Wednesday, June 27, 2018

Etrigansauria, the unnecessary demon

For this week's post, we have a new paper on ceratosaurs by Delcourt (2018).  The paper discusses anatomy, behavior and such (and provides some good photos of Limusaurus), but here I only want to deal with the phylogenetic taxonomy proposed.  Delcourt uses the topology of Analyses 1 and 2 of Wang et al. (2016) from the Limusaurus ontogeny paper, which seems to have been well done from what I've seen.  Tons of taxa, tons of characters, and some sage commentary on OTUs and anatomy.  It's a shame the full tree is never presented in the paper, and I hope that analysis or a derivative is used for a stand alone phylogeny paper in the future.  Wang et al. interestingly find noasaurids to group with Elaphrosaurus, Limusaurus, Spinostropheus and Deltadromeus in a clade outside ceratosaurids plus abelisaurids, which is also what the Lori analysis found weirdly enough.

Ceratosaur portion of Analysis 1 and 2 of Wang et al. (2016).  Numbers are GC jacknife supports from Analysis A (above branches) and B (below branches).  After Wang et al., 2016.

So I have no issue with the phylogeny, but Delcourt's proposed phylogenetic taxonomy is... bad.  Let's start with his new taxon- Etrigansauria, named after DC Comics character Etrigan who is a demon bound to the human Jason Blood.  Now I love the DC Animated Universe as much as the next person, but what's the phylogenetic definition of Etrigansauria? "The most inclusive clade containing Carnotaurus sastrei and Ceratosaurus nasicornis but not Noasaurus leali."  But wait a second, we already have a Carnotaurus plus Ceratosaurus node-based clade- Neoceratosauria from Novas 1991, most recently refined by Hendrickx et al. (2015) as "The least inclusive clade containing Ceratosaurus nasicornis and Carnotaurus sastrei."  So if we have a standard topology with abelisauroid noasaurids, Etrigansauria self destructs, and if we have a Wang et al. style topology then Etrigansauria is just a junior synonym of Neoceratosauria.  [Edit: I noticed when commenting on the journal's website that the definitions are slightly different in that Etrigansauria is stem-based, so that there could be non-neoceratosaurian etrigansaurs under a Wang et al. style topology.  But the only such taxon in Wang et al.'s trees that were used is the skull-less Berberosaurus, which falls out other places in their other analyses- elaphrosaurid, stem-ceratosaur, etc..  Indeed, I doubt Delcourt had this distinction in mind because his figure 1 actually places Etrigansauria at the neoceratosaur node, not the stem containing Berberosaurus as his definition would have it.]  The word "neoceratosaur" only appears once in Delcourt's paper, as a brief mention- "In some analyses, Berberosaurus is considered as a basal ceratosaurian, a neoceratosaurian, ...".  This seems weird, and I urge everyone not to forget Novas's decades of work on these animals, and use Neoceratosauria instead of Etrigansauria published twenty-seven years later.

I don't know why everyone has such a hard time with Phylocode Article 11.7, which reads in part "when a clade name is converted from a preexisting typified name or is a new or converted name derived from the stem of a typified name, the definition of the clade name must use the type species of that preexisting typified name or of the genus name from which it is derived (or the type specimen of that species) as an internal specifier."  Let's keep that rule in mind as we look at the rest of the definitions...

Delcourt's other big blunder is with Abelisauroidea versus Ceratosauroidea.  Delcourt uses Wilson et al.'s (2003) definition of Abelisauroidea which is (Carnotaurus sastrei + Noasaurus leali).  That's a bad definition since it doesn't include Abelisaurus as a specifier, but we'll ignore that for the moment.  He also uses Wilson et al.'s definition for Abelisauridae- (Carnotaurus sastrei < - Noasaurus leali).  Which is also bad in not including Abelisaurus, but whatever.  Using these bad definitions in Wang et al.'s phylogeny gets us the bad result of making Ceratosaurus an abelisaurid abelisauroid.  Which Delcourt correctly notes it can't be, because Ceratosauridae/oidea has priority over Abelisauridae/oidea.  Delcourt's weird solution is to instead use Wilson et al.'s Abelisauroidea definition for Ceratosauroidea, so that Ceratosauroidea is now Carnotaurus plus Noasaurus. Ack!

Okay, first of all, that doesn't work because Ceratosaurus nasicornis needs to be an internal specifier of Ceratosauroidea (Phylocode Article 11.7!).  Second, we have much earlier and better definitions to use than Wilson et al.'s.  Holtz (1994) defined Abelisauroidea as taxa closer to abelisaurids than Ceratosaurus, which can be easily modified to (Abelisaurus comahuensis < - Ceratosaurus nasicornis).  See, that's a good definition that follows Article 11.7, maps correctly on to Novas' (1991) topology when he created the taxon, and never includes Ceratosaurus to avoid that whole kerfuffle.  In Wang et al.'s topology, noasaurids aren't abelisauroids, simple as that.  What is Ceratosauroidea?  It's only ever been defined before this as an alternative to Neoceratosauria when that clade was thought to be sister to coelophysoids, so those definitions make it a junior synonym of Neotheropoda sensu Bakker.  Given current taxonomy, it doesn't seem like a useful clade to redefine unless what we call Ceratosauridae now expands a LOT.

Ceratosauria in a version of the Lori analysis.  I'd ignore Kayentavenator and bissektensis as flukes based on their very fragmentary holotypes.  Not bad for analyzing ceratosaurs using maniraptoromorph characters...

The rest of Delcourt's definitions aren't any better.

Ceratosauria: Most inclusive clade containing Ceratosaurus but not Neornithes

That's the standard ever since Rowe (1989) so is fine.

Noasauridae: Most inclusive clade containing Noasaurus but not Carnotaurus

That's the original definition from Wilson et al. (2003), and is fine.

Elaphrosaurinae: Most inclusive clade containing Elaphrosaurus but not Noasaurus

This is attributed to Rauhut and Carrano (2016), but that's wrong.  Those authors used the better definition "all noasaurids that are more closely related to Elaphrosaurus than to Noasaurus, Abelisaurus, Ceratosaurus, or Allosaurus" to cover alternative topologies so that we don't get stupid results like abelisaurid Ceratosaurus.

Noasaurinae: Most inclusive clade containing Noasaurus but not Elaphrosaurus

Ditto here. Delcourt falsely attributes that definition to Rauhut and Carrano, but they actually used the much better "all noasaurids that are more closely related to Noasaurus than to Elaphrosaurus, Abelisaurus, Ceratosaurus, or Allosaurus."  As an obvious illustration of why Delcourt's definition is bad, in a standard topology where Noasaurus is an abelisauroid but Elaphrosaurus is not (e.g. Carrano and Sampson, 2008), Ceratosaurus and abelisaurids are all noasaurines.

Ceratosauridae: (new definition) the most inclusive clade containing Ceratosaurus but not Carnotaurus.

We actually already have an equivalent definition for this family- Rauhut (2004) wrote "the name is used here for a clade containing all ceratosaurs that are more closely related to Ceratosaurus than to abelisaurids." But even if one disputed that because Rauhut stated "it is premature to give such a formal definition at present", Hendrickx et al. (2015) defined it as "The most inclusive clade containing Ceratosaurus nasicornis but not Carnotaurus sastrei and Noasaurus leali." 

Abelisauridae: (new definition) the most inclusive clade containing Carnotaurus but not Ceratosaurus.

Article 11.7!  Abelisaurus comahuensis needs to be an internal specifier for Abelisauridae, again why is this so hard?  No argument for using Carnotaurus makes any sense.  Sure it's more complete, and may be more deeply nested, but if Abelisaurus somehow ends up not closer to Carnotaurus than Ceratosaurus, you're not going to be calling the Carnotaurus group Abelisauridae anyway.  The sad part is that we actually do need a new good definition for Abelisauridae.  Novas' (1997) definition is a node including the fragmentary Xenotarsosaurus which has an unstable position in recent analyses.  Rowe et al.'s (1997), Wilson et al.'s (2003) and Sereno's (perpetually in press) definitions all use Carnotaurus.  Sereno's (1998) is a node using Abelisaurus and Carnotaurus that would work (except for Rugops) in Wang et al.'s topology, but exclude all taxa except the two specifiers and Aucasaurus in Filippi et al.'s (2016) topology, for instance.  Plus none of the stem-based definitions exclude Ceratosaurus.  Delcourt's definition is bad because if noasaurids are abelisauroids as in most topologies, noasaurids are abelisaurids.  Here's what a good definition of Abelisauridae looks like- All taxa more closely related to Abelisaurus comahuensis than to Ceratosaurus nasicornis, Noasaurus leali, Elaphrosaurus bambergi or Allosaurus fragilis.  Someone publish that.

Ceratosauria phylogeny from Filippi et al. (2016), after Filippi et al. (2016).

Carnotaurinae: Most inclusive clade containing Carnotaurus but not Abelisaurus

That's fine and classic, taken from Sereno (1998) who named the clade.  Honestly, I think this and Abelisaurinae have proven to be pretty useless due to the varying position of Abelisaurus and should probably be ignored by future authors.  In Filippi et al.'s trees, Carnotaurus is the only carnotaurine, but in Wang et al.'s trees all abelisaurids except Abelisaurus and Rugops are.  Instead of abelisaurines vs. carnotaurines, the more useful split seems to be between majungasaurs and brachyrostrans (in the Lori trees too, incidentally).  It would be great to have a name for the Majungasaurus plus Carnotaurus node too, so we could easily refer to "basal" abelisaurids like Rugops, Abelisaurus and Ilokelesia in Wang et al.'s trees, Kryptops and Rugops in Filippi et al.'s trees, or Rugops, Genusaurus and Eoabelisaurus in the Lori tree.

