Speaking of the Ornithoscelida paper, coauthor and fellow theropod blogger Andrea Cau just got a big new paper published using his MegaMatrix character list. So congrats! It's a summary of theropod evolution focusing on the path from Teleocrater to Meleagris, detailing the changes in each node from Pan-Aves (well, technically that's a stem) to Aves, and using that data to examine the trends and rates of change along that line. We get two new clade names as well. Dracohors is (Megalosaurus bucklandii < - Marasuchus lilloensis), so covers silesaurs and dinosaurs. The use of a stem instead of a node like Silesaurus+Megalosaurus was wise considering some analyses (especially those recovering ornithischian silesaurids) recover Lewisuchus and such at an uncertain position relative to Silesauridae, but it's always closer to dinosaurs than Marasuchus. But come on, 'Dracohors'? Dragonian prostitutes? Did no one learn from Ascendonanus?! Oh, and the plural is 'dracohorsians', which sounds like a hybrid race from My Little Pony. Maniraptoromorpha is (Vultur gryphus < - Tyrannosaurus rex) and is a sorely needed name that I could have used in the Lori paper, since we ended up limiting the taxon sample to maniraptoromorphs. Recall that the results of TWG characters get worse as you get further from Norell et al.'s (2001) or Clarke's (2002) original scopes, and I didn't want to be Petersian and tackle e.g. the Megaraptora problem without the Carrano et al. (2012) or Novas et al. (2013) characters while using a batch of maniraptoromorph characters. The name Maniraptoromorpha also fits the -morpha > -formes > basic clade pattern, which I like.
|Sacrum of the maniraptoromorph Bambiraptor feinbergi (holotype AMNH 30556) in ventral view, anterior to left (courtesy of the AMNH).|
"14): Premaxilla, fifth alveolus: absent (0); present (1). ...
1717): Premaxilla, sixth alveolus: absent (0); present (1).
1718): Premaxilla, seventh alveolus: absent (0); present (1).
1759): Premaxilla, fourth alveolus: absent (0); present (1)."
Or instead of "Sacral vertebrae - number - two or less (0); three (1); four (2); five (3); six (4); seven (5); eight (6); nine (7); ten (8); eleven or more (9)", he has-
"343): Third sacral vertebra: absent (0); present (1). ...
1707): Fourth sacral vertebra: absent (0); present (1).
1708): Fifth sacral vertebra: absent (0); present (1).
1709): Sixth sacral vertebra: absent (0); present (1).
1710): Seventh sacral vertebra: absent (0); present (1).
1711): Eight sacral vertebra: absent (0); present (1).
1712): Ninth sacral vertebra: absent (0); present (1).
1713): Tenth sacral vertebra: absent (0); present (1).
1714): Eleventh sacral vertebra: absent (0); present (1)."
Now this is largely fine, as both ordered and unordered multistate characters can generally be scored this way using certain procedures to avoid weighting. Cau does it to make Bayesian analyses easier (pers. comm.). But the Lori character list would be 25% longer (875 non-zero states in my 700 characters) using this method, for instance. Of course the MegaMatrix was designed for a larger taxonomic scope, so will necessarily have more characters, those meant for carnosaurs, ceratosaurs, basal dinosauromorph phylogeny, etc.. Limiting the taxon sample to maniraptoromorphs finds 1170 parsimony-informative characters in Cau's dataset. There are also 14 parsimony-uninformative characters in the Lori dataset, since some TWG characters were designed for tyrannosauroids or positioning outgroups like Dilophosaurus, Monolophosaurus, etc.. This would leave 861 Cau-style characters in the Lori analysis, so 74% as many as the MegaMatrix. Not so bad...
