Monday, July 24, 2017

Theropod Database pilfered again? Teihivenator edition

Back when I was sorting through obscure theropod species, I noticed the case of "Laelaps" macropus.  Ignored for almost a century, I examined the syntypes at the AMNH and wrote the first substantive comparison and diagnosis on The Theropod Database back in 2009.  Eight years later, and I see Yun (2017) has published a paper on the specimen and named it Teihivenator.  Well, it's good someone finally did something with the taxon, except....

My proposed diagnosis- "lateral tibial malleolus at same level as medial malleolus; paired proximoventral processes on pedal phalanges II-1 and III-2."
Yun's last two characters in his diagnosis- "lateral malleolus is at same level as medial malleolus; paired ventral processes proximally on all preserved pedal phalanges."
Hmmm...

My materials list- "... distal tibia (100 mm wide)
....(AMNH 2551) phalanx II-1 (109 mm), phalanges III-2 (93, 96 mm)"
Yun's discussion- "and distal ends of a tibia (Fig. 1A, C), about 100 mm wide.
... Phalanx II-1 is about 109 mm long, and each phalanges III-2 are about 93, 96 mm long."
And no, these aren't measurements from the literature, they're from my photos with scale bar taken at the AMNH. Hmm...

My discussion- "The material is tyrannosauroid based on the anterior process of the lateral tibial condyle..."
Yun's- "the material clearly belongs to tyrannosauroid based on the presence of the anterior process on the lateral tibial condyle.
Me- "All phalanges are ... more robust than similar-sized ornithomimids (e.g. Gallimimus' holotype)."
Yun- "Also, preserved pedal phalanges are much more robust than similarly sized ornithomimosaurs..."
Me- "The proximal metatarsal is II, and has a sharper posterior corner, more rounded anteromedial corner and shallower lateral notch than Alectrosaurus, Appalachiosaurus and Tyrannosaurus."
Yun- "The posterior corner is more narrow and triangular compared to other derived tyrannosauroids, and the medial corner is more rounded. The notch for metatarsal III is much shallower than most tyrannosauroids."
Hmmm...

Some syntypes of "Teihivenator" macropus.  Top left- proximal metatarsal II AMNH 2553. Top right- distal metatarsal IV AMNH 2552. Bottom- proximal and distal tibiae AMNH 2550.  Courtesy of the AMNH.

I want to make clear that this isn't a hack job like Easter's "Ajancingenia" copy-paste nonsense.  Yun came up with quite a few features of his own and his own conclusion, that macropus is closer to tyrannosaurids than Dryptosaurus and thus deserves a new genus name.  But I think it's inarguable Yun used the Database for information, but did not cite it or myself in the Acknowledgements.

There's "good" news though!   As noted by Marjanovic on the DML, the name is not valid because there was no physical publication or ZooBank registration.  So here's my proposal to Yun- Add me as a second author for a brief follow-up paper, we can correct a few things like -venator being Latin as opposed to Greek, add my high res photos from the AMNH to give the genus a proper illustrative debut, and with a ZooBank registration make it official.  Deal?

[Edit- When I wrote this, I was unaware of Brownstein's preprint placed online today arguing macropus is a chimaera of tyrannosaur and ornithomimosaur specimens.  While I haven't had a chance to study the chimaera issue, Brownstein does provide detailed descriptions and high resolution photographs, so that I don't think any further contribution by myself is necessary.  So, uh, proposal retracted.  Though if Yun does publish a corrective paper with ZooBank registry, I would like to be in the acknowledgements.  Man, that story changed fast.

Brownstein, 2017. Theropod specimens from the Navesink Formation and their implications for the diversity and biogeography of ornithomimosaurs and tyrannosauroids on Appalachia. PeerJ Preprints. 5:e3105v1.]