Majungasaurini: Most inclusive clade containing Majungasaurus but not Carnotaurus

Here, Delcourt correctly notes that in Wang et al.'s topology, Majungasaurinae as originally defined falls out inside Carnotaurinae.  So it's yet another case where the Phylocode clashes with the ICZN.  Which is a fair observation, but I think the better solution would be to propose Majungasauria for that clade, which could go in either position and work fine. 

Brachyrostra: Most inclusive clade containing Carnotaurus but not Majungasaurus

The original definition, so that's fine.

Furileusauria: Most inclusive clade containing Carnotaurus but not Skorpiovenator.

This is credited to Filippi et al. (2016), but those authors actually had Ilokelesia and Majungasaurus as external specifiers too.  Since those two are also outside Furileusauria in Wang et al.'s trees, I don't see why the change was made.  I'm also not sure how useful the clade Furileusauria is yet.  It obviously works in Filippi et al.'s phylogeny, but has uncertain content in Wang et al.'s since Carnotaurus and Skorpiovenator are part of a polytomy.  I should note here that it's not at all certain whether Wang et al.'s or Filippi et al.'s trees are better supported.  Filippi et al. includes 6-8 more ceratosaur taxa and 416 characters with just a few outgroups, while Wang et al. have 744 characters but also densely sample and test coelophysoids and have quite a lot of tetanurines, so many of those characters are probably not parsimony-informative for ceratosaurs.

So that's Delcourt's (2018) phylogenetic taxonomy.  I honestly don't see how Neoceratosauria was never brought up in peer review.  It's also ironic that Delcourt goes through hoops to try to adjust Wilson et al.'s bad definitions because they only work in Wilson et al.'s topology, only to propose new definitions that only work in Wang et al.'s topologies.  I don't know about the other portions of the paper, but the phylogenetic taxonomy section is an utter failure of peer review in my opinion.  If people start using Etrigansauria and this butchered Ceratosauroidea... *cringe*

Look, if you were tasked with making good definitions for Ceratosauria, it's easy-
Ceratosauria- (Ceratosaurus nasicornis < - Passer domesticus)
Noasauridae- (Noasaurus leali < - Abelisaurus comahuensis)
Elaphrosaurinae- (Elaphrosaurus bambergi < - Noasaurus leali, Abelisaurus comahuensis, Ceratosaurus nasicornis, Allosaurus fragilis)
Noasaurinae- (Noasaurus leali < - Elaphrosaurus bambergi, Abelisaurus comahuensis, Ceratosaurus nasicornis, Allosaurus fragilis)
Neoceratosauria- (Ceratosaurus nasicornis + Abelisaurus comahuensis)
Ceratosauridae- (Ceratosaurus nasicornis < - Abelisaurus comehuensis)
Abelisauroidea- (Abelisaurus comehuensis < - Ceratosaurus nasicornis)
Abelisauridae - (Abelisaurus comahuensis < - Ceratosaurus nasicornis, Noasaurus leali, Elaphrosaurus bambergi, Allosaurus fragilis)
NEW CLADE- (Majungasaurus crenatissimus + Carnotaurus sastrei)
Majungasauria- (Majungasaurus crenatissimus < - Carnotaurus sastrei)
Brachyrostra- (Carnotaurus sastrei < - Majungasaurus crenatissimus)

Follows Article 11.7, works in everyone's topologies, ta da. 

References- Rowe, 1989. A new species of the theropod dinosaur Syntarsus from the Early Jurassic Kayenta Formation of Arizona. Journal of Vertebrate Paleontology. 9(2), 125-136.

Novas, 1991. Phylogenetic relationships of ceratosaurian theropod dinosaurs. Ameghiniana. 28, 401.

Holtz, 1994. The phylogenetic position of the Tyrannosauridae: Implications for theropod systematics. Journal of Paleontology. 68(5), 1100-1117.

Novas, 1997. Abelisauridae. In Currie and Padian (eds.). Encyclopedia of Dinosaurs. Elsevier Inc. 1-2.

Rowe, Tykoski and Hutchinson, 1997. Ceratosauria. In Currie and Padian (eds.). Encyclopedia of Dinosaurs. Elsevier Inc. 106-110.

Sereno, 1998. A rationale for phylogenetic definitions, with application to the higher-level taxonomy of Dinosauria. Neues Jahrbuch für Geologie und Paläontologie Abhandlungen. 210(1), 41-83.

Wilson, Sereno, Srivastava, Bhatt, Khosla and Sahni, 2003. A new abelisaurid (Dinosauria, Theropoda) from the Lameta Formation (Cretaceous, Maastrichtian) of India. Contributions from the Museum of Paleontology. 31(1), 1-42.

Rauhut, 2004. Provenance and anatomy of Genyodectes serus, a large-toothed ceratosaur (Dinosauria: Theropoda) from Patagonia. Journal of Vertebrate Paleontology. 24(4), 894-902. 

Carrano and Sampson, 2008. The phylogeny of Ceratosauria (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 6, 183-236. 

Hendrickx, Hartman and Mateus, 2015. An overview of non-avian theropod discoveries and classification. PalArch's Journal of Vertebrate Palaeontology. 12(1), 1-73.

Filippi, Mendez, Juarez Valieri and Garrido, 2016. A new brachyrostran with hypertrophied axial structures reveals an unexpected radiation of latest Cretaceous abelisaurids. Cretaceous Research. 61, 209-219. 

Rauhut and Carrano, 2016. The theropod dinosaur Elaphrosaurus bambergi Janensch, 1920, from the Late Jurassic of Tendaguru, Tanzania. Zoological Journal of the Linnean Society. 178(3), 546-610.

Wang, Stiegler, Amiot, Wang, Du, Clark and Xu, 2016. Extreme ontogenetic changes in a ceratosaurian theropod. Current Biology. 27(1), 144-148.

Delcourt, 2018. Ceratosaur palaeobiology: New insights on evolution and ecology of the southern rulers. Scientific Reports. 8:9730.

Monday, June 18, 2018

Confuciusornithiform taxonomy in Wang et al 2018

Well I missed a week, but this post is on Wang et al.'s (2018) new paper on confuciusornithiforms.  Note that's not confuciusornithids, as that family was poorly defined by Chiappe et al. (1999) as Confuciusornis plus Changchengornis.  Martyniuk (2012) thus defined Confuciusornithiformes as the stem-based clade of taxa closer to Confuciusornis than Enantiornis and Passer.  The Lori analysis did recover some non-confuciusornithid confuciusornithiforms, so the distinction seems valuable.  In any case, I spent a lot of time working out the taxonomy of these taxa back in 2002, the results of which have made their way into the Database.  So how do Wang et al.'s interpretations compare?

First, Tim Williams already noted this on the DML, but Wang et al.'s phylogenetic definition of Confuciusornithidae as "The most-inclusive clade that contains Eoconfuciusornis zhengi Zhang et al., 2008, but not Sapeornis chaoyangensis Zhou & Zhang, 2002, or Passer domesticus Linnaeus, 1758" is wrong in not including Confuciusornis sanctus.  I don't know why it's so hard to use eponymous taxa...

Confuciusornis suniae
This was erected by Hou (1997), but we both agree it's just a Confuciusornis sanctus.  There are a few characters Hou mentions as distinctive (ten free caudals, slightly developed olecranal fossa, radial groove and patella) but are not in his diagnosis, so go unmentioned by Wang et al..  But based on Hou's inaccuracy in other areas, I maintain these are probably misinterpretations.

Confuciusornis chuonzhous
Also named by Hou (1997), this is just based on a hindlimb.  Wang et al. provide good photos and interestingly find the specimen is a left leg instead of a right one.  While Chiappe et al. thought the lack of proximal tarsal fusion was equivocal, Wang et al. view it as genuine and ontogenetic.  I said "Finally, Hou lists "metatarsal V is present and is isolated, except for its articulated proximal end", but it is present in C. sanctus as well. The discussion indicates it is metatarsal V's robusticity and lack of fusion with the tarsometatarsus that Hou belives is unique. Examination of photos leads me to believe that what's identified as metatarsal V is actually a broken proximal end of metatarsal II. This would explain why the metatarsus is so narrow, and why metatarsals I and V are on the same side."  Wang et al. confirm this with "Furthermore, the element identified as metatarsal V by Hou (1997) is in fact the incomplete metatarsal II, as indicated by its medial position and robust size."  We both agree it's indeterminate within confuciusornithids.

Holotype of Confuciusornis chuonzhous (IVPP V10919) as illustrated in Hou (1997) (left) and Wang et al. (2018) (right).

Confuciusornis dui
Regarding only known specimens (holotype and paratype), Wang et al. report "unfortunately, neither of these specimens can be located at this time."  This is yet another example of IVPP specimens being lost and is rather concerning.  I wrote "(proposed) narrow, tapered and vertical ascending process of maxilla" as a diagnostic character, and Wang et al. agree and write "we identify two new cranial features diagnostic of C. dui: the dorsal process of the maxilla rapidly tapers dorsally, forming a triangular shape in lateral view."  Of course, Elzanowski et al.'s (2018) recent paper shows that we were all wrong about the maxilla in Confuciusornis and that it actually has a low internal ascending process and no external ascending process.  Their other supposedly new cranial feature is "the ventral margin of the surangular is straight in C. dui lacking the ventral process seen in C. sanctus and E. zhengi", but this was actually listed in its original description ("without the distinctive anteroventral expansion of the dentary found in C. sanctus") and is a plesiomorphy anyway.

