Monday, December 3, 2012

Is Ichthyovenator a spinosaurid?

So I've been adding taxa to Carrano et al.'s (2012) tetanurine analysis for a Database update, and most positions are expected (I suppose I should note that I ordered characters properly in the matrix, which had the minor effects of putting Chuandongocoelurus, Monolophosaurus and Orionides in a trichotomy, and making Xuanhanosaurus a non-allosaurian carnosaur instead of necessarily a metriacanthosaurid).  Erectopus is a non-allosaurian carnosaur, Kaijiangosaurus is a non-megalosaurian and non-avetheropod tetanurine, etc..  But Ichthyovenator came out sister to Concavenator as a carnosaur sister to Allosauria.  Interesting....

Well, Cau found it as a basal spinosaurid instead of a baryonychine like Allain et al. (2012) found, so this wasn't totally unexpected.  So I constrained it to be a spinosaurid and found it takes five extra steps, which isn't too bad.  Next I constrained it to be a non-allosaurian carnosaur in Allain et al.'s matrix and it takes nine extra steps, which is getting into improbable territory.  Let's look at the details.

It's a sauropod pubis... er no wait.... Ichthyovenator's ischium (after Allain et al., 2012).

In Allain et al.'s matrix...
- Ichthyovenator is a megalosauroid due to having a vertical ridge anterior to the hyposphene in the dorsal vertebra.  But this is miscoded and is actually absent.
- It is a spinosaurid due to the tall dorsal neural spine, but these are also present in Concavenator, which was not included in their analysis.
- It is placed in Baryonychinae due to four characters- the basally webbed dorsal neural spine.
- ... An accessory centrodiapophyseal lamina on the dorsal, which is also present in the unincluded Concavenator.
- ... A mediolaterally expanded pubic boot.
- ... And a posterior pubic boot "reduced to a small flange". But this is correlated with the last character, as a reduced posterior pubic boot (with insignificant anterior boot) leads to a transversely expanded distal pubis, and indeed the only taxa coded as having the first state are also the only ones coded as having the second.
- It is excluded from Avetheropoda due to the small pubic boot as well.
- It is excluded from Allosauroidea because the posterior dorsal neural spine is not anteriorly inclined, but this is also true in Concavenator).
- It's also excluded from Allosauroidea because the ischial obturator foramen is closed.  Yet the two coelurosaurs are miscoded as lacking an obturator notch; when that's corrected, Ichthyovenator's closed foramen becomes an autapomorphy.

So of the nine characters, three are due to Allain et al. not including Concavenator in their matrix.  Two are due to miscodings. The two pubic boot characters are correlated, so are really only one. Yet this character was not used by Carrano et al..  Finally, the neural spine webbing is valid and used by Carrano et al..

In Carrano et al.'s matrix...
- Ichthyovenator is sister to Concavenator due to three characters.  The tall dorsal neural spine (also in spinosaurids).
- ... The accessory centrodiapophyseal lamina (also in baryonychines).
- ... And a peg-and-socket ilioischial articulation (not included by Allain et al.).
- It is an avetheropod because of four characters.  It has a narrow brevis fossa (coded more strictly in Allain et al.).
- ... An m. cuppedicus shelf (not included by Allain et al.).
- ... An open pubic obturator notch.  However, Suchomimus and Baryonyx are miscoded by Carrano et al. (Rauhut, 2003; Charig and Milner, 1997).
- ... And a large and oval pubic obturator notch/foramen (not included by Allain et al.).
- It is excluded from Megalosauroidea due to lacking a vertical ridge anterior to the hyposphene (miscoded by Allain et al.).
- ... And having a vertical ilial ridge (not included by Allain et al.).

So of these nine characters, two are correctly coded as also present in baryonychines, and another is miscoded as being absent in baryonychines.  Five others aren't used by Allain et al., and another was miscoded by Allain et al.

After recoding...
In Allain et al.'s matrix, after recoding Ichthyovenator's hyposphene ridge and the coelurosaurs' obturator notches, and excluding the correlated pubic boot character, Ichthyovenator is still a baryonychine.  Constraining it to be a non-allosauroid carnosaur takes five extra steps, which is down from the nine it took before (though it was slightly more nested in Carnosauria before, but only by two steps).  If we add the five characters Allain et al. didn't use that support this position (the brevis fossa expansion counts too since it is an additional state of a character), then either alternative is equally parsimonious.

In Carrano et al.'s matrix, after recoding Baryonyx and Suchomimus for their obturator notches, Ichthyovenator is now a non-allosauroid carnosaur and Concavenator is back to Carcharodontosauridae (in case you're wondering, making them sister taxa like before is now one step longer).  It now takes three more steps to make Ichthyovenator a spinosaurid, so that's dropped from five.  If we add on the transversely wide pubic boot character that they didn't include, we could say it only takes two more steps to make Ichthyovenator a spinosaurid.

In conclusion...
Amazingly, after only six corrections and taking into account the unused characters in each, both matrices give almost the same answer- Ichthyovenator is either equally likely or two steps more likely to be a basal carnosaur instead of a baryonychine.  The main flaw was that Allain et al. didn't include several useful characters, which is expected considering their total character number is 51% of Carrano et al.'s.  I'd put it in Orionides incertae sedis for now.

References- Charig and Milner, 1997. Baryonyx walkeri, a fish-eating dinosaur from the Wealden of Surrey. Bulletin of the Natural History Museum of London (Geology). 53, 11-70.

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

Allain, Xaisanavong, Richir and Khentavong, 2012. The first definitive Asian spinosaurid (Dinosauria: Theropoda) from the Early Cretaceous of Laos.  Naturwissenschaften. 99(5), 369-377.

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

Wednesday, November 28, 2012

"Allosaurus/Chilantaisaurus" sibiricus is probably a megaraptoran

So the Database is still up for some reason, but I've come through with my promise to examine what Riabinin named Allosaurus sibiricus and which has been going by Molnar et al.'s reassignment as Chilantaisaurus sibiricus.  The description's in Russian (translations are welcome), but the holotype is figured clearly in all views, allowing us to make comparisons to other taxa (thanks to Molnar for sending it to me).  I can send the pdf to any who ask.