It also doesn't use any polymorphic scoring, so there are no 0+1 scores in Cau's matrix. I'm not sure if this matters analytically, since I assume he scores a polymorphic taxon unknown, and I don't know how TNT treats polymorphies when it's making trees. Not that the standard method is without its problems, since TNT is stupider than PAUP in treating uncertainty polymorphies (could have either four or five teeth) the same as actual polymorphies (some have four teeth, others five). He also doesn't differentiate inapplicable (-) and unknown (?) scorings, which is fine functionally as I believe TNT treats them the same, but this and the lack of polymorphic scores do make the matrix itself more opaque to users since a lot of question marks there aren't technically unknown. For the Lori matrix, we're providing both a TNT and a NEXUS file, with the latter showing uncertainty polymorphies vs. actual polymorphies, plus when taxa can but shouldn't be scored due to ontogeny (e.g. a juvenile with unfused bones, when adults are unknown).
Fake Ornithuromorpha instead of sister to Pygostylia. Cau states on page 4 that taxon choice was based on a subjective (or at least not objectively justified) "balanced series of criteria" and I get that the point of the paper is trends leading to Aves, but having the quite complete Jianchangosaurus as the first branching of four alvarezsaurs, and eliminating a major step by placing therizinosaurs sister to oviraptorosaurs, seem like problems. I'm sure the main trends are only very minorly affected, but still. I think if I needed a reduced taxon sample (which was a real concern during part of the Lori process...) and was being subjective anyway, I would fiddle with the sample until I got a topology that matched the full analysis. Or maybe Jianianhualong, Chongmingia and/or the added eight characters changed the topology, and this whole paragraph is misled. Or maybe the reduced outgroup in the Halszkaraptor matrix affected the topology (only eight non-maniraptoromorphs compared to 58 here), which would be problematic for coelurosaur analyses since most have just been using 2-5 of the same outgroup taxa (Sinraptor dongi, Allosaurus, Monolophosaurus, Dilophosaurus, and/or Coelophysis...)..
|Parsimony-based strict consensus of Cau (2018)with clade names along the bird lineage and Decay Indices > 1 (after Cau, 2018).|
Interestingly, Cau also performed a Bayesian analysis. In these, herrerasaurs are sister to Dinosauria like Baron and Williams (2018), but Eodromaeus is a basal ornithoscelidan. Allosauroid relationships now match the Carrano et al. consensus, and Zuolong is a basal coelurosaur but Chilesaurus follows it. Gualicho is now closer to tyrannosaurids than to megaraptorans. Jianchangosaurus is back to being a therizinosaur, but Ornitholestes and Haplocheirus are basal ornithomimosaurs. Weird. Therizinosaurs are no longer sister to oviraptorosaurs, and actually move down an extra node to be stemward of alvarezsaurids too. Especially interesting is that scansoriopterygids move way down from being avialans to being basal oviraptorosaurs. Are they the missing Jurassic oviraptorosaurs? This lets Xiaotingia go back to Anchiornithidae. Rahonavis is now sister to Jeholornithidae instead of a couple nodes stemward of it, and Sapeornis is a confuciusornithiform. Protopteryx is always an enantiornithine (aw...), but Patagopteryx is still way crownward, though now Vorona joins it (basal fake ornithuromorph in the parsimony analysis). Well, that does match their Late Cretaceous age at least. Considering all of these changes, I like a few things better about the parsimony version and a few things better about the Bayesian version.
How does Cau's Maniraptoromorpha topology compare to Lori's? Quite different on both a broad level and with regard to the detailed relationships within the clades, although there are a few things that aren't common but popped up in both. I'm dying to say more, but that post has got to wait. Congrats again to Andrea.
References- Norell, Clark and Makovicky, 2001. Phylogenetic relationships among coelurosaurian theropods. In Gauthier and Gall (eds.). New Perspectives on the Origin and Early Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom. 49-67.
Clarke, 2002. The morphology and systematic position of Ichthyornis Marsh and the phylogenetic relationships of basal Ornithurae. PhD thesis, Yale University. 532 pp.
Livezey and Zusi, 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society. 149. 1-95.
Novas, Agnolin, Ezcurra, Porfiri and Canale, 2013. Evolution of the carnivorous dinosaurs during the Cretaceous: The evidence from Patagonia. Cretaceous Research. 45, 174-215.
Cau, 2018. The assembly of the avian body plan: A 160-million-year long process. Bollettino della Società Paleontologica Italiana. 57(1), 1-25.