The authors interestingly report some Confuciusornis specimens have a posteriorly grooved furcula like Changchengornis.  They also interpret the supposed maxillary fenestra more correctly than Chiappe et al. (1999) as being within the lacrimal, although missing Elzanowski et al.'s idea that the lacrimal and ethmoid complex are fused.  Finally, they include "tarsometatarsus without plantar excavation" in the diagnosis despite that being plesiomorphic compared to Confuciusornis (sanctus, at least).

This is a very useful section of the paper, since both species of the genus were described in Chinese and only Chiappe et al. (2008) have examined their validity in print, albeit briefly.  Regarding J. yixianensis, I wrote "Characters like "braincase small" and "second manual digit not particularly expanded" appear to differ at first glance, but I have a feeling examination of the specimen would show otherwise" and indeed Wang et al. provide excellent photos showing the skull is exposed in lateroventral view and that manual phalanx II-1 is not exposed (covered by manual ungual I and sediment if present).  Supposedly different in having more than 12 dorsal vertebrae, I said "Confuciusornis may have had over twelve dorsal vertebrae" but it seems the answer's actually the opposite and that the posterior dorsals of J. yixianensis are missing so that it can't be shown to have twelve dorsals in the first place.  For J. zhangjiyingia, Chiappe et al. (2008) stated the supposed quadratojugal-orbit contact cannot be confirmed, and Wang et al. show that this portion of the 'quadratojugal' is actually part of the postorbital.  Indeed, one of the weird findings of Elzanowski et al. is that the quadratojugal of confuciusornithids has yet to be identified, and that laterally exposed bone in that area of the skull could easily be non-homologous elements as in some recent birds.  In any case, the authors agree with Chiappe et al. and I that Jinzhouornis is a junior synonym of Confuciusornis sanctus.

I proposed Eoconfuciusornis zhengi was closer to Confuciusornis than Changchengornis and potentially closer to Confuciusornis sanctus than C. dui based on characters like the surangular process invading the external mandibular fenestra.  I said "The only character which would place zhengi outside Confuciusornis (sanctus + dui) is the absent humeral foramen, but this may be ontogenetic and seems to be developing as a fossa in the specimen", and the authors note referred specimen BMNHC-PH870 (Navalon et al., 2018) has a humeral foramen.  BMNHC-PH870 wasn't published when I examined confuciusornithid taxonomy, but would seem to have relevance.  Notably Wang et al. didn't defend placing Eoconfuciusornis outside Confuciusornithidae or diagnose the genus Confuciusornis, although it did fall out at the base on Confuciusornithiformes in their tree.

Confuciusornis feducciai
In a rare exception to the norm, I think the authors are correct to synonymize a taxon that I kept separate.  Turns out its original describers were wrong in claiming the humeral foramen was absent and that manual phalanx I-1 is subequal in width to III-3.  Pending detailed examination of the situation, I agree with Wang et al. that C. feducciai is just a large C. sanctus with longer wings than average.

Holotype of Confuciusornis jianchangensis (PMOL-AM00114) pelvis in right lateral view as illustrated by Li et al. (2010) (top), photographed by Wang et al. (2016) (middle) and interpreted here (bottom).

Confuciusornis jianchangensis
Continuing the exceptions, I might have been wrong not to synonymize this species with C. sanctus.  I've so far agreed with Cau's (2010) blogpost that found this species to share some characters with Ornithothoraces.  However, Wang et al. provide better photos that show the ornithuromorph-style ischium illustrated by Li et al. (2010) isn't there.  Instead, there is a large proximodorsal process like Confuciusornis and enantiornithines, and the distal ischium is missing so we can't tell if a mid-dorsal process was present or what the ischiopubic ratio was.  While Li et al. provided a short fibular measurement suggesting complete and reduced fibulae, the right fibula definitely goes underneath the tibia and the left one might.  Wang et al. correctly note metatarsal V is easily lost or hidden, so that it's not necessarily truly absent.  The final supposedly different character is the reduced dorsal count, but I can't verify Li et al.'s cervicodorsal transition in the photos.  Interestingly, what might be the tip of a scapula projects dorsally from below the pectoral vertebrae, so maybe the forelimb lies under the sediment and could resolve the issue definitively.

References- Hou, 1997. Mesozoic birds of China. Taiwan Provincial Feng Huang Ku Bird Park. Taiwan: Nan Tou, 228 pp.

Chiappe, Ji, Ji and Norell, 1999. Anatomy and systematics of the Confuciusornithidae (Theropoda: Aves) from the Late Mesozoic of Northeastern China. Bulletin of American Museum of Natural History. 242, 1-89.

Chiappe, Marugan-Lobon, Ji and Zhou, 2008. Life history of a basal bird: morphometrics of the Early Cretaceous Confuciusornis. Biology Letters. 4(6), 719-723.

Li, Wang and Hou, 2010. A new species of Confuciusornis from Lower Cretaceous of Jianchang, Liaoning, China. Global Geology. 29(2), 183-187.

Martyniuk, 2012. A Field Guide to Mesozoic Birds and Other Winged Dinosaurs. Vernon, New Jersey. Pan Aves. 189 pp.

Elzanowski, Peters and Mayr, 2018. Cranial morphology of the Early Cretaceous bird Confuciusornis. Journal of Vertebrate Paleontology. 38(2), e1439832.

Navalón, Meng, Marugán-Lobón, Zhang, Wang, Xing, Liu and Chiappe, 2018. Diversity and evolution of the Confuciusornithidae: Evidence from a new 131-million-year-old specimen from the Huajiying Formation in NE China. Journal of Asian Earth Sciences. 152, 12-22.

Wang, O'Connor and Zhou, 2018. A taxonomical revision of the Confuciusornithiformes (Aves: Pygostylia). Vertebrata PalAsiatica. DOI: 10.19615/j.cnki.1000-3118.180530

Friday, June 1, 2018

Basal theropods in the Lori analysis

In lieu of my original post plan, I just got results from Scott on the most recent analysis of the Lori matrix.  This includes the Archaeopteryx, Ichthyornis and confuciusornithid skull updates unlike the version in the manuscript, plus some added taxa.  The good news is that basic maniraptoromorph topology and Lori's position stayed the same, but you won't be getting any of that today.  Previously, I looked at the non-theropod Lori matrix topology to demonstrate how using maniraptoromorph characters for basal dinosauromorphs will fail even given several hundred accurately scored characters with complete taxonomic coverage.  Well, here's the non-tyrannoraptoran results of the full taxonomic coverage analysis.  It's a majority rule tree, and you can see that fragmentary taxa can fall out in the wrong place due to both a lack of certain characters and the vagaries of tree generation.  So no, I don't think Archaeornithomimus bissektensis' holotype femur is abelisaurian, and the analysis presumably found it to fall out in numerous positions within Avepoda in the most parsimonious trees.  But this gives you a good overall view of what the Lori characters have to say, and it's pretty interesting in some areas.  I would never publish this tree without including characters relevant to carnosaurian, megalosauroid, ceratosaurian, etc. phylogeny, so I don't mind sharing it here.

It's largely good.  The weirdest part is tetanurine coelophysoids.  Also odd is that Sciurumimus and Chuandongocoelurus don't fall out close to their published positions.  Gualicho is a ceratosaur here, so take take from that what you will.  Valdoraptor emerged as a ceratosaur, but the Angeac taxon came out as an ornithomimosaur and Thecocoelurus as a therizinosaur.  None of these taxa are in the Lori manuscript matrix since they had such unstable positions and so little of the Angeac taxon has been published (based on the mounted specimen, it looks very ceratosaurian).  The coelophysoid grade section actually looks pretty good.  Gasosaurus as a piatnitzkysaurid?  Reminds me of PDW.  Xuanhanosaurus and the contemporaneous Kaijiangosaurus sisters?  Synonyms?  I'm rather surprised at the retention of Megalosauroidea, which I usually think is a tenuous grouping.  I don't trust the structure in it, though there is a Spinosauridae (with probably wrongly placed Magnosaurus).  We get a paraphyletic sinraptorid base instead of a big Carnosauria.  Yangchuanosaur Bicentenaria might be worth looking into.  Australovenator and Fukuiraptor are allosaurids/carnosaurs unlike other megaraptorans.  Congrats, Molnar. ;)  Kelmayisaurus as a carcharodontosaur is surprisingly in line with Brusatte et al.'s results given how fragmentary the material is, and Labocania as one is certainly interesting.  Megaraptorans sister to Tyrannoraptora has been my pet hypothesis for a while and shows up again.  Hmm.

It all goes to show you that you can't just take one character list and expect it to give you the right results.  Topology is highly dependent on both character and taxon inclusion, and even if a matrix has more taxa and/or characters than another, you should never trust it to be better unless it includes all the competing data. 

Tuesday, May 22, 2018

The Missing Maniraptoromorphs

For this week's post, it's time for an installment of "What can I write about the Lori analysis without giving away any results?"  I figure I can reveal the taxa that didn't make it into the analysis.  As I've said before, my goal was to include every named Mesozoic maniraptoromorph known from more than teeth or a single kind of element.  I ended up including thirty unnamed specimens and plenty of taxa known from single elements, but it turns out TWG characters are better at placing taxa known from e.g. femora than frontals.  So which taxa didn't make it into the Lori analysis?

Taxa known only from teeth- Zapsalis, Richardoestesia? isosceles and R? asiatica, Dromaeosauroides, Paronychodon spp., Koparion, "Saurornithoides" asiamericanus.