"Allosaurus" sibiricus Riabinin, 1915
= Antrodemus sibiricus (Riabinin, 1915) Huene, 1932
= Chilantaisaurus? sibiricus (Riabinin, 1915) Molnar, Kurzanov and Dong, 1990
Berraisian-Hauterivian, Early Cretaceous
Tignin Formation or Turgin Formation or Zugmar Formation, Chitinskaya Oblast, Russia
- (PIN coll.) distal metatarsal II (~300-400 mm)
Late Barremian-Mid Aptian, Early Cretaceous
Mogoito Member of Murtoi Formation, Buryatia, Russia
- ? bone (Ivanov, 1940)
Diagnosis- (suggested) (combination of) metatarsal II lateral condyle with ventral surface width ~46% of condylar depth; metatarsal II medial condyle dorsal surface ~73% as wide as surface of lateral condyle and angled 35 degrees from lateral edge of lateral condyle.

Holotype of "Allosaurus" sibiricus, distal left metatarsal II in (top left to right) medial, dorsal, lateral, ventral, (bottom left to right) distal and proximal views (after Riabinin, 1915).  The distal end is 68 mm wide.

Comments- Note the description was actually published in 1915, though the volume was intended for 1914. The holotype was discovered in 1912 and deposited in what was then the Geological Museum of the Russian Academy of Sciences in Petrograd (Tolmachoff, 1924) (now St. Petersburg), which has since moved to Moscow. Riabinin (1915; partially translated in Chure, 2000) named it Allosaurus (?) sibiricus based on what he identified as a distal metatarsal IV. Huene (1932) said only that it did not permit exact characterization and probably belonged to an allosaurid (he renamed it Antrodemus? sibiricus as he thought that was a senior synonym of Allosaurus). Molnar et al. (1981) felt sibiricus resembled Ceratosaurus so closely that they "hesitate to accept it as an allosaurid". Molnar et al. (1990) on the other hand stated it was "almost identical with that of C. tashuikouensis in form and proportions of the distal condyle", so questionably referred it to Chilantaisaurus. Nessov (1995) agreed the species were similar and that sibiricus may belong in Chilantaisaurus. He noted stratigraphic data gave three possible formations the specimen was discovered in. Chure (2000) incorrectly said Riabinin did not illustrate the material, as he apparently had only a small portion of the original document. This error was repeated by Benson and Xu (2008). Chure excluded it from Allosauridae because he believed the distal outline was rectangular, but it is actually trapezoidal in both Allosaurus and sibiricus. Both Benson and Xu and Carrano et al. (2012) incorrectly credited Holtz et al. (2004) as being responsible for assigning it to Chilantaisaurus, though Carrano et al. correctly identified it as a second metatarsal. They believed it "too fragmentary to be assigned to a known taxon or identified as a distinct form" and noted similarity to Allosaurus, Neovenator, Torvosaurus and Afrovenator (though no metatarsal II has been reported for the latter).

Ivanov (1940) reported a bone referred to Allosaurus sibiricus from the Mortoi Formation, though without more data this referral is uncertain.

The holotype is ~70% the size of Chilantaisaurus tashuikouensis in distal width and depth, which would make it ~286 mm if similarly stout. If from an elongate metatarsus like Australovenator's though, it would be ~398 mm long. It differs from Allosaurus in having a more medially oriented dorsal curve to the lateral condyle, having a larger and more medially flaring medial condyle, having a lateral condyle which is recessed ventrally, and lacking the lateral flare on the ventral edge of Allosaurus' lateral condyle. Chilantaisaurus' medial condyle flares slightly more than Allosaurus' and it has a ventrally recessed lateral condyle, but it has the small medial condyle and a lateral flare like Allosaurus and has the dorsal curve oriented even further laterally. Of course, Riabinin and Molnar et al. were comparing sibiricus with the fourth metatarsals of Ceratosaurus, Allosaurus and Chilantaisaurus, not the second metatarsals (all three fourth metatarsals differ from sibiricus in having a ventrally pointed medial condyle and lacking a ventrally inset medial condyle, while Ceratosaurus' and  Allosaurus' element is much narrower, and Chilantaisaurus' has a larger dorsolateral bulge; Molnar et al. were correct that Chilantaisaurus' is more similar, but it is not almost identical). Taxa with similarly medially flaring medial condyles are Ceratosaurus, Torvosaurus, Sinraptor, Acrocanthosaurus, Fukuiraptor, Australovenator, Megaraptor and Harpymimus, though only Australovenator's and Acrocanthosaurus' are close in size. Taxa with a ventrally inset lateral margin are Rajasaurus, Megalosaurus, Chilantaisaurus, Fukuiraptor, Australovenator, Megaraptor, Appalachiosaurus and Alxasaurus.

Comparison of metatarsals in distal view (some reversed; scaled to equal depth). Top row, left to right- right metatarsal IV (medial to right) of Chilantaisaurus tashuikouensis (after Hu, 1964),  Allosaurus fragilis (after Madsen, 1976) and Ceratosaurus (after Gilmore, 1920).  Middle row, left to right- left metatarsal II (medial to left) of Chilantaisaurus tashiukouensis (after Benson and Xu, 2008), Allosaurus fragilis (after Madsen, 1976), Megaraptor (after Lamanna, 2004), "Allosaurus" sibiricus (after Riabinin, 1915), Australovenator (after Hocknull et al., 2009), Neovenator (after Brusatte et al., 2008), Torvosaurus (after Britt, 1991) and Alxasaurus (after Russell and Dong, 1994).  Bottom row, left to right- left metatarsal II (medial to left) of Ceratosaurus (after Gilmore, 1920), Rajasaurus (after Wilson et al., 2003), Megalosaurus (after Benson et al., 2010), Sinraptor (after Churrie and Zhao, 1994), Acrocanthosaurus (after Harris, 1998), Fukuiraptor (after Azuma and Currie, 2000), Appalachiosaurus (after Carr et al., 2005) and Harpymimus (after Kobayashi, 2004).

