Butler et al., 2008)." This should have states 1 and 2 flipped, since tear-drop shaped is the intermediate shape.
The authors didn't take ontogeny into account when coding fusion characters (351, 422, 438 and 445), so that taxa known only from young individuals (e.g. Tawa, Pantydraco, Panguraptor, Liliensternus) are coded as if they are adults.
A final minor note that doesn't affect the analysis itself is there are way too many characters credited as "NEW" which are anything but. I don't expect every other matrix to be scoured, but there are some basic characters credited as new here- nasolacrimal crests (48); deep basisphenoid recess (100); posterior exposure of basiphenoid recess/plate (108); dorsal expansion of the anterior dentary (125); fan-shaped dorsal neural spines (211); fused sacral neural spines (219); presence of a caudosacral vertebra (225); metacarpal V absence (278); highly reduced ischial peduncle of ilium (316); obturator and pubic foramen presence (338); distal notch between pubes (348); pelvic fusion (351), etc., etc..
Overall, even if it was coded correctly, I don't think I'd trust this analysis within the 15 steps needed to dump Ornithoscelida. So consider my earlier support withdrawn. So disappointing. And that's not even getting to the coding accuracy, which is coming next time...
References- Xu, Clark, Mo, Choiniere, Forster, Erickson, Hone, Sullivan, Eberth, Nesbitt, Zhao, Hernandez, Jia, Han and Guo, 2009. A Jurassic ceratosaur from China helps clarify avian digital homologies. Nature. 459, 940-944.
Baron, Norman and Barrett, 2017. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature. 543, 5601-506.