Taxa known from a single kind of element- "Archaeornithomimus" bissektensis (attempted), "Coelosaurus", Ilerdopteryx, Thecocoelurus (attempted), Ojoraptorsaurus, Kuszholia (though Caenagnathasia was; I didn't use any Bissekty composite taxa), Boreonykus (I agree with Cau only the frontal should be referred to this taxon; attempted), Cretaaviculus, "Dromaeosaurus" gracilis, Saurornitholestes? sullivani (attempted), Yaverlandia (attempted), "Saurornitholestes" robustus (attempted), Lenesornis, Platanavis, Abavornis, Catenoleimus, "Enantiornis" walkeri, "Ichthyornis" minusculus, Incolornis spp., Explorornis, Kizylkumavis, Sazavis, Martinavis? saltariensis (attempted), M? whetstonei (attempted), Nanantius, "Zhyraornis kashkarovi", Guildavis, Zhyraornis spp., Judinornis, Parascaniornis, Brodavis americanus (attempted), Apatornis, Laornis, Palaeotringa spp., Volgavis, Novacaesareala, Torotix, Austinornis, Anatalavis rex, Cimolopteryx spp., Lamarqueavis spp., Graculavis spp., Telmatornis, "Lonchodytes" pterygius, Neogaeornis, Lonchodytes, Tytthostonyx.  Note there was a single Hesperornis spp. OTU.  You can see I'm pretty certain there aren't enough TWG sacral or coracoid characters to usefully place taxa, and that including fragmentary Aves wasn't considered useful when the sampling of the clade is so low.

Taxa published too late to be included- Anomalipes, Eogranivora and Microenantiornis, to date.  But hey, we got Halszkaraptor, Ostromia, Caihong and Almas in there.  I don't think these three taxa are that important to Lori's position, though Eogranivora may be important for taxa around the base of Carinatae.

Holotype of Dalianraptor cuhe (D2139), a composite specimen. Top- confuiusornithid manus; Middle- jeholornithid distal tail; Bottom- probable enantiornithine pes. (after Gao and Liu, 2005)

The chimaerical Beipiaognathus and Dalianraptor.  For the former, I have no way of knowing which elements are from one individual given the three humeri and multiple pieces placed incorrectly, while the latter seems to be a jeholornithid skull, confuciusornithid wing and possibly enantiornithine feet.

There was a lot of crunch time at the end, so despite including ~70 enantiornithines I decided that several enants with poor descriptions and schematic illustrations could be skipped for now- Alethoalaornis (whose holotype is missing), Cathayornis? aberransis (ditto), Cuspirostrisornis, Dapingfangornis, Largirostrornis and Longchengornis.  Also the partial leg that is Confuciusornis chuonzhous.  Hou (1997) is a particularly flawed paper describing four of these taxa, with illustrations that do not match the material when the latter has been redescribed as is the case for Songlingornis and Houornis (= Cathayornis caudatus).  I did include Jibeinia though, since it's potentially important to ornithothoracine origins (or maybe just a misinterpreted Hebeiornis).  In any case, I've since scored Alethoalaornis, Longchengornis and Dapingfangornis, and plan to do so for all of these taxa for future analyses.

Juvenile enantiornithines- Liaoxiornis, Dalingheornis and Gobipipus.  I did include the Catalan nestling LP-4450-IEI and Cratoavis.  I've since scored Dalingheornis and Gobipipus and will have Liaoxiornis and GMV 2158 and 2159 scored for future analyses.  LP-IEI-4450 and Cratoavis don't group together, so my precautions when scoring ontogenetically variable characters may have been effective.

Holotype of Gallornis straeleni, right proximal femur (Royal Belgian Institute of Natural Sciences coll.) in (a) anterior, (b) posterior and (c) proximal views (after Lambrecht, 1931).

The others- There were several named taxa known from multiple elements that had very unstable positions when tested.  Aepyornithomimus, Tototlimimus, Valdoraptor (ceratosaurian?), Unquillosaurus (carnosaurian?), "Ornithomimus" minutus, Soroavisaurus, Canadaga, Maaqwi and Gallornis.  The former two are known mostly from hindlimb fragments that allow a lot of leeway under TWG characters.  "Ornithomimis" minutus has never been illustrated and is now lost, so we only have Marsh's description.  TWG matrices were not designed to include enantiornithine or hesperornithine characters, so Soroavisaurus (tarsometatarsi plus some pedal phalanges) and Canadaga (cervicodorsal vertebrae and rib fragments) aren't well constrained.  Maaqwi is only known from a coracoid and forelimb shafts. Gallornis is known from a possibly referrable fragmentary proximal humerus that was undescribed and has a photo which basically no characters can be scored from ("probably beyond evaluation" in Hope's [2002] words), and a proximal femur photographed in three views.

Corythoraptor- I somehow completely missed this taxon until last week, the billionth oviraptorid from the Nanxiong Formation.  Looks similar to the Khermeen Tsav taxon with the tall cranial crest (PMO X678 cast; UALVP 49394 cast; UALVL 49393 cast). Its absence shouldn't affect much, since I don't include any of the oviraptorosaur characters from Maryanska et al. (2002) derivatives.

And that's it.  In the end, we analyzed 356 Mesozoic maniraptoromorphs, plus four Cenozoic birds.  We were able to make a fairly resolved tree by excluding 53 taxa a posteriori.  Now back to Ornithoscelida...

References- Lambrecht, 1931. Gallornis straeleni n. g. n. sp., ein Kreidevogel aus Frankreich. Bulletin de Musee Royal d'Histoire Naturelle de Belgique. 7, 1-6.

Hou, 1997. Mesozoic Birds of China. Phoenix Valley Bird Park, Lugu Hsiang, Taiwan. 221 pp.

Hope, 2002. The Mesozoic radiation of Neornithes. In Chiappe and Witmer (eds). Mesozoic birds: Above the heads of dinosaurs. Berkeley: University of California Press. 339-388.

Maryanska, Osmolska and Wolsan, 2002. Avialan status for Oviraptorosauria. Acta Palaeontologica Polonica. 47 (1), 97-116. 

Gao and Liu, 2005. A new avian taxon from Lower Cretaceous Jiufotang Formation of western Liaoning. Global Geology. 24(4), 313-316.

Wednesday, May 16, 2018

Testing alternative stem bird topologies in Cau, 2018

In the comments to my last post describing Cau's (2018) new paper detailing the acquisition of characters on the line to Aves, reader AOF requested a post similar to what I did six years ago with the Carrano et al. (2012) tetanurine analysis.  Namely, testing alternative topologies using constraint analyses to see how many more steps they would require.  I think these kinds of things can be illuminating.  I've often said that we shouldn't think of a new cladogram as just 'the best new hypothesis', but rather check individual components of the tree to see how likely or unlikely they are to be correct.  Cau's 2018 matrix has a reduced taxon sample, which could easily change the number of steps compared to a complete sample.  On the other hand, I think Andrea tries to include all proposed characters in his MegaMatrix, which could make this a more honest measure of comparative topology length than most studies.  I'm not sure which variable overrides the other.  Then we have score correctness, which I've never checked in a Cau matrix, so I'm taking that at face value.

Andrea sent me his NEXUS file, but whereas the paper reports 3072 MPTs of 6790 steps, I found 10872 MPTs of that length.   Eoraptor and Buriolestes aren't always sauropodomorphs, Pisanosaurus is sometimes an ornithischian, Asilisaurus, Silesaurus and Sacisaurus are an unresolved trichotomy, Enantiornithes can be paraphyletic with Zhongjianornis among them, and Fake Ornithuromorpha is less resolved, as Patagopteryx and Apsaravis can be outside Hongshanornis+Aves, Archaeornithura can be a songlingornithid, etc..  I think Andrea's philosophy would be that these things vary with taxon inclusion, so aren't a definite part of his data.  The absence of any included spinosaurids, carcharodontosaurines, parvicursorines or Avimimus unfortunately makes some weird 80s and 90s hypotheses untestable.  After six more years of experience, I've added a new category "less likely" because I think that factors like scoring accuracy and taxon inclusion can have a larger influence.  As I said in the 2012 post, the corrected TWG matrix needed 15 more steps to get a monophyletic Deinonychosauria which is the most common outcome for TWG matrices today.  I'll say the Lori matrix recovers at least one hypothesis found to be "unlikely" here, so even that's not the kiss of death.

Basically ambiguous

0 steps- Maniraptoromorph Compsognathus.

0 steps- Megaraptoran Gualicho.

1 step- Ceratosaurus closer to abelisauroids than Elaphrosaurus.

1 step- Megalosauroid piatnitzkysaurids.

1 step- Coelurosaurian Zuolong.  Ends up as a basal maniraptoromorph between Coelurus and Ornitholestes.

1 step- Coelurid Aorun, as in its original description.  It moves to Maniraptoromorpha with Coelurus.

1 step- Coelurid Tanycolagreus, as in its original description.  Coelurus moves into Tyrannosauroidea with Tanycolagreus.

1 step- Compsognathid Sinosauropteryx and/or Sinocalliopteryx.

1 step- Tyrannosauroid Sinocalliopteryx or Coelurus.

1 step- Anchiornithid or archaeopterygid Xiaotingia.

1 step- Scansoriopterygids closer to Aves than Archaeopteryx.

1 step- Sapeornis closer to Aves than Confuciusornis.

1 step- Zhongjianornis sister to Pygostylia, as in its original description.

1 step- Ichthyornis closer to Aves than Hesperornis, the consensus until the recent cranial redescription of Ichthyornis.

2 steps- Theropodan Eodromaeus.

2 steps- Chilesaurus just outside Avepoda, which was my best guess back in 2015 considering the results of its original misscored matrices and my subjective feelings of what would plausibly reverse.

2 steps- Ceratosaurian Gualicho.  It has an uncertain placement within the clade, though is excluded from Abelisauria.

2 steps- Megaraptora as coelurosaurs just outside of Tyrannoraptora.  This was my result back in 2010 after adding Benson's Neovenatoridae data to my theropod supermatrix (since superseded by the Lori analysis).  Bicentenaria is at this level too, while Guanlong and Tanycolagreus become maniraptoromorphs.