 Overall, it is most similar to Australovenator, differing in being 9% broader compared to depth, a broader lateral condyle ventrally, and having a more medially oriented dorsal surface of the lateral condyle. Next most similar is Megaraptor, which it differs from in having a broader lateral condyle ventrally with ventral surface angled more laterally, and a less rounded dorsal surface of the lateral condyle. The amount of ventral inset of the lateral condyle and dorsal exposure of the medial condyle is in between these two taxa. This suggests sibiricus may be a megaraptoran, which is congruent with its age, size and location. As it is intermediate in two variables, more similar to Megaraptor in depth, more similar to Australovenator in the orientation of the lateral condyle's ventral surface, and differs from both in the lateral condyle's ventral width, placing it in any named genus is not possible. As it does differ from all known theropod metatarsals, it is not a nomen dubium, contra Rauhut (2003), Holtz et al. and Carrano et al..

References- Riabinin, 1915. Zamtka o dinozavry ise Zabaykalya [A note on a dinosaur from the trans-Baikal region]. Trudy Geologichyeskago Muszeyah Imeni Petra Velikago Imperatorskoy Academiy Nauk. 8(5), 133-140.

Tolmachoff, 1924. On dinosaurs in northern Asia. American Journal of Science. 5(7), 489-490.

Huene, 1932. Die fossile Reptil-Ordnung Saurischia, ihre Entwicklung und Geschichte. Monographien zur Geologie und Palaeontologie. 4(1), viii + 361 pp.

Ivanov, 1940. [On the age of the coal-bearing deposits of Transbaikalia]. Sovietskaya Geologiya. 11, 45-54.

Molnar, Flannery and Rich, 1981. An allosaurid theropod dinosaur from the early Cretaceous of Victoria, Australia. Alcheringa. 5, 141-146.

Molnar, Kurzanov and Dong, 1990. Carnosauria. In Weishampel, Dodson and Osmolska (eds.). The Dinosauria. Berkeley: University of California Press. 169-209.

Nessov, 1995. Dinozavri severnoi Yevrazii: Novye dannye o sostave kompleksov, ekologii i paleobiogeografii [Dinosaurs of northern Eurasia: new data about assemblages, ecology, and paleobiogeography]. Institute for Scientific Research on the Earth's Crust, St. Petersburg State University, St. Petersburg. 156 pp.

Chure, 2000. A new species of Allosaurus from the Morrison Formation of Dinosaur National Monument (Utah-Colorado) and a revision of the theropod family Allosauridae. Ph.D. thesis. Columbia University. 964 pp.

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

Holtz, Molnar and Currie, 2004. Basal Tetanurae. In Weishampel, Dodson and Osmolska (eds.). The Dinosauria Second Edition. University of California Press. 71-110.

Benson and Xu, 2008. The anatomy and systematic position of the theropod dinosaur Chilantaisaurus tashuikouensis Hu, 1964 from the Early Cretaceous of Alanshan, People’s Republic of China. Geological Magazine. 145(6), 778-789.

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

Saturday, November 24, 2012

"New" name for Megalosaurus? lydekkeri

When checking if Walgettosuchus woodwardi had in fact been reassigned to Megalosaurus as listed by Olshevsky (1991), I found a theropod name no one has noticed since its announcement.

Megalosaurus lydekkeri is a tooth first mentioned by Dawkins (in Huxley, 1869) as Megalosaurus, then called Zanclodon(?) sp. b. by Lydekker (1888), named Megalosaurus (gen. ?) lydekkeri by Huene (1926) and reassigned as Magnosaurus (?) lydekkeri by Huene (1932).  It's Early Jurassic, so probably not Megalosaurus or Magnosaurus, and has since been relegated to Theropoda indet. status and never compared in detail to anything.

Holotype tooth and maxillary or dentary fragment of Megalosaurus? woodwardi (BMNH 41352) (after Lydekker, 1888).

However, no one has noticed that in 1909, Lydekker designated the tooth as the type of a new species, Megalosaurus woodwardi (along with the tibia that would later be named Sarcosaurus andrewsi).  While he included no description or definition, he did provide an indication in the form of referencing Woodward (1908) who distinguished the tibia from M. bucklandii, Ceratosaurus and Allosaurus in its slenderness and "trochlear" shape of the astragalar facet, and from Triassic taxa in its tall astragalar ascending process.

Because Megalosaurus woodwardi has priority over Megalosaurus lydekkeri, but has not been used since it was named, ICZN Article 23.9.1 should be consulted to check if the former is a nomen oblitum. Usage of Megalosaurus lydekkeri must be maintained if ( M. woodwardi has not been used as a valid name after 1899 (false, as Lydekker used it in 1909) and ( M. lydekkeri has been used as a valid name "in at least 25 works, published by at least 10 authors in the immediately preceding 50 years and encompassing a span of not less than 10 years" (false as far as I can tell, as an extensive search located only 13-15 works since 1962*). Thus Megalosaurus woodwardi is the valid name, unless a worker were to petition the ICZN to suppress it.

* Neaverson (1962), Steel (1970), Kuhn (1972)?, Waldman (1974), Chure and McIntosh (1989), Molnar et al. (1990), Olshevsky (1991), Glut (1997), Carrano and Sampson (2004), Holtz et al. (2004), Naish and Martill (2007), Benson and Barrett (2009), Fastovsky and Weishampel (2009)?, Benson (2010), Carrano et al. (2012).

The ironic thing here is that the tibia has also been called Megalosaurus woodwardi, though for completely different reasons.  The specimen was accidentally made the type of two species simultaneously by Huene (1932) (Sarcosaurus andrewsi and Magnosaurus woodwardi). In that paper, Huene also lists Megalosaurus woodwardi in the section on Magnosaurus nethercombensis, stating both should be Megalosaurus subgenus Magnosaurus. As Magnosaurus is explicitly named as a new genus on that same page, this was probably an earlier opinion that was mistakenly retained. Note Huene uses "n. sp." and does not reference Lydekker's 1909 paper, suggesting he was not merely using Lydekker's name.  Though even if he did it wouldn't matter since Lydekker made the tooth the type, not the tibia.  The tibia is now called Sarcosaurus andrewsi because Huene was first revisor in 1956.

