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.