2 steps- Maniraptoran Ornitholestes.

2 steps- Hongshanornithid Parahongshanornis, as in its original description.

Cast YPM 56693 of the Mononykus olecranus holotype pes in plantar view, courtesy of Senter.

Quite likely to be true

3 steps- Saurischia.  Herrerasaurs and Eodromaeus are theropods.  Note that while some of these constraints were tested in the Ornithoscelida paper, the studies differ in both taxonomic content and characters used, so that MegaMatrix results don't necessarily correlate with Ornithoscelida paper results and should not be seen as scooping anything we find. 

3 steps- Ornithischian Daemonosaurus. Chilesaurus is sister to Averostra.

3 steps- Theropodan Herrerasaurus/Tawa/Daemonosaurus.  These each take three steps more, and other herrerasaurs follow when one is constrained.

3 steps- Dilophosaurid Liliensternus, as in Paul (1988).

3 steps- Ceratosauria sensu lato, combining Neoceratosauria and Coelophysoidea.  Chilesaurus is the most basal theropod, Elaphrosaurus plus Limusaurus are the basal neoceratosaurs, and Gualicho is the most basal tetanurine.

3 steps- Eustreptospondylus and/or Megalosaurus outside Avetheropoda.  If one is constrained, the other follows.

3 steps- Megaraptoran Eotyrannus, as in Novas et al. (2013).

3 steps- Maniraptoran Coelurus.

3 steps- Troodontid Aurornis, Anchiornis and/or Xiaotingia.

3 steps- Chongmingia sister to Ornithothoraces, as in p2 of its original description. 

4 steps- Ornithischian silesaurids.  Lewisuchus is outside Dinosauria, Saurischia exists, and Asilisaurus and Pisanosaurus form a silesaur grade to either side of Silesauridae.

4 steps- Phytodinosauria.  Eoraptor and Buriolestes are sister to Dinosauria, while herrerasaurs and Eodromaeus are theropods.

4 steps- Ornithischian Chilesaurus.  Ornithoscelida occurs.

4 steps- Theropodan EoraptorBuriolestes, herrerasaurs and Eodromaeus also theropods.

4 steps- Abelisaurid Eoabelisaurus, as in its original description.

4 steps- Metriacanthosaurids outside Allosauria (Allosaurus plus Carcharodontosaurus).  Acrocanthosaurus joins Neovenator, so this also covers carcharodontosaurid Neovenator.

4 steps- Tyrannosauroid Compsognathus, as in Olshevsky (1991).  Surprised this one is so parsimonious.  A Compsognathidae with Aorun, Bicentenaria and Sinosauropteryx are the basalmost tyrannosauroids, with Sinocalliopteryx, Coeluridae including Tanycolagreus and Guanlong successively closer to core tyrannosauroids.

4 steps- Maniraptoromorph Tanycolagreus and/or Guanlong.

4 steps- Ornithomimosaurian Gualicho.  Tested due to Rauhut (2003) finding the very similar Deltadromeus in this position.  Note that ornithomimosaurian Elaphrosaurus is 36 steps longer, so the cases aren't that similar.

4 steps- Therizinosaurian Jianchangosaurus.  Still outside Falcarius plus Beipiaosaurus, and Cau said in a comment to the last post Jianchangosaurus was still an alvarezsauroid even after adding Erlikosaurus and Shuvuuia.  I'm not revealing much by saying the Lori analysis finds Jianchangosaurus to be a therizinosaur between Falcarius and Beipiaosaurus as in its original description.  Seems fishy...

4 steps- Archaeopterygid Jinfengopteryx, as in its original description.

4 steps- Archaeopterygid Anchiornis.

4 steps- Oviraptorosaurian scansoriopterygids.  They have an uncertain position within the clade, and therizinosaurs are still sister to oviraptorosaurs.

Allosaurus fragilis holotype tooth (YPM 1930) in ?lingual view.  Courtesy of the YPM.

5 steps- Dilophosaurus/Cryolophosaurus closer to Averostra than Coelophysis.

5 steps- Non-avetheropod Compsognathus, as in Novas (1992).  Very surprised this is so easy to get.  It's even more extreme than Novas' version, where Compsognathus was at least closer to avetheropods (his Tetanurae) than Piatnitzkysaurus and Eustreptospondylus, because in the constrained trees Carnosauria still has the same content as Cau's MPTs.  Sinosauropteryx joins it.

5 steps- Maniraptoromorph Eotyrannus.  I'm surprised by this, since I figured the result in other matrices was due to a lack of tyrannosauroid characters, which I think are all in the MegaMatrix.

5 steps- Non-tyrannoraptoran Coelurus, as in Paul (1988).

5 steps- Avemetatarsalian alvarezsauroids, as in Sereno (1999).  Jianchangosaurus is still a basal alvarezsauroid.

5 steps- Haplocheirus compsognathid/coelurid grade, as in Alifanov and Saveliev (2011).  Wasn't there some analysis that recovered it here too?  I just constrained it to be outside Maniraptoriformes (including alvarezsaurids).

5 steps- Non-pennaraptoran therizinosaurs, which fall out sister to Pennaraptora like the current consensus.

5 steps- Chongmingia a basal ornithurine (sensu Gauthier) outside Shenzhouraptor and Pygostylia, as in p1 of its original description.  The Lori analysis recovers it in a different position than  p1, p2 or Cau's analysis.

Less likely

6 steps- Non-eusaurischian saurischian EoraptorBuriolestes follows, but herrerasaurs and Eodromaeus are theropods.

6 steps- Theropodan Guaibasaurus.  Non-dinosaurian Eoraptor and Buriolestes, and this recovers Phytodinosauria.

6 steps- Eustreptospondylus closer to Neotetanurae than Megalosaurus, as in Holtz (2000).  I'm actually surprised this is so unlikely.

6 steps- Carnosaurian Sinosauropteryx, as in Longrich (2002).  Though Longrich's phylogeny was a bit different in having megalosaurids and metriacanthosaurids outside Avetheropoda.

6 steps- Ornithomimosaurian Haplocheirus, as in the Bayesian analyses of Cau and Lee and Worthy (2011).

6 steps- Arctometatarsalian therizinosaurs, as in Sereno (1999).

6 steps- Shenzhouraptor closer to Aves than Sapeornis.  

7 steps- Sauropodomorph Staurikosaurus but not Herrerasaurus, as in pachypodosaur Staurikosaurus of Kischlat (2000).

7 steps- Megalosauroid Monolophosaurus.  Megalosauroidea remains in Carnosauria.

7 steps- Coelurosaurian Neovenator.  Not sure if this has been suggested in print before, but I noticed quite a few coelurosaur-like characters when scoring Neovenator for the Lori matrix.  It forms the most basal coelurosaur clade with Aorun and Gualicho.

7 steps- Maniraptoran Compsognathus.

7 steps- Paravian alvarezsaurids, though note the lack of parvicursorines probably affects these numbers.  They (including Jianchangosaurus and Haplocheirus) emerge as the most basal paravians.

7 steps- Basal paravian Anchiornis, Aurornis, scansoriopterygids, Serikornis and/or Xiaotingia.

7 steps- Archaeopterygid Rahonavis, as in Forster et al. (1998).

7 steps- Fake-Ornithuromorphan Confuciusornis, as in Kurochkin (2006).  I really thought this would be more difficult to achieve than enantiornithine Confuciusornis (below).

Box of Archaeornithimimus asiaticus elements from AMNH 6576, with my identifications (dc- distal caudal, dt- distal tarsal, pedal except m 1-1 and m 3-2).  Is that a proximal metatarsal I in the upper left?  Courtesy of the AMNH.

8 steps- Non-eusaurischian saurischian HerrerasaurusEodromaeus and sometimes Eoraptor become herrerasaurs and Buriolestes is one node more stemward.

8 steps- Tetanurine Cryolophosaurus, as in Carrano et al. (2002).  Dilophosaurus stays in Coelophysoidea.

8 steps- Ceratosaurian megalosaurids, as in Britt (1991).  Chilesaurus falls out in a polytomy with megalosaurids and other ceratosaurs.

8 steps- Megalosauroid piatnitzkysaurids, with Megalosauroidea outside Avetheropoda.  Since this is the Carrano et al. consensus, I thought it would take less steps.

8 steps- Monolophosaurus sister to Avetheropoda, as in Smith et al. (2007).  Megalosaurids and piatnitzkysaurids fall out as more basal tetanurines.

8 steps- Arctometatarsalian tyrannosauroids, AKA Tyrannosaurus closer to Ornithomimus than to birds as in Holtz (1994).  I'm very surprised this is so parsimonious.  Coelurus and Bicentenaria join Tyrannosauroidea, but Gualicho leaves to be a ceratosaur.

8 steps- Maniraptoran tyrannosauroids, as in Sereno (1999).  This is accomplished more by moving ornithomimosaurs (including Gualicho) stemward to be the most basal coelurosaurs except for Zuolong

Somewhat possible

9 steps- Classic late 80s to early 90s topology where Staurikosaurus is sister to Herrerasaurus plus Dinosauria.  Tawa plus Daemonosaurus are closer to dinosaurs than both, while Sanjuansaurus follows Herrerasaurus.

9 steps- Piatnitzkysaurus outside Orionides, as in Rauhut (2003).  Condorraptor follows Piatnitzkysaurus, and megalosauroids fall outside Avetheropoda.  Surprised this is so high.

9 steps- Carnosaurian Tyrannosaurus, which brings megaraptorans, Gualicho and Bicentenaria to form the sister group of Allosauroidea (including Monolophosaurus).  I bet this is more parsimonious than most readers would assume given published topologies over the past two decades.