And in case you're wondering, I think Olshevsky was mistaken in thinking Walgettosuchus had been explicitly assigned to Megalosaurus as Megalosaurus woodwardi.

References- Huxley, 1869. On the upper jaw of Megalosaurus. Quarterly Journal of the Geological Society of London. 25, 311-314.

Lydekker, 1888. Catalogue of the Fossil Reptilia and Amphibia in the British Museum (Natural History), Cromwell Road, S.W., Part 1. Containing the Orders Ornithosauria, Crocodilia, Dinosauria, Squamta, Rhynchocephalia, and Proterosauria: British Museum of Natural History, London. 309 pp.

Woodward, 1908. Note on a megalosaurian tibia from the Lower Lias of Wilmcote, Warwickshire. Annals and Magazine of Natural History. 8(1), 257-259.

Lydekker, 1909. Vertebrate paleontology in 1908. Science Progress in the Twentieth Century: A Quarterly Journal of Scientific Work & Thought. 3(11), 450-471.

Huene, 1926 The carnivorous Saurischia in the Jura and Cretaceous formations, principally in Europe. Revista Museo de La Plata, 29, 35-167.

Huene, 1932. Die fossile Reptil-Ordnung Saurischia, ihre Entwicklung und Geschichte [The fossil reptile order Saurischia, their development and history]. Monographien zur Geologie und Palaeontologie, serie 1. 4(1-2), 1-361.

Huene, 1956. Paleontologie und Phylogenie der niederen Tetrapoden. Fischer-Verlag, Jena.

Olshevsky, 1991. A revision of the parainfraclass Archosauria Cope, 1869, excluding the advanced Crocodylia. Mesozoic Meanderings. 2, 196 pp.

Friday, November 16, 2012

Wang et al. 2012 - for once I'm against a paper synonymizing Jehol birds?!

Wang et al. have a new paper in press synonymizing Jixiangornis with Shenzhouraptor (their Jeholornis).

EDIT: I've been in communication with Dyke (who has been an exemplary scientist in his response) since posting this and it seems the paper was not supposed to be online yet and was taken down since Creisler's DML post so that more work could be done.  Gotta love the consequences of publishing submitted manuscripts early, and how things like this and Brontomerus' early surprise publication happened. ;)  Actually, the consequences here might be very good indeed....

Before I get into the meat of the paper, I'd like to express my continuing disappointment with how Yandangornis is handled by everyone, when it's mentioned at all.  Wang et al. claim Zhou and Zhang (2006) "reviewed Yandangornis longicaudus and concluded that it 'lacks the diagnostic characters of birds' and thus may also be a non-avian dinosaur".  In actuality, Zhou and Zhang merely said "Unfortunately, this fossil was only preliminarily described, showing no diagnosis of birds.  As a result, it remains a mystery whether it is a bird or bird-like dinosaur."  That counts as a review?!  Especially when Yandangornis was described as having numerous characters of basal ornithurine (sensu Gauthier) birds including the toothless upper jaw (with pointed symphysis), reduced number of caudal vertebrae (with rod-like distal caudals), fused sternum with median bulge, trochanteric crest, completely fused tibiotarsus, fibula not contacting tarsus and fused metatarsus.  I fear Yandangornis is becoming the Longisquama of birds- being curtly dismissed as an unknown factor without even trying to evaluate it.

On to the main topic.  Wang et al. present a new specimen of basal ornuthurine from the Yixian Formation, YFGP-yb2.  They claim this specimen combines characters of Shenzhouraptor and Jixiangornis, showing both to be synonymous.

First they say it has no maxillary teeth, unlike 'Jeholornis palmapenis' but like 'J. prima' and Jixiangornis (wouldn't this be itself a reason to separate the former species, if it were true and thus notable enough to comment on?).  Yet jeholornithid teeth are often unpreserved due to their small size and low number, as seen by palmapenis' lack of dentary teeth (considered preservational by O'Connor et al., 2010) and LPM 0193's (the Shenzhouraptor holotype) lack of any recognizable teeth. Even palmapenis only preserves one of the at least two maxillary teeth it had on that side. Thus the absence of maxillary teeth in other specimens may easily be preservational, so that Wang et al. simply accept reportedly absent teeth as such seems naive.

The scapula is said to narrow distally as in Shenzhouraptor, but this is true of almost all ornithurines including Jixiangornis, so means little.  The scapula was known to be curved in Jixiangornis previously (Nesbitt et al., 2009; and in Sapeornis), so that means little too.  The coracoid is correctly stated to be more elongate than Shenzhouraptor or Jixiangornis, which is interesting.  It's stated to be strut-like as in Jixiangornis (and by implication unlike Shenzhouraptor), but Jixiangornis has the less strut-like coracoid as can be seen in figure 82 of Turner et al. (2012).  Though Wang et al. claim the new specimen shares a well developed lateral coracoid process with Jixiangornis and not Shenzhouraptor, the latter has a better developed process than either (ironically making Wang et al.'s pairing right, but for the wrong reason).  [Edit: actually some individuals of both species have large processes, and some small ones] They claim the new specimen has the distal half of the medial coracoid margin convex as in Jixiangornis and unlike Shenzhouraptor, but in fact it differs from all prior specimens in having a completely concave medial margin distally.  The supposed furcula is said to be V-shaped and slender, so more like Shenzhouraptor, but what's identified is extremely slender like enantiornithines' and Jixiangornis' furcula is actually more V-shaped than Shenzhouraptor's (though nothing near this specimen's supposed anatomy).  Both would differ from the new specimen in lacking a large hypocleidium.  In fact, I'm nearly certain what Wang et al. think is a furcula is a dorsal rib and parts of dorsal vertebrae [Edit: I've since found the actual furcula under the coracoids].
Supposed furcula of basal ornithurine YFGP-yb2 (top) as photographed by Wang et al. (2012- figure 2A), (middle) as illustrated by Wang et al. (2012- figure 2B), (bottom) from an unpublished photo.