[Edit #2- News continues to fly in.  As McCabe commented on below, Yun has left feedback on another preprint of Brownstein's indicating he thought the macropus syntypes were lost, though he really should have mentioned this in his paper.  Creisler also informed me via the DML that Yun registered the genus on ZooBank, but without a mention of this in the paper itself it still violates ICZN Article 8.5.3 (a name must "be registered in the Official Register of Zoological Nomenclature (ZooBank) (see Article 78.2.4) and contain evidence in the work itself that such registration has occurred.").  Thus a corrigendum is still necessary, which Yun's been informed of.  Whew.  This is going to be a messy Database entry to write...]

Reference- Yun, 2017. Teihivenator gen. nov., a new generic name for the tyrannosauroid dinosaur "Laelaps" macropus (Cope, 1868; preoccupied by Koch, 1836). Journal of Zoological and Bioscience Research. 4(2), 7-13.

Tuesday, March 28, 2017

Ornithoscelida Tested- Adding taxa and checking characters

So the last post reported on Baron et al.'s (2017) new paper that recovered a theropod-ornithischian clade excluding sauropodomorphs, which they inaccurately resurrected the name Ornithoscelida for.  Now that I've been able to construct a TNT file from their matrix and have coded a few relevant taxa for it, we can explore it in further depth.

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.

Friday, March 24, 2017

Ornithoscelida Lives!

Back in 2010, I wrote a post about how surprisingly theropod-like Heterodontosaurus was, and ended by stating "Not that I'm saying Saurischia is wrong, I just think we can get so comfortable with an idea that we stop looking at alternatives."  This week I was surprised to learn of a new paper by Baron, Norman and Barrett (2017) which uses a phylogenetic analysis to recover that heterodox ornithichian+theropod topology.  In particular, they recover herrerasaurids as basal sauropodomorphs, while ornithischians and theropods are joined together in the resurrected clade Ornithoscelida*.   Vindication?

* Baron et al. redefine some clades (see below), but here I'm using the traditional concepts since I dislike some of their definitions.

"Reduced strict consensus tree of [Baron et al.'s] main
analysis ..., after the exclusion of Saltopus elginensis, Agnosphitys
cromhallensis, Eucoelophysis baldwini
and Diodorus scytobrachion." (after Baron et al., 2017)

Well, let's see how good the study is first.  I should preface this by noting that while traditional Saurischia has been recovered in every single previously published numerical cladistic analysis, most of these were crap by today's standards.  The only exceptions are really Nesbitt et al.'s (2009) Tawa analysis, which used 30 dinosauromorphs and 315 characters, Ezcurra's (2006) Eucoelophysis analysis that used 26 dinosauromorphs and 287 characters, and Cabreira et al's Ixalerpeton/Buriolestes analysis that used 42 dinosauromorphs and 256 characters  Yates' is large but focuses mainly on sauropodomorphs, and others are small (11 taxa, 98 characters for Langer and Benton, 2006; 18 taxa, 139 characters for Martinez et al., 2011; etc.).  Baron et al. include 72 dinosauromorphs and 456 characters, so by that measure is much better.

It also uses only species-level OTUs and properly orders characters, so that's good.  And it has excellent taxon sampling, including basically every basal dinosauromorph except Ixalerpeton, Buriolestes and Isaberrysaura (which were presumably published too late) and a couple fragmentary taxa (Teyuwasu, Alwalkeria) [Edit: I did not realize at the time it doesn't have Daemonosaurus, Scutellosaurus or rhodesiensis, and less importantly the fragmentary Chromogisaurus.  The absence of Daemonosaurus is particularly odd given it's somewhat heterodontosaury features...].  In particular, ornithischians are well represented unlike any prior analysis (14 taxa vs. 5 in Nesbitt et al., 3 in Ezcurra, and 5 in Cabreira et al.).  I'd say sauropodomorphs are almost over-represented, except that with this heterodox topology, it might have been a good thing to include even the basal gravisaurs they did just in case those ended up being the earliest diverging branches.  Sauropodomorpha has the standard topology in their trees btw, except Eoraptor is recovered as a theropod.