9 steps- Avialan Caudipteryx, as in its original description.  The rest of Oviraptorosauria follows it, though troodontids are still closer to Aves.

9 steps- Avialan Microraptor, as in Agnolin and Novas (2013).  Weirdly becomes the most basal troodontid, with that family closer to Aves than scansoriopterygids and anchiornithids.

9 steps- Avialan Unenlagia, as in its original description and Agnolin and Novas (2013).  Halszkaraptorines are unenlagiids, which are outside the Troodontidae plus Ornithes clade.

9 steps- Deinonychosauria.  Scansoriopterygids are oviraptorosaurs, while Jinfengopteryx and anchiornithids are avialans.

9 steps- Archaeopterygidae sister to Troodontidae.  Anchiornithines fall out as archaeopterygids. 

10 steps- Monolophosaurus outside Orionides, as in Carrano et al. (2002).  Megalosaurids and piatnitzkysaurids form successively closer outgroups to Avetheropoda.

10 steps- Fukuivenator excluded from Alvarezsauridae plus Therizinosauria plus Pennaraptora as in its original description.  It emerges as the sister to other maniraptorans.

10 steps- Eumaniraptora excluding troodontids as in Agnolin and Novas (2013).  Scansoriopterygids are oviraptorosaurs.

10 steps- Dromaeosaurid Xiaotingia, as in Senter et al. (2012).  Falls out in Microraptoria.

10 steps- Dromaeosaurid Balaur, as in its original description.  Falls out sister to Unenalagiinae plus Halszkaraptorinae.

11 steps- Tyrannosauroid Acrocanthosaurus, as in Bakker et al. (1988).  Tyrannosauroids become carnosaurs, with Sinraptor, Acrocanthosaurus and Bicentenaria successively closer to the 'core tyrannosauroid' clade of Eotyrannus, Gualicho, megaraptorans and TyrannosaurusTanycolagreus and Guanlong are now maniraptoromorphs.

11 steps- Alvarezsauroid Nqwebasaurus.  Alvarezsauroids emerge sister to ornithomimosaurs, with Haplocheirus and Jianchangosaurus forming a basal [edit] arctometatarsalian clade.

11 steps- Mahakala outside Unenlagiinae plus Eudromaeosauria (Halszkaraptor follows), as in most TWG matrices (though Senter et al. 2012 recovered it sister to unenlagiines like Cau).


12 steps- Alvarezsauroid Chilesaurus, where it emerged in the Lori matrix back in 2015.

12 steps- Ornithuran (sensu Gauthier) oviraptorosaurs, as in Maryanska et al. (2002).  Constraining Khaan to be closer to Meleagris than Archaeopteryx results in oviraptorosaurs (including scansoriopterygids) being the first clade to diverge from the avian stem after Archaeopteryx.

12 steps- Basal paravian Jinfengopteryx, as in Foth et al. (2014). 

13 steps- Coelophysoid Elaphrosaurus, as in Paul (1988).  Ceratosauria sensu lato forms, Elaphrosaurus is outside core coelophysoids and Limusaurus and sometimes Gualicho follow.

13 steps- Compsognathid Nqwebasaurus, as in Novas et al. (2013).  Compsognathids (including Aorun) become ornithomimosaurs.

13 steps- Dromaeosaurid Rahonavis.  Emerges in the unenalgiine plus halszkaraptorine clade.

14 steps- Neovenatorid megaraptorans, though this actually moves Neovenator out of Carnosauria into Tyrannosauroidea, so isn't that similar to Benson's topology.

14 steps- Enantiornithine Confuciusornis.

15 steps- Sauropodomorphan Chilesaurus, where it emerges as the most basal member.

15 steps- Carnosaurian Ceratosaurus, as in Currie (1995).  Other ceratosaurs follow.

15 steps- Alvarezsaurids closer to Aves than dromaeosaurids or troodontids.  Haplocheirus and Jianchangosaurus remain behind as ornithomimosaurs.  Note the lack of parvicursorines probably affects this number.

15 steps- Archaeopterygid Unenlagia, as in Forster et al. (1998).  Buitreraptor remains in Dromaeosauridae.

Cladogram of archosauromorphs after Kischlat (2000).  Note saurischian Marasuchus and sauropodomorph Staurikosaurus.

16 steps- Saurischian Marasuchus, as in Kischlat (2000).  Ornithischian silesaurs result, and Lewisuchus sister to Eodromaeus plus avepods.

16 steps- Non-avetheropod Sinraptor as in Longrich (2002).  Carnosauria becomes a grade, Acrocanthosaurus joins Neovenator, and Guanlong and Tanycolagreus become maniraptoromorphs. 

18 steps- Basal paravian Archaeopteryx.  Deinonychosauria forms, and anchiornithids and scansoriopterygids are further from Eumaniraptora.

19 steps- Coelophysoid ornithischians or ornithischians sister to Neotheropoda, as in Baron (2017).  Chilesaurus is the most basal theropod.

19 steps- Basal deinonychosaur Archaeopteryx, as in Xu et al. (2011).   Anchiornis, Aurornis and Serikornis are one node closer to Dromaeosauridae plus Troodontidae.

20 steps- Monolophosaurus sister to Guanlong, as in Carr (2006) who proposed they were an adult and juvenile of the same species.  The pairing resolves as sister to Tyrannoraptora.

21 steps- Carnosaurian megaraptorans.  Er, wow.  The Carrano et al. consensus is blown out of the water.  They don't even group with Neovenator, instead (including Gualicho and Bicentenaria) being in a trichotomy with megalosaurids and an Allosauroidea including piatnitzkysaurids.

I'm drawing the line here for plausibility

22 steps- Theropodan Marasuchus, as in Olshevsky (1991). Silesaurids, Eoraptor+Buriolestes and herrerasaurians are also theropods.

23 steps- Avialan therizinosaurs, as in Maryanska et al. (2002).  One of the odder parts of the classic 'oviraptorosaurs are birds' analysis is that they recovered therizinosaurs as closer to birds than dromaeosaurids or troodontids, which was only briefly mentioned in the text, while they removed Troodontidae and Therizinosauria from their figured cladogram.  Constraining this result leads to oviraptorosaurs being dragged along, and the whole of Caenagnathiformes is sister to taxa closer to Aves like scansoriopterygids, anchiornithids, Archaeopteryx, etc..

24 steps- 'Allosaur' Ornitholestes, as in Paul (1988).   Although Paul includes Ornitholestes in his Allosauridae, he views that family as paraphyletic to tyrannosaurids and his figure 10-1 shows Allosaurus closer to tyrannosaurids than Ornitholestes.  I thus only specified Ornitholestes to be closer to Allosaurus than megalosaurids, piatnitzkysaurids, Compsognathus and birds.  The resulting tree has ornitholestiids (including Zuolong) sister to core allosauroids including Monolophosaurus (which was considered closer to Allosaurus by Paul too- pg. 307), but tyrannosauroids and compsognathids are coelurosaurs.

24 steps- Ornithuran (sensu Gauthier) alvarezsaurids.  The most crownward alvarezsaurids were ever proposed to be, closer to Aves than Archaeopteryx.  They end up just crownward of anchiornithids, and weirdly form a clade there with scansoriopterygids and oviraptorosaurs.  As usual, the absence of parvicursorines probably affects the numbers.

24 steps- Archaeopterygid Protarchaeopteryx, as in Paul (2002).  Xiaotingia and scansoriopterygids are also closer to Archaeopteryx than Aves in these trees.

25 steps- Tyrannosauroids sister to Pennaraptora, as in Sereno (1999).  Like Sereno's trees, alvarezsauroids and therizinosaurs (Beipiaosaurus) form an expanded Arctometatarsalia, though now joined by Ornitholestes, Aorun and CompsognathusCoelurus becomes a tyrannosauroid.

26 steps- Ornithischian alvarezsaurids, as in Alifanov and Barsbold (2009).  Chilesaurus emerges as an alvarezsauroid.  Note the true number is probably much higher since neither included alvarezsaurid has cranial material.

30 steps- Ceratosaurian ornithomimosaurs, as in my half-joking post.  They don't even come out by Limusaurus or Elaphrosaurus, instead Ornithomimosauria (including Zuolong and Gualicho) are sister to other ceratosaurs.  How disappointing.

35 steps- Sauropodomorphan BeipiaosaurusFalcarius stays by oviraptorosaurs, while Beipiaosaurus ends up sister to Guaibasaurus.

35 steps- Phytodinosaurian BeipiaosaurusFalcarius stays by oviraptorosaurs, while Beipiaosaurus is sister to Chilesaurus as an ornithischian.

36 steps- Ornithomimosaurian ElaphrosaurusGualicho follows, and ornithomimosaurs move stemward to be sister to Tyrannoraptora.

36 steps- Megalosaurid abelisauroids, as in Paul (1988).  Megalosaurus moves to Abelisauria.

36 steps- Dromaeosaurid Ornitholestes, as in Makovicky (1995).  Fukuivenator emerges as the most basal dromaeosaurid, and dromaeosaurids are the most basal pennaraptorans with oviraptorosaurs, scansoriopterygids, anchiornithids and troodontids successively closer to birds.  This is equivalent to my old post about getting dromaeosaurid evolution backwards.

37 steps- Bullatosauria.  This actually moves ornithomimosaurs plus alvarezsauroids into Avialae to be sister to troodontids.  I had to specify both Zanabazar and Sinornithoides as troodontids, because specifying Zanabazar alone moves it into Ornithomimosauria without the other troodontids at a lower cost of 21 steps.

37 steps- Oviraptorosaurian Sapeornis, as in Paul (2010).  Oviraptorosaurs move to just closer to Aves than Archaeopteryx, with scansoriopterygids closer to core oviraptorosaurs than Sapeornis.