Wang et al. claim the new specimen is closer in radioulnar width ratio (claimed 50%) to Shenzhouraptor, citing a 50% ratio in 'Jeholornis prima', but Zhou and Zhang's (2002) figures show it closer to 65% in the latter.  Shenzhouraptor's holotype is ~71% and the new specimen's is ~64% based on an unpublished photo.  What's sad is that they cite Jixiangornis' ratio as "less than 0.7", basing this on a matrix coding by O'Connor et al., when Ji et al. (2002) explicitly listed widths in their forelimb measurement table (4.5 / 6.8 mm = 66%).  Did they not even read its original description?  Wang et al. claim the new specimen is more similar to Shenzhouraptor than Jixiangornis in lacking an intermetacarpal scar, saying it was "coded as potentially present in Jixiangornis by O’Connor et al.".  Potentially present?  Yuan (2005) and Turner et al. (2012) both code it as absent in Jixiangornis.  The new specimen (106%) supposedly resembles 'Jeholornis prima' (105-108%) more than Jixiangornis (104%) in its short manuohumeral ratio, but this isn't true.  And it's only a single percent difference anyway.  How is that important to note?  Annoyingly, this ratio isn't listed in the measurement comparisons table, nor is manual length, so you have to multiply the listed ulnohumeral and manuoulnar ratios to get it.  Shenzhouraptor's type has a ratio of 117% btw.  The ratio between manual unguals I and II is said to be more similar to Jixiangornis, with the new specimen having a larger ungual I, but the schematic drawing of Jixiangornis by Ji et al. (2002) would suggest it had a larger ungual II.  Shenzhouraptor has a larger ungual I, so is actually the taxon closest to the new specimen, but the schematic nature of Ji et al.'s drawing, small amount of difference in all specimens and difficult to separate claw sheaths makes any comparison unimportant.  The length of manual digit II is said to be more similar to Shenzhouraptor, but the ratio is identical to Jixiangornis (98% for II-1+II-2 / mcII). 

The high tibiofemoral ratio was suggested to be ontogenetic despite the smaller palmapenis type (which they cited earlier) having a larger ratio.  Wang et al. are wrong in claiming Jixiangornis has an incompletely fused tibiotarsus (Ji et al., 2002; Turner et al., 2012).  They claim the pedal unguals of 'Jeholornis prima' and the new specimen are more slender and less curved than Jixiangornis, but the opposite is true comparing Ji et al.'s illustration with figure 3 of Zhou and Zhang (2006), and the new specimen shows variation caused by keratin sheaths.

Wang et al. end with this paragraph, with my interjections bracketted- "To sum up, YFGP-yb2 shares the following features with Jeholornis prima that are absent in Jixiangornis: subequal manus and humerus lengths [untrue and a 1% difference]; similar ratio between the radius and ulna shaft widths [~1% difference]; and the absence of an intermetcarpal tubercle on metatarsal II [wow, the intermetAcarpal scar on metaCARPAL II, with the same mistake also in the abstract; in any case probably absent in Jixiangornis too]. YFGP-yb2 shares the following features with Jixiangornis that are absent in Jeholornis prima: large sized ungual [er, luckily we know this is manual ungual I from the discussion, but is probably untrue in Jixiangornis, difficult to evaluate in any specimen due to claw sheaths and is a small difference anyway] and coracoid with less convex medial margin [true, though the completely concave distal margin is unlike either of them] and less developed external process [true, though contradicting the earlier text Edit: false, as it varies in both species]."

Their discussion merely compares the new specimen, Jixiangornis and Shenzhouraptor with Zhou and Zhang's (2006) diagnosis for Jeholornis prima.  And yes, Zhou and Zhang used a lot of bad characters that are also found in Jixiangornis.  But what about Ji et al.'s diagnosis for Jixiangornis?  What about the differences noted by Yuan (2005), Turner (2008) and Nesbitt et al. (2009)?

This paper is flawed for so many reasons.  It presents incorrect data often.  Several times it contradicts itself, and has frequent grammatical and spelling errors.  The new specimen isn't even described, with only one photo and a schematic illustration.  Very odd features of the specimen aren't even noted- ~16 caudals [Edit: only the first twelve are preserved]; completely concave medial coracoid margin distally; only two non-ungual phalanges on manual digit III [Edit: it actually has three, which are interestingly twice the length of Shenzhouraptor's; the right digit III appears articulated but isn't]; subarctometatarsalian pes [Edit: not different from Shenzhouraptor or Jixiangornis] (the furcular morphology would be way too weird to pass by as well if it were real).  That whole furcular misidentification issue.  Many times facts are brought up that have no bearing on the synonymy issue, as when the new specimen resembles both taxa.  The main argument of the paper is because this specimen shows exclusive features of each taxon, those taxa are synonymous, yet these differences are often ~1% ratios and most proposed differences aren't even mentioned (dentary teeth; caudal count; fused sternum; stratigraphic level; just to take some mentioned by Ji et al., 2002).  There's no attempt to examine the literature for differences between each taxon, let alone the specimens.  The measurement table lacks both IVPP V13550 and palmapenis, not to mention the CAGS Jixiangornis specimen Turner (2008) and Nesbitt et al. (2009) used, and lacks one of the basic measurements mentioned in the text.  Perhaps most sad is they didn't even seem to read the original description of the taxon they're sinking, not citing its diagnosis and citing a matrix coding by someone else instead of a measurement explicitly listed in the description's Table 1.

Luckily, "This file will be reviewed by the authors and editors before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content."  I'm sending this critique to the authors in hope that this paper is fixed before publication, though honestly fixing it destroys its entire point.  Are Shenzhouraptor and Jixiangornis synonyms?  This would require evaluation of over 50 supposed differences mentioned in the literature I noted above, but not by Wang et al..  In the meantime, I think YFGP-yb2 is certainly not Shenzhouraptor, and probably not Jixiangornis (may be a small adult?).  It makes for a more exciting paper in my opinion.