The next thing to check is if this result is robust, and at a whopping 20 extra steps needed to recover Saurischia, is it ever*!  For comparison, the original TWG matrix needs 22 more steps to recover Bullatosauria and 23 steps to get Russell and Dong's (1994) crazy topology.  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.  Baron et al. also deleted various sets of taxa but found "the recovery of Ornithoscelida as a monophyletic clade, as well as Sauropodomorpha+Herrerasauridae (Saurischia, new definition), occurred in all of these analyses, regardless of which taxa were included or excluded."  So that's impressive.  They also tested Dimorphodon as an alternate outgroup (the defaults are Euparkeria and Postosuchus which is wrongly called an ornithosuchid; an ornithosuchid would have been better ironically, since they're the first branching pseudosuchian group if parasuchians aren't), and found the same topology.

* To those who noted the 66% bootstrap for Ornithoscelida (Cerny on the DML, *cough cough*), realize that with very incomplete taxa like most fossils, bootstrap percentages mean very little.  It's easy for a fragmentary taxon like Nyasasaurus to fall inside Ornithoscelida, for example.  And every time it does, that lowers the bootstrap score.

The Lori analysis if limited to the taxonomic scope of Barron et al. (2017).  The topology changed from my last post after the inclusion of non-dinosauromorph outgroups, but is still unlike either the traditional topology or Baron et al.'s.  Instead, it features non-dinosaurian herrerasaurids and a Phytodinosauria with paraphyletic sauropodomorphs.

Of course, I just posted about recovering a heterodox dinosaur topology using the Lori matrix, which has more characters than even Baron et al.'s (481 are parsimony informative for basal dinosauromorphs) and 71 dinosauromorphs within Baron et al.'s scope (more coelophysoids, less plateosaurs).  Yet I don't trust that part of the Lori tree.  That's because the Lori matrix wasn't designed to sort basal dinosauromorphs, so lacks many of the proposed characters that support traditional clades.  Is Baron et al.'s similar?  To determine that, we need to check and see if the characters traditionally used to support Saurischia are included.  Of the 28 characters recovered as supporting the clade in Nesbitt et al.'s study, 27 are included by Baron et al., and one is even (correctly) divided into two characters since it was a composite.  The one excluded character ("Femur, surface between the lateral condyle and crista tibiofibularis on the distal surface: smooth (0); deep groove (1)") doesn't actually support Saurischia anyway.  Cabreira et al.'s analysis was published after Baron et al. had done their analysis, so the latter can't be faulted for not including all of their characters.  Ironically, they also found 28 characters, but 16 of these are different than Nesbitt et al.'s.  Five of these sixteen are not in Baron et al.'s matrix, which considering the 20 steps needed to get Saurischia there, aren't a help even assuming coding accuracy.  Finally, Ezcurra had 39 characters of which 23 aren't used in the prior two, and 9 of these aren't in Baron et al.'s.  Even adding these nine to the preceding five, it doesn't match the twenty.  So I'd say Baron et al. did a decent job testing saurischian monophyly character-wise, and that adding published suggested saurischian characters aren't going to overturn Ornithoscelida.  For comparison, only 5 of Nesbitt et al.'s characters are in the Lori matrix and only 5 of Cabreira et al.'s new ones and 5 of Ezcurra's new ones, though the Lori topology eliminates Saurischia by recovering Phytodinosauria instead.