Phylogram from Huene (1923) showing his idea of what were carnosaurs vs. coelurosaurs.

39 steps- Huene's (1923) Carnosauria vs. Coelurosauria dichotomy.  For such an archaic concept, this works surprisingly well.  The trick is that Huene's and Cau's Carnosauria are basically the same.  By 1923, Huene had moved Ceratosaurus to Coelurosauria and placed tyrannosaurids and Elaphrosaurus there as well.  His carnosaurs are Megalosaurus, Eustreptospondylus and Allosaurus.  Even looking at the taxa not included in Cau's analysis, most shake out right- coelurosaurian Sarcosaurus, Halticosaurus, Procompsognathus, Podokesaurus, Betasuchus, Genyodectes, Proceratosaurus and Thecocoelurus vs. carnosaurian Magnosaurus, Poekilopleuron, Spinosaurus and Metriacanthosaurus.  There's a load of non-theropods in there and Huene got Sarcosaurus? andrewsi, Dryptosaurus and Valdoraptor wrong, but still impressive.  So this basically how many steps it takes to force carnosaurs stemward of Ceratosauria sensu lato.

43 steps- Sauriurine enantiornithines, as in Martin (1983).  Basically constraining enantiornithines (Bohaiornis and Cruralispennia here) as closer to Archaeopteryx than to Aves.  Rahonavis and Balaur emerge as sauriurines, but surprisingly scansoriopterygids, Sapeornis, jeholornithids, Confuciusornis, Zhongjianornis and Protopteryx remain as closer to Aves ('Ornithurae' in BANDit terminology).

57 steps- Sauriurine enantiornithines and Confuciusornis, as in Hou et al. (1995).  This is more in line with BANDit thought, as not only enantiornithines, Archaeopteryx and Confuciusornis fall out as sauriurines, but also Protopteryx, Sapeornis, jeholornithids (Martin, 2004),  Vorona (Kurochkin, 2006), Rahonavis and Xiaotingia (those two as archaeopterygids).  Unlike the plus 43 step tree, scansoriopterygids are outside Sauriurae plus 'Ornithurae' similar to Czerkas' hypothesis.

58 steps- Abelisaurid Piatnitzkysaurus, as in Currie and Zhao (1994).  Condorraptor follows, Eoabelisaurus also becomes an abelisaurid.

75 steps- 'Carnosauria' vs. 'Oviraptorosauria' of Russell and Dong (1994).  The Alxasaurus description is my most nostalgic technical paper, because it was the first I tracked down that wasn't in Science or Nature.  The authors presented a strange new analysis of theropods, where tetanurines fell into 'Carnosauria' (Baryonyx, Yangchuanosaurus, Allosaurus, dromaeosaurids and tyrannosaurids in successive order) and 'Oviraptorosauria' (ornithomimosaurs, therizinosauroids, oviraptorosaurs and troodontids in successive order).  Needless to say, it doesn't hold up, even when topology within each clade is allowed to vary like it is here.  Birds end up in 'Oviraptorosauria', so that would be Coelurosauria under current nomenclature.

78 steps- "Pneumatocrania", Holtz's (1994) concept combining oviraptorids, 'elmisaurids', tyrannosaurids, troodontids and ornithomimosaurs to the exclusion of dromaeosaurids and birds.  Cau's matrix doesn't result in anything close to Holtz's topology for this clade, with troodontids sister to oviraptorosaurs (including scansoriopterygids), and ornithomimosaurs sister to tyrannosauroids with alvarezsauroids and therizinosaurs in a trichotomy with Tyrann+Ornithom.  As with Bullatosauria, Sinornithoides had to be specified as well.

81 steps- Arctometatarsalia sensu Holtz (1994).  This is like "Pneumatocrania" except it excludes oviraptorids.  In Cau's analysis, this results in most oviraptorosaurs (including scansoriopterygids) being maniraptorans, but 'elmisaurid' Anzu being sister to Zanabazar deep within Troodontidae.  Again unlike Holtz's topology, tyrannosauroids, ornithomimosaurs, alvarezsauroids, therizinosaurians and Fukuivenator are successively closer to troodontids.

84 steps- Huene's Pachypodosauria, where his carnosaurs are closer to sauropodomorphs than his coelurosaurs.  Pachypodosauria ends up containing sauropodomorphs and ceratosaurs plus Cau's expanded Carnosauria, with every other theropod a coelurosaur.

[Edit] 100 steps- Conservative BANDit topology.  Here I specified taxa with stage III or IV feathers as birds, and retained Heterodontosaurus, Plateosaurus, Herrerasaurus, Coelophysis, Majungasaurus, Megalosaurus, Allosaurus and Sinosauropteryx as dinosaurs theropodsForcing birds outside Saurischia, Dinosauria, Dracohors, Dinosauriformes, etc. is difficult as it is actually easier to get Teleocrater up in basal Coelurosauria than to break up those clades.  But just breaking up Theropoda into these two clades takes 83 steps.  Tyrannosauroids, ornithomimosaurs, alvarezsauroids and therizinosaurs group with birds.  

140 steps- Coelophysoid birds, as in Raath (1985).  Other theropods known at the time were constrained as monophyletic relative to a Coelophysoidea containing rhodesiensis, Archaeopteryx, Hesperornis, Ichthyornis and MeleagrisBicentenaria, Fukuivenator, halszkaraptorids, scansoriopterygids and paraphyletic anchiornithids end up bridging the gap between coelophysoids and birds.

Paul's (1984) cladogram of predatory dinosaurs, after Raath (1990).  It differs from Paul's actual printed cladogram where compsognathids are better interpreted as in an unresolved trichotomy between 'allosaurs' and other coelurosaurs, ornithomimids merely extend with a '?' falling between tyrannosaurids and Archaeopteryx, and oviraptorids extend with a '?' that falls on the troodontid plus bird branch.  Note this differs from the PDW phylogeny in that megalosaurids are down by Procompsognathus and tyrannosaurids are sister to Protoavia.

191+ steps- Kurochkin's (2006) diphyletic birds.  BANDit Kurochkin had a weird hypothesis that Archaeopteryx and enantiornithines were theropods, but Confuciusornis, Patagopteryx, Ichthyornis, Hesperornis and of course Aves are birds.  These diverged at the typically vague BANDit level of Archosauromorpha or Archosauria, with no comment on where crocodylians, ornithischians, sauropodomorphs, etc. go.  It's again very hard to constrain in TNT since the program doesn't let the outgroup (Euparkeria) be specified, so if you constrain the next closest taxon (Teleocrater) to be outside of dinosauromorphs on one side and 'Ornithurae' on another, it's more parsimonious for TNT to force Teleocrater into Ornithothorces than to make that basal divergence.  But even a weak version of Kurochkin's hypothesis where Coelophysis and Allosaurus are still theropods and lead to enantiornithines but are more closely related to 'Ornithurae' than Teleocrater, Lagerpeton, Marasuchus, Heterodontosaurus and Plateosaurus results in 191 more steps.  Fukuivenator, halszkaraptorids, scansoriopterygids, Balaur and Zhongjianornis end up on the 'ornithurine' line.

Ignoring maniraptoromorphs (so as not to hint at Lori's topology) I'm most surprised by the robusticity of Cau's expanded Carnosauria, the rootward mobility of compsognathid-grade taxa, how unparsimonious carnosaurian megaraptorans are, and how parsimonious ceratosaurian megalosaurids and arctometatarsalian tyrannosaurids are.  I think Gualicho is the most interesting theropod right now in terms of just what it is, since its remains are decent but it can pretty easily move between ceratosaurs, tyrannosauroids and ornithomimosaurs.  Bicentenaria also finds its way into a suprisingly large number of hypotheses, so deserves a more detailed description.

References- Huene, 1923. Carnivorous Saurischia in Europe since the Triassic. Bulletin of the Geological Society of America. 34, 449-458.

Martin, 1983. The origin and early radiation of birds. in Brush and Clark, (eds.). Perspectives in Ornithology. 291-338.

Paul, 1984. The archosaurs: A phylogenetic study. In Reif and Westphal (eds.). Third Symposium on Mesozoic Terrestrial Ecosystems, Short Papers. 175-180.

Raath, 1985. The theropod Syntarsus and its bearing on the origin of birds. In Hecht, Ostrom, Viohl and Wellnhofer (eds.). The Beginnings of Birds. Freunde des Jura-Museums Eichstätt, Eichstätt. 219-227.

Bakker, Williams and Currie, 1988. Nanotyrannus, a new genus of pygmy tyrannosaur, from the latest Cretaceous of Montana. Hunteria. 1, 1-30.

Paul, 1988. Predatory Dinosaurs of the World. Simon & Schuster, New York. 464 pp.

Raath, 1990. Morphological variation in small theropods and its meaning in systematics: Evidence from Syntarsus rhodesiensis. In Carpenter and Currie (eds.). Dinosaur Systematics: Approaches and Perspectives. Cambridge University Press, Cambridge. 91-105.

Britt, 1991. Theropods of Dry Mesa Quarry (Morrison Formation, Late Jurassic), Colorado, with emphasis on the osteology of Torvosaurus tanneri. Brigham Young University Geology Studies. 37, 1-72.

Olshevsky, 1991. A Revision of the Parainfraclass Archosauria Cope, 1869, Excluding the Advanced Crocodylia. Mesozoic Meanderings. 2, 196 pp.

Novas, 1992. La evolucion de los dinosaurios carnivoros. In Sanz and Buscalioni (eds.). Los Dinosaurios y Su Entorno Biotico: Actas del Segundo Curso de Paleontologia in Cuenca. Instituto "Juan Valdez", Cuenca, Argentina. 126-163.

Currie and Zhao, 1994. A new carnosaur (Dinosauria, Theropoda) from the Jurassic of Xinjiang, People's Republic of China. Canadian Journal of Earth Sciences. 30(10), 2037-2081.

Holtz, 1994. The phylogenetic position of the Tyrannosauridae: Implications for theropod systematics. Journal of Paleontology. 68(5), 1100-1117.

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.

Currie, 1995. Phylogeny and systematics of theropods (Dinosauria). Journal of Vertebrate Paleontology. 15(3, 25A.

Hou, Zhou, Gu and Zhang, 1995. Confuciusornis sanctus, a new Late Jurassic sauriurine bird from China. Chinese Science Bulletin. 40(18), 1545-1551.

Forster, Sampson, Chiappe and Krause, 1998. The theropod ancestry of birds: New evidence from the Late Cretaceous of Madagascar. Science. 279, 1915-1919.

Sereno, 1999. The evolution of dinosaurs. Science. 284, 2137-2147.

Holtz, 2000. A new phylogeny of the carnivorous dinosaurs. GAIA. 15, 5-61.

Kischlat, 2000. Tecodoncios: A aurora dos Arcosaurios no Triassico. in Holz and De Rose (eds.). Paleontologia do Rio Grande do Sul. 273-316.

Longrich, 2002. Systematics of Sinosauropteryx. Journal of Vertebrate Paleontology. 22(3), 80A.

Maryanska, Osmolska and Wolsan, 2002. Avialan status for Oviraptorosauria. Acta Palaeontologica Polonica. 47(1), 97-116.

Paul, 2002. Dinosaurs of the Air. The Johns Hopkins University Press, Baltimore. 460 pp.

Rauhut, 2003. The interrelationships and evolution of basal theropod dinosaurs. Special Papers in Palaeontology. 69, 1-213.

Martin, 2004. A basal archosaurian origin for birds. Acta Zoologica Sinica. 50(6), 978-990.

Carr, 2006. Is Guanlong a tyrannosauroid or a subadult Monolophosaurus? Journal of Vertebrate Paleontology. 26(3), 48A.

Kurochkin, 2006. Parallel evolution of theropod dinosaurs and birds.  Entomological Review. 86 (Supp. 1),  S45-S58.

Smith, Makovicky, Hammer and Currie, 2007. Osteology of Cryolophosaurus ellioti (Dinosauria: Theropoda) from the Early Jurassic of Antarctica and implications for early theropod evolution. Zoological Journal of the Linnean Society. 151, 377-421.

Alifanov and Barsbold, 2009. Ceratonykus oculatus gen. et sp. nov., a new dinosaur (?Theropoda, Alvarezsauria) from the Late Cretaceous of Mongolia. Paleontological Journal. 43(1), 94-106.

Paul, 2010. The Princeton Field Guide to Dinosaurs. Princeton University Press. 320 pp.

Alifanov and Saveliev, 2011. Brain structure and neurobiology of alvarezsaurians (Dinosauria), exemplified by Ceratonykus oculatus (Parvicursoridae) from the Late Cretaceous of Mongolia. Paleontological Journal. 45(2), 183-190.

Lee and Worthy, 2011. Likelihood reinstates Archaeopteryx as a primitive bird. Biology Letters. 8(2),

Carrano, Benson and Sampson, 2012. The phylogeny of Tetanurae (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 10(2), 211-300.

Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790.

Agnolin and Novas, 2013. Avian ancestors: A review of the phylogenetic relationships of the theropods Unenlagiidae, Microraptoria, Anchiornis and Scansoriopterygidae. Springer Netherlands. 96 pp.

Novas, Agnolin, Ezcurra, Porfiri and Canale, 2013. Evolution of the carnivorous dinosaurs during the Cretaceous: The evidence from Patagonia. Cretaceous Research. 45, 174-215.

Foth, Tischlinger and Rauhut, 2014. New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers. Nature. 511, 79-82.

Baron, 2017. Pisanosaurus mertii and the Triassic ornithischian crisis: Could phylogeny offer a solution? Historical Biology. DOI: 10.1080/08912963.2017.1410705 

Cau, 2018. The assembly of the avian body plan: A 160-million-year long process. Bollettino della Società Paleontologica Italiana. 57(1), 1-25.

Tuesday, May 8, 2018

Cau's 2018 theropod tree

Hi all.  Work's been rapid on the Ornithoscelida project, which has improved due to David Marjanovic's request that I provide a citation for each character state we think was inaccurately coded by Baron et al..  It's time consuming, but has revealed several times where I was mistaken in my scoring, and forces you to really evaluate whether you think the evidence is good enough to truly call someone's character state choice wrong.  As tedious as it is, this should really become the standard for scoring justification in any analysis (and no, I didn't do that for the Lori analysis, though I have the preliminary steps for a far future offshoot of it).

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).
Cau's analysis itself has positives and negatives.  What everyone knows about the MegaMatrix is that it's HUGE.  I'm talking 1781 characters.  That's more than all Mesozoic theropod analyses except the poorly coded Livezey and Zusi (2007), which used 2954 characters and focused on living birds though technically included 30 non-avian theropods too.  But if you look at the matrix, the size is a tiny bit misleading because Cau doesn't use any multistate characters.  So instead of a single character of "Premaxilla - number of teeth - three or less (0); four (1); five (2); six (3); seven or more (4)", he has-
"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).

Cranial elements of the maniraptoromorph Microvenator celer (holotype AMNH 3041), with supposed right lacrimal of Makovicky and Sues in lateral view (upper left, anterior to right), dentary in dorsal view (lower right, anterior to top) and unidentified elements (scale bar in cm) (courtesy of the AMNH).
The taxon sample is interesting because it is very reduced compared to the Halszkaraptor analysis (Cau et al., 2017) that used the same character list (plus eight new characters; though among maniraptoromorphs, Jianianhualong and Chongmingia were added).  Alvarezsaurids are only represented by Alvarezsaurus and Patagonykus, caenagnathoids by Anzu and Khaan, therizinosaurs by Beipiaosaurus and Falcarius (and Jianchangosaurus... see below), etc..  Which still leaves it as the best large scale Mesozoic theropod analysis published, but without e.g. undisputed alvarezsaur skulls (since Haplocheirus finds itself elsewhere in some analyses), it's bound to get things wrong.  And it does differ from Cau et al.'s 2017 trees which focused on maniraptoromorphs.  Zuolong is outside Neotetanurae instead of a coelurosaur, Coelurus is a maniraptoromorph [see how useful this clade name is!] instead of a tyrannosauroid, Jianchangosaurus is an alvarezsaur(!), therizinosaurs are caenagnathiforms instead of outside Pennaraptora, Fukuivenator is a paravian instead of a therizinosaur, halszkaraptorines are unenlagiines, Xiaotingia is a scansoriopterygid instead of an anchiornithid, scansoriopterygids are further from Aves than Archaeopteryx, and Zhongjianornis is in 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).
What of the phylogenetic results themselves?  Eodromaeus and herrerasaurs are in an unresolved polytomy with sauropodomorphs and ornithoscelidans, which matches their increasingly uncertain position now that people are using large taxon samples for more than Nesbitt-derived matrices and Sereno's non-testing 'analyses' from the 90s are fading into history.  Ornithoscelida itself is recovered, but with only Heterodontosaurus and Tianyulong representing Ornithischia, I don't give that much credit regardless of the character count.  Heterodontosaurids are very theropody in some ways few other ornithischians are and generally fall out as the first branching clade in analyses (now that Pisanosaurus is a silesaurid, which Cau also recovers) and ignoring Chilesaurus for the moment.  But I'm co-writing a whole paper on that, so let's move on to theropods.  Cryolophosaurus is a dilophosaurid coelophysoid, which is counter the recent consensus of finding it closer to averostrans or even a tetanurine itself.  As stated above, Zuolong is outside Neotetanurae, which is weird since it generally falls out as a basal coelurosaur.  Chilesaurus is also here, matching its authors' conclusion, but I think the poor ornithischian sample keeps this analysis from adequately dismissing an ornithischian identity.  But I'm co-writing a paper on that and etc. etc..  Back to theropods.  Cau recovers a Rauhut-like Carnosauria including megalosaurids, piatnitzkysaurids, Monolophosaurus and allosaurs.  Neovenator is sister to Allosaurus and Sinraptor sister to Acrocanthosaurus among the latter, which harkens back to late 90s phylogenies.  Megaraptorans (including Gualicho) are tyrannosauroids closer to Tyrannosaurus than Eotyrannus, matching Novas et al. (2013).  The tree is untraditional in placing compsognathid-grade taxa outside Tyrannoraptora, though Novas had that opinion back in the early 1990s.  As stated above, the maniraptoran section has the out of vogue caenagnathiform therizinosaurs and the very weird alvarezsauroid Jianchangosaurus, but those might be glitches due to the taxon sample.  Fukuivenator is sometimes a dromaeosaurid and sometimes the basalmost paravian, which its authors recovered with the addition of three steps.  Cau finds avialan troodontids, standard for his published analyses.  Like his Halszkaraptor version, Rahonavis is close to jeholornithids and Protopteryx can be outside Ornithothoraces (it always is in the 2017 trees).  The latter is funny because I had that idea way back in 2000 on the DML ("My analysis of 31 characters and 6 taxa resulted in a single most parsimonious teee (CI .81, HI .19, RI .78)" ... how quaint), so if it turns out to be true that would be something.  Finally, presumably due to excluding fragmentary taxa like Teviornis, the huge ornithuromorph polytomy of the 2017 paper is resolved and Patagopteryx falls out by Apsaravis, Ichthyornis and Hesperornis+Aves.  Wha?

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.

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