References- Ji, Ji, You, Zhang, Yuan, Ji, Li and Li, 2002. Discovery of an Avialae bird - Shenzhouraptor sinensis gen. et sp. nov. - from China. Geological Bulletin of China. 21(7), 363-369.
Ji, Ji, Zhang, You, Zhang, Wang, Yuan and Ji, 2002. A new avialian bird - Jixiangornis orientalis gen. et sp. nov. - from the Lower Cretaceous of Western Liaoning, NE China. Journal of Nanjing University (Natural Sciences). 38(6), 723-736.
Zhou and Zhang, 2002. A long-tailed, seed-eating bird from the Early Cretaceous of China. Nature. 418, 405-409.
Zhou and Zhang, 2003. Jeholornis compared to Archaeopteryx, with a new understanding of the earliest avian evolution. Naturwissenschaften. 90, 220-225.
Yuan, 2005. Restudy on sapeornithids from the Lower Cretaceous of Yixian County, Liaoning. PhD Thesis. China University of Geosciences. 157 pp.
Zhou and Zhang, 2006. Mesozoic birds of China- A synoptic review. Vertebrata PalAsiatica. 44(1), 60-98.
Turner, 2008. Phylogenetic relationships of paravian Theropods. PhD Thesis. Columbia University. 666 pp.
Nesbitt, Turner, Spaulding, Conrad and Norell, 2009. The theropod furcula. Journal of Morphology. 270, 856-879.
O'Connor, Sun, Xu, Wang and Zhou, 2012. A new species of Jeholornis with complete caudal integument. Historical Biology. 24(1), 29-41.
Turner, Makovicky and Norell, 2012. A review of dromaeosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History. 371, 1-206.
Wang, Dyke and Godefroit, in press. A new specimen of a Jeholornis-like long-tailed bird shows that Jixiangornis is a junior synonym of Jeholornis prima. Acta Palaeontologica Polonica. 14 pp.

Sunday, November 4, 2012

The Theropod Database will be down for a while

Due to a recent move, my Comcast domain will be discontinued starting 11-4, so the Theropod Database will go offline then too.  Luckily, Nick Gardner has offered to host it, but I'll need to get my room and computer set up first, as all of the files are on there.  It should all be back up at a new address some time this week though.  The good news for all of you is that the newly uploaded version will be updated with many new taxa and studies from 2012, which were originally scheduled to go up in December.  The blog will not be affected, as it is hosted by Blogger.

In additional good news, once I'm set up for research again, we can figure out what Chilantaisaurus/Allosaurus/Antrodemus sibiricus is, because contra Chure, Riabinin (1914) did illustrate it.  In all six cardinal positions no less. I can tell you right now that it's not Chilantaisaurus though.

Sunday, October 28, 2012

Did Dromiceiomimus really have long vaned secondaries?

For what will possibly be my last post before the big move (the blog will keep the same address, but we'll see how the Database itself is affected), Zelenitsky et al. (2012) recently reported a somewhat surprising discovery- wings in ornithomimids.

First, note it's not actually Ornithomimus edmontonicus the paper is about.  The supposed secondary shaft marks are from RTMP 95.110.1, which is Dromiceiomimus* samueli.  The other two, being from the Hoseshoe Canyon Formation, are probably D. brevitertius.  For some reason, everybody seems to want to ignore that edmontonicus was named in 1933, while brevitertius was named in 1926 and samueli in 1928.  Zelenitsky et al. follow Makovicky et al.'s (2004) Dinosauria II chapter which synonymized all of these species, but the name would still be brevitertius, not edmontonicus, as both published references state.  Principle of priority people!

 * Russell only placed edmontonicus in Ornithomimus because of its long metacarpal I, and Makovicky et al. did not list any additional justification. Yet O. velox has never been included in a published cladistic analysis as a separate OTU, and when it is (unpublished data), it does not clade with brevitertius (= edmontonicus) or samueli. For instance, O. velox lacks appressed metacarpals II and III and seems to have a medial distal condyle on metacarpal I positioned higher than its lateral condyle, both less similar to Dromiceiomimus than Anserimimus is.

With that out of the way, vaned feathers in ornithomimids shouldn't really be that surprising.  As Martyniuk (online 2012) stated, Currie and Chen (2001) noted Sinosauropteryx's seemingly stage 1 feathers were probably vaned, and there have been a few references since that discovered modern vaned feathers become difficult to diagnose as such after crushing and decay.  So the supposedly simple body feathers we have in e.g. Beipiaosaurus or Scuirumimus may have originally been vaned.  Pelecanimimus does have large paired sterna with ossified ribs and possibly uncinates, so maybe basal ornithomimosaurs were more flight-y anyway.  Not only that, but the seemingly solid position of ornithomimosaurs outside Oviraptorosauria+Paraves isn't quite as definite as it seems.  It's just that basically all recent coelurosaur matrices inherit the character bias and miscodings of the TWG matrix.  So no surprise their topologies are all similar.

I was however surprised that Horseshoe Canyon and Dinosaur Park specimens could preserve feathers.  The two Horseshoe Canyon specimens both show what have been commonly identified as stage 1 or 2 feathers, but which may be degraded state 3 feathers as noted above.  Those on the forelimb are short, but who knows how complete they are.  The Dinosaur Park specimen has been known for a while and is the source of the supposedly adult winged morphology described in the new paper.  This is based on black marks on the radius and ulna which trend posterodistally to distally, and sometimes are U- or hook-shaped as if they had hollow centers.  Now maybe these are feather remains, though I don't know of any other theropod which has preserved feathers this way.  Yet as Mcfeeters noted on the DML, they only show the shaft, not any vane.  Couldn't these just be stage 1 feathers, quills, etc.?  They certainly don't indicate Zelenitsky et al.'s conclusion that adults had long wing feathers while juveniles didn't, as the length is unknown in both (>15 mm in a juvenile; >6.5 mm in an adult).  Sure they're three times wider than the filaments of the juveniles, but the adult is 2.4 times as large, bases of feathers are thicker than other parts, and secondary quills are plausible without vanes.

So while the new paper is interesting in showing Dromiceiomimus had feathers and possibly thick quills/shafts on the lower arm in D. samueli, I don't think it successfully shows the genus had long secondaries, vaned secondaries, or changed its plumage ontogenetically.  This makes their oft-copied figure 4A/B of the little unwinged individual and adult with ostrich-like wings possibly misleading. 