So far it's looking very good for Ornithoscelida.  However- here are some caveats.  First, Baron et al.'s matrix has some correlated characters.  Examples are "Third cervical vertebra, centrum length: 0, subequal to the axis centrum; 1, longer than the axis centrum (Gauthier, 1986; Langer and Benton, 2006; Nesbitt, 2011)" compared to "Elongation of cervical centrum (cervicals 3–5): 0, less than 3.0 times the centrum height, 1, 3.0-4.0 times the centrum height, 2, >4.0 times the centrum height (Upchurch, 1998; Pol et al., 2011b). ORDERED"; "Digit I with metacarpal: 0, longer than the ungual; 1, subequal or shorter than the ungual (Sereno, 1999; Langer and Benton, 2006; Nesbitt, 2011)" compared to "Manual digit I, first phalanx: 0, is not the longest non-ungual phalanx of the manus; 1, is the longest non-ungual phalanx of the manus (Gauthier, 1986; Langer and Benton, 2006; Nesbitt, 2011)", and "Deltopectoral crest: 0, less than 30% the length of the humerus; 1, more than 30% the length of the humerus (Bakker and Galton, 1974; Benton, 1990; Juul, 1994; Novas, 1996; Benton, 1999)" compared to "Humerus, apex of deltopectoral crest situated at a point corresponding to: 0, less than 30% down the length of the humerus; 1, more than or equal to 30% down the length of the humerus but less than 50% down the length of the humerus; 2, more than 50% down the length of the humerus (modified from Bakker and Galton, 1974; Benton, 1990; Juul, 1994; Novas, 1996; Benton, 1999, Nesbitt, 2011)."  There are also no polymorphies in the matrix, which is impossible in reality with taxa like Coelophysis and Plateosaurus known from tons of variable individuals.  So it's not an excellent character list.

Second, despite the great taxon sample, Buriolestes would seem to be a most relevant taxon to include, being a supposed basalmost sauropodomorph that is very theropod-like.  Maybe it'd fall out as a theropod in Baron et al.'s trees, since Eoraptor does, but who knows until it's added.  Another issue is that no neotheropods are included, unlike Nesbitt et al.'s and Ezcurra's matrices.  If coelophysoid-grade taxa are paraphyletic, that's fine.  But if Dilophosaurus, Cryolophosaurus, Dracovenator and (?)Sinosaurus are coelophysoids, we're missing a whole side of the avepod tree.  And that could be important since heterodontosaurids seem particularly similar to coelophysoids among avepods.  So add Ceratosaurus, Elaphrosaurus, Piatnitzkysaurus and Monolophosaurus?

Also, how accurate is the coding?  There's no premade TNT file and the matrix is presented in a way that without copy-pasting it's basically impossible to check codings.  But the last character is an obvious one to code- "Singular and unbranched filamentous integumentary structures covering, or partially covering, the outer body: 0, absent; 1, present. NEW".  Depressingly, the following taxa are coded as lacking filamentous integument- Saltopus, Silesaurus, Lewisuchus, Pisanosaurus, Fruitadens, Abrictosaurus, Heterodontosaurus, Eocursor, Lesothosaurus, Scelidosaurus, Emausaurus, Agilisaurus, Hexinlusaurus, Jeholosaurus, Dracoraptor, Massospondylus carinatus, Guaibasaurus, Unaysaurus, Plateosaurus, Efraasia, Pantydraco, Herrerasaurus, Eodromaeus, Coelophysis, Eoraptor, Procompsognathus, Euparkeria, Dilophosaurus, Sinosaurus, Pampadromeus and Dimorphodon.  Obviously none of these taxa preserve integument (does Dimorphodon preserve pterofuzz?), excluding osteoderms in a few.  So this is a massive and worthless miscoding (only Tianyulong preserves filaments among the OTUs and none is known to lack them).  I can only hope this misrepresents the coding accuracy of the matrix.

So where does this leave us?   Honestly, I'm rather strongly in favor of Ornithoscelida.  For all my caveats, I could say the same for at least Nesbitt et al.'s matrix.  I haven't examined Ezcurra's or Cabreira et al.'s in depth.  Also, Baron et al. did include a lot of new ornithischian info, both taxon- and coding-wise.  Given the apparent robusticity of the result, the size of the matrix, and the coverage of proposed saurischian characters, any analysis that aims to disprove Ornithoscelida needs to use this study as its base.

Holotype and referred specimen of Nyasasaurus, Middle Triassic massopod? (after Nesbitt et al., 2013)

One other unexpected result of this analysis is the position of Nyasasaurus.  In its unofficial pre-cladistic days, considered a prestosuchid or thecodontosaurid (heh, what are those? ;) ), Nesbitt et al. (2013) recovered it as closer to Dinosauria than silesaurids, but outside examined ornithischians, sauropodomorphs and Tawa+avepods.  Well, Baron et al. recovered it as... a massopod sauropodomorph outside Anchisauria.  In the Middle Triassic.  Which would be weird.  Oddly enough, Nyasasaurus emerges sister to Plateosaurus in the Lori result.  Hmm...

FINALLY (long post), Baron et al. redefine several clades given their new topology.  This is where I have some serious issues.

First, Dinosauria becomes "The least inclusive clade that includes Passer domesticus, Triceratops horridus and Diplodocus carnegii."  I'm generally of the Kischlat school of phylogenetic definitions, where only taxa originally considered part of the clade (or not) are used.  But sauropodomorphs weren't included when Dinosauria was coined, so I'll make an exception here.  Since Sauropodomorpha is based on Sauropoda, and Sauropoda was based on Atlantosaurus, Apatosaurus, Morosaurus and Diplodocus, I'm fine with Diplodocus being used (better than the standard Saltasaurus).  But of course I'm a defender of D. longus remaining the type species (and submitted a Comment to the BZN over it), so would use it instead of D. carnegii, which was unknown to Marsh.  Similarly, I don't like making birds dinosaurs by fiat, so would rather use Allosaurus fragilis for the theropod specifier since it was what Marsh based Theropoda on in 1881.  For ornithischians, I follow Kischlat's arguments that Stegosaurus armatus is ideal since Triceratops was unknown to Seeley in 1887.  So I'd suggest-
The least inclusive clade that includes Allosaurus fragilis, Stegosaurus armatus and Diplodocus longus.

Ornithoscelida is defined as "The least inclusive clade that includes Passer domesticus and Triceratops horridus."  It's not a great name for the clade, because Huxley included sauropodomorphs in the group- Thecodontosaurus as a scelidosaurid and Cetiosaurus as an iguanodontid.  Huxley's point was to use it to relate all dinosaurs with Compsognathus, which was not considered dinosaurian at the time.  But since there are honestly no preexisting names for this concept, and this is a landmark paper, we might as well accept it.  Just as in the above example though, birds were never considered ornithoscelidans, and ceratopsians were still unknown back in 1870.  As Huxley's dinosaurian families were Megalosauridae, Scelidosauridae and Iguanodontidae, I'd suggest the following definition-
The least inclusive clade that includes Megalosaurus bucklandii and Iguanodon bernissartensis.

Saurischia is defined as "The most inclusive clade that contains Diplodocus carnegii but not Triceratops horridus", which is easily the worst definition of the bunch.  A clade of just herrerasaurids and 1990's+ standard sauropodomorphs is NOT Saurischia.   Seeley clearly constructed Saurischia to combine theropods and sauropods based on e.g. pelvic structure and axial pneumaticity.  All proposed definitions either self destruct in this topology or ironically include only theropods.  So I say if Ornithoscelida is a thing, then Saurischia just goes away.

Theropoda is defined as "The most inclusive clade that contains Passer domesticus but not Diplodocus carnegii or Triceratops horridus."  Again, birds shouldn't be theropods by definition, and neither Mesozoic taxon was known when Marsh named Theropoda.  Using the logic from the above examples, I'd suggest- The most inclusive clade that contains Allosaurus fragilis but not Diplodocus longus or Stegosaurus armatus.

Ornithischia is defined as "The most inclusive clade that contains Triceratops horridus but not Passer domesticus or Diplodocus carnegii."  So again, I would suggest- The most inclusive clade that contains Stegosaurus armatus but not Allosaurus fragilis or Diplodocus longus.

Sauropodomorpha is defined as "The most inclusive clade that contains Diplodocus carnegii but not Triceratops horridus, Passer domesticus or Herrerasaurus ischigualastensis."  This is the second most troubling definition because there's no reason to bring herrerasaurids in to it.  Indeed, Herrerasaurus was regarded AS a sauropodomorph by basically every author after its initial description and before the mid 80's cladistic revolution.  I even state on the Database "While these historical comparisons of Herrerasaurus to sauropodomorphs were generally vague, unpublished analysis suggests herrerasaurids can be moved to a position as basalmost sauropodomorphs without adding many extra steps" based on my experiments with a partially corrected Nesbitt et al. dataset.  Just regard herrerasaurids as basal sauropodomorphs in this topology and use the definition- The most inclusive clade that contains Diplodocus longus but not Stegosaurus armatus or Allosaurus fragilis.

The take away- I provisionally accept Ornithoscelida as better supported than Saurischia, but just get rid of the latter in this topology and let herrerasaurids be sauropodomorphs.

As a last question- what does this say about Chilesaurus?  It wasn't included, but is the prime example of an ornithischian-theropod cross after all....

References- Russell and Dong, 1994. The affinities of a new theropod from the Alxa Desert, Inner Mongolia, People’s Republic of China. Canadian Journal of Earth Sciences. 30(10), 2107-2127.

Ezcurra, 2006. A review of the systematic position of the dinosauriform archosaur Eucoelophysis baldwini Sullivan & Lucas, 1999 from the Upper Triassic of New Mexico, USA. Geodiversitas. 28(4), 649-684.

Langer and Benton, 2006. Early dinosaurs: A phylogenetic study. Journal of Systematic Palaeontology. 4(4), 309-358. 

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.

Martinez, Sereno, Alcober, Columbi, Renne, Montanez and Currie, 2011. A basal dinosaur from the dawn of the dinosaur era in Southwestern Pangaea. Science. 331, 206-210.

Nesbitt, Barrett, Werning, Sidor and Charig, 2013. The oldest dinosaur? A Middle Triassic dinosauriform from Tanzania. Biology Letters. 9(1), 20120949.

Cabreira, Kellner, Dias-da-Silva, da Silva, Bronzati, Marsola, Muller, Bittencourt, Batista, Raugust, Carrilho, Brodt and Langer, 2016. A unique Late Triassic dinosauromorph assemblage reveals dinosaur ancestral anatomy and diet. Current Biology. 26(22), 3090-3095.

Baron, Norman and Barrett, 2017. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature. 543, 5601-506.


Wednesday, March 1, 2017

Basal Dinosauromorpha in the Lori tree

Hi everyone!  Sorry for being away so long.  As an interesting experiment, after adding every decently preserved theropod to the Lori matrix, I added every decently preserved basal dinosauromorph as well.  As you all know, the Lori matrix is basically every TWG analysis through 2012 combined together with a complete taxon sample.  This yields 700 characters designed to sort out coelurosaurian phylogeny, excluding crown Aves, tyrannosaurids (fixed with Brusatte's later additions), enantiornithines and caenagnathoids.  Only a few non-coelurosaurian theropods have ever been included in TWG analyses- Sinraptor dongi and Allosaurus as outgroups from the beginning, with a few authors adding Coelophysis, Dilophosaurus and Monolophosaurus as well.  It actually performs pretty well at approximating avepod phylogeny, but once we get to the base of Dinosauromorpha, this happens-

Initial majority rule consensus of the non-avepod section of the Lori tree.  Running a traditional TBR search from this shows that Nyasasaurus, Lagosuchus, Teyuwasu and Dromomeron gregorii all have uncertain positions, as does Pisanosaurus within Neornithischia.  Also the pairing of Guaibasaurus and Saturnalia within their basal phytodinosaur clade lowers to 97%.  TNT crashed before I could screen capture the reduced consensus however.

Notice how Peters-ian it is.  Not that it has a similar topology to Peters' Large Reptile Tree, though there are a few similarities (Phytodinosauria, ornithischian Chilesaurus, Buriolestes and Marasuchus as theropods...).  Indeed, our ornithischian topologies are completely different.  No, what I mean is that while there are some consensus clades recovered (in my case Ornithischia, Scelidosaurus+Huayangosaurus, the Agilisaurus+ clade, herrerasaurids, avepods), it's largely a novel tree with newly paraphyletic groups (e.g. Silesauridae) and misplaced taxa (e.g. Diodorus and Dromomeron romeri in Ornithischia; Eucoelophysis and Dromomeron gregorii in a clade of basal sauropodomorphs).  Like Peters' trees, mine actually has a bigger taxon sample than prior basal dinosauromorph analyses.  Superior to Peters' analyses, I use far more characters than prior analyses (700 vs. 228 in Peters, online 2016; 315 in Nesbitt et al., 2009; 256 in Cabreira et al., 2016; 139 in Martinez et al., 2011; 221 in Butler et al., 2008; 255 in Boyd, 2015; ~370 characters in the newest version of Yates' basal sauropodomorph analysis), and these are formed well and the taxa coded accurately.

Yet despite the latter facts, I wouldn't even think of claiming e.g. Tawa and Daemonosaurus aren't dinosaurs, or that sauropodomorphs are diphyletic and partly paraphyletic to ornithischians.  This is because I haven't included the characters supporting the consensus topology in most cases, so I haven't really tested those ideas.  Conversely, it may be that some TWG characters actually do overwealm those used in basal dinosauromorph analyses to support novel relationships.  But we'll never know that until we combine the character sets.

I do find it interesting that Chilesaurus falls out basally by ornithischians, and not all that far away from the Tawa+Daemonosaurus clade I proposed it belonged to in my last post on the taxon.  Certainly it never clades with basal tetanurans, and still emerges as a basal alvarezsaur if it's an avepod.  Of course in the Lori tree, it emerges within a paraphyletic derived Thyreophora which is itself the basalmost group of ornithischians within a paraphyletic Sauropodomorpha.  So the combination of character states there probably doesn't reflect the combination of character states in a traditional basal Ornithischia, where they're sister to Saurischia or various silesaurids.  Ideally without adding the hundreds of characters involves with this part of the tree, I could constrain a traditional topology here, but that's assuming the traditional topology is correct.  Honestly there's no easy way to test such a controversial taxon as Chilesaurus.

Finally, I'd like to mention the excellent new paper by Marjanovic and Laurin (2016), which is basically a published version of what I do on the Evaluating Phylogenetic Analyses portion of the Database, targeting an analysis of basal tetrapods.  It's incredibly detailed and finds "thousands of suboptimal scores" (I'd like to know the percentage changed, but it's not listed AFAIK) and a very different topology from the original.

References- Butler, Upchurch and Norman, 2008. The phylogeny of the ornithischian dinosaurs. Journal of Systematic Palaeontology, 6(1), 1-40.

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.

Martinez, Sereno, Alcober, Columbi, Renne, Montanez and Currie, 2011. A basal dinosaur from the dawn of the dinosaur era in Southwestern Pangaea. Science. 331, 206-210.

Boyd, 2015. The systematic relationships and biogeographic history of ornithischian dinosaurs. PeerJ. 3:e1523.

Cabreira, Kellner, Dias-da-Silva, da Silva, Bronzati, Marsola, Muller, Bittencourt, Batista, Raugust, Carrilho, Brodt and Langer, 2016. A unique Late Triassic dinosauromorph assemblage reveals dinosaur ancestral anatomy and diet. Current Biology. 26(22), 3090-3095.

Marjanovic and Laurin, 2016. Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates. PeerJ Preprints. 4:e1596v2.