References- Currie and Chen, 2001. Anatomy of Sinosauropteryx prima from Liaoning, northeastern China. Canadian Journal of Earth Science. 38, 1705-1727.

Makovicky, Kobayashi and Currie, 2004. Ornithomimosauria. In Weishampel, Dodson and Osmolska (eds). The Dinosauria Second Edition. University of California Press. 861 pp.

Martyniuk, 2012 online. 

McFeeters, 2012 online.

Zelenitsky, Therrien, Erickson, DeBuhr, Kobayashi, Eberth and Hadfield, 2012. Feathered non-avian dinosaurs from North America provide insight into wing origins. Science. 338(6106), 510-514.

Monday, October 15, 2012

Microraptor hanqingi and Senter's (2011) split

Hi readers.  I've been away due to the fun of unemployment and moving (which might shut down the Database for a short while), but here's a little something I did while deciding whether to make Microraptor/Cryptovolans multiple OTUs.  Though many species and specimens have been described, Senter et al. (2004) synonymized them, which was followed by Turner et al. (2012).  However, Senter (2011) recently reversed his opinion and has M. zhaoianus, the CAGS specimens (20-7-004 and 20-8-001 described by Hwang et al., 2002), M. gui and Cryptovolans all separate.  In addition, Gong et al. (2012) described a new species M. hanqingi which has yet to receive taxonomic commentary.

Senter states "recent personal examination of the holotype of M. zhaoianus (IVPP V 12330), a specimen referred to M. gui (IVPP V 13320), and a cast of the holotype of M. gui (IVPP V 13352) has revealed that the previous assertion that these taxa were synonymous (Senter et al. 2004) is incorrect.  These four OTUs differ from each other in too many character states to be considered synonymous (Table S1)."  Table S1 shows eight characters-

1. Lateral groove on maxillary and dentary teeth. Supposedly present in Cryptovolans but absent in the others.  Yet not only is this polymorphic in most theropods (check Currie et al.'s 1990 illustrations of Saurornitholestes, Dromaeosaurus, Richardoestesia and Troodon for instance), it is present in some teeth of the M. zhaoianus holotype, unpreserved in the M. gui holotype and CAGS 20-8-001, and is indeterminable in photos of CAGS 20-7-004's ~15 preserved teeth.

2. Serrations on maxillary and dentary teeth.  Supposedly present in Cryptovolans and the CAGS specimens (only preserved in 20-7-004) but absent in M. zhaoianus and M. gui.  This is actually present in M. zhaoianus' holotype (Xu et al., 2000) and referred specimen IVPP V13475 (Xu, 2002).  It is unpreserved in the M. gui holotype, though absent in referred specimen IVPP V13320.

3. Fusion of sternal plates.  Present in M. gui's holotype and both Cryptovolans specimens but absent in CAGS 20-8-001.  Unknown in CAGS 20-7-004 and unreported in the referred M. gui.

4. Manual phalanx I-1 significantly longer than metacarpal II.  Supposedly present in the CAGS specimens but not M. gui or Cryptovolans.  However, Hwang et al. state in CAGS 20-7-004 "Phalanx I-1 is very long; it extends almost as far as the distal articulations of metacarpals II and III."  It can be seen in figure 23 to be shorter than the incomplete metacarpal II, while the condition in CAGS 20-8-001 is unpreserved.

5. Manual phalanges II-1 and II-2 together longer than metacarpal II + carpus.  Supposedly present in Cryptovolans but absent in M. gui and the CAGS specimens.  Yet ignoring the carpus, Cryptovolans' paratype has a ratio of 91% and M. gui's holotype a ratio of 102%.  CAGS 20-7-004 has an incomplete metacarpal II so can only be said to have at least 95% and CAGS 20-8-001's ratio is unpreserved. 

6. Arching of first manual ungual.  Supposedly present in M. gui and the CAGS specimens but absent in Cryptovolans.  Yet this is impossible to determine in the Cryptovolans paratype due to the proximal portion of ungual being broken (the holotype's hands are impossible to evaluate in Czerkas et al.'s photos).

7. Strong lip on first manual ungual.  Supposedly present in M. gui and the CAGS specimens but absent in Cryptovolans.  Not only is this variable in other taxa (e.g. Archaeopteryx, Sapeornis, Confuciusornis), it is an illusion in Cryptovolans' paratype caused by the aforementioned broken proximal portion of that ungual.

8. Tibia bowed.  Supposedly present in Cryptovolans but absent in the others. Yet M. gui was originally diagnosed partially on having tibiotarsal bowing, though it is more developed in IVPP V13320 than the holotype.  M. zhaoianus' holotype is also stated to have a bowed tibia by Turner et al., which is true.  That of CAGS 20-8-001 is also bowed (Hwang et al., 2002 figure 28A).  The truth is most Microraptor specimens have some degree of bowing, and Turner et al. proposed the differences are largely taphonomic.

Note a recurring issue is that certain characters are only determinable in one specimen of a species, and there have been no valid characters proposed to e.g. group IVPP V13320 with the M. gui holotype, or group the CAGS specimens together to the exclusion of M. zhaoianus.  The only valid differences noted above are that referred M. gui IVPP V13320 lacks tooth serrations and CAGS 20-8-001 lacks sternal fusion.

Moving on to Microraptor hanqingi, Alexander et al. (2010) used LVH 0026 for their biomechanical work, considering it "probably a different species of Microraptor but is morphologically closely similar to M. gui, including the presence of flight-adapted feathers on the tarsometatarsus" (though remember M. zhaoianus' holotype merely doesn't preserve metatarsal remiges, and may have had them in life). Gong et al. (2012) later described it as the new species Microraptor hanqingi. They diagnosed it based on several characters-

"Largest known species of Microraptor; sternals not fused; robust pubis with squared distal end (more pointed in M. gui) and not as bent backwards as in M. gui; pubic boot tapering posteriorly; ischia with posterior edge straight and ventral edge concave while in M. gui they are sinuous and flat; differs from M. zhaoianus and resembles M. gui in having a proportionally short manual digit I; metatarsals II and IV about the same length (mt II slightly shorter); differs from M. gui in having fewer caudal vertebrae (23)."

The larger size (11-14% larger than M. gui or Cryptovolans) could be ontogenetic or individual variation. Unfused sternals are also present in CAGS 20-80-001 and NGMC 00-12-A, and vary within other species like "Ingenia" yanshini. The pubis is not more robust than in M. gui's holotype, and it cannot be determined if the pubic boot is more squared since most of M. gui's is hidden behind the tibiotarsus. The pubis is indeed bent ~10 degrees less than in the M. gui holotype, but some other specimens lack much bending at all (e.g. IVPP V13475). Contra Gong et al., the ischia of M. hanqingi are posteriorly sinuous and those of M. gui are anteriorly concave, so do not differ in these respects. Additionally, the short manual digit I (83% of mcII) was said to be like M. gui (87%) but unlike M. zhaoianus, and this is true for a referred M. zhaoianus IVPP V13475 (98%) and the Cryptovolans paratype (110%), while NGMC 00-12-A (85%) is also like M. hanqingi and M. gui.  The supposedly longer metatarsal II compared to IV was also supposed to be more similar to M. gui than to M. zhaoianus, but the latter's holotype has a ratio of 98% compared to 91% in M. gui's holotype. Other Microraptor specimens fall between those two ratios, and 7% differences or more are known in other coelurosaur species (e.g. Archaeopteryx lithographica and Dromiceiomimus brevitertius). Finally, its 23 caudal vertebrae are less than M. gui's ~26, but M. zhaoianus' holotype has 24, CAGS 20-7-004 and 20-8-001 have 26 and Cryptovolans has 28-30.  Other maniraptoriform species (e.g. Gallimimus bullatus and Shenzhouraptor sinensis) are known to have individual variation in caudal count within 3-4 vertebrae.

So besides the possibly ontogenetic large size, sternal fusion, pubic curvature, manual digit I length, metatarsal II/IV ratio and caudal number all vary compared to some other specimens.  Variation from other specimens is never significant (e.g. 10 degrees of pubic angle; 2% manual digit I length; one caudal centrum), often falls within the range of other specimens, and most are known to vary within other coelurosaur species.

In conclusion, the problem with splitting the Microraptor-Cryptovolans clade into species is not the absence of variation, as most of the described specimens have some proportions or characters which differ from all or most other specimens (see The Theropod Database's Microraptor entry for more examples, though it's not yet updated with this post's details). Instead, the problem is that these differences don't vary in a systematic, congruent way. While we might argue the Cryptovolans specimens and M. gui holotype should be grouped together to the exclusion of M. hanqingi, CAGS 20-80-001 and NGMC 00-12-A based on their fused sterna, we could equally as well argue the Cryptovolans specimens, M. hanqingi and NGMC 00-12-A should be grouped together to the exclusion of the M. gui holotype and CAGS 20-7-004 based on their long manual phalanx III-1. Or that Cryptovolans, M. hanqingi and CAGS 20-7-004 should be grouped together to the exclusion of the M. gui holotype and NGMC 00-12-A based on their long manual phalanx I-1. There is no obvious answer. One possibility would be to diagnose a separate species for each specimen, and indeed the variation may be due to several different species living in the Jiufotang fauna.  The more conservative approach taken by Senter et al. and Turner et al. is followed here, where differences are ascribed to individual and ontogenetic variation.

References- Xu, Zhou and Wang, 2000. The smallest known non-avian theropod dinosaur. Nature, 408, 705-708.
Czerkas, Zhang, Li and Li, 2002. Flying dromaeosaurs. in Czerkas (ed.). Feathered Dinosaurs and the Origin of Flight. 97-126.
Hwang, Norell, Qiang and Keqin, 2002. New specimens of Microraptor zhaoianus (Theropoda: Dromaeosauridae) from northeastern China. American Museum Novitates. 3381, 1-44.
Xu, 2002. Deinonychosaurian fossils from the Jehol Group of Western Liaoning and the coelurosaurian evolution. PhD Thesis. Chinese Academy of Sciences. 325 pp.
Senter, Barsbold, Britt and Burnham, 2004. Systematics and evolution of Dromaeosauridae. Bulletin of Gunma Museum of Natural History 8: 1-20.
Alexander, Gong, Martin, Burnham and Falk, 2010. Model tests of gliding with different hindwing configurations in the four-winged dromaeosaurid Microraptor gui. Proceedings of the National Academy of Sciences. DOI 10.1073/pnas.0911852107
Senter, 2011. Using creation science to demonstrate evolution 2: Morphological continuity within Dinosauria. Journal of Evolutionary Biology. 24, 2197-2216.
Gong, Martin, Burnham, Falk and Hou, 2012. A new species of Microraptor from the Jehol Biota of northeastern China. Palaeoworld. 21(2), 81-91.
Turner, Makovicky and Norell, 2012. A review of dromaeosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History. 371, 1-206.

Tuesday, September 25, 2012

Bennett's new paper with non-archosaurian pterosaurs

So you all know the basic history of pterosaur affinities.  Viewed as avemetatarsalians since the 1980s, this result has been found in basically every analysis.  Yet Peters (2000) argued they were actually related to non-archosauriforms like Longisquama, Cosesaurus and Sharovipteryx.  Indeed, he now thinks all of these taxa are lepidosauromorphs based on his analysis with too few characters, correlated characters and his ever un-trusty digital segregation technique of determining anatomy.  Peters rightly points out that no analysis has included the above three genera, many use suprageneric taxa, and most only examine archosaurs, so pterosaurs nesting with dinosaurs is an artifact.  Thus so far we have flawed analysis versus flawed analysis, so Bennett's new paper finding pterosaurs to be basal archosauriforms between proterosuchids and erythrosuchids has a chance to help.

Unfortunately, I don't think it does.  The basic premise is that Bennett is checking his 1996 analysis to see if hindlimb characters are causing pterosaurs and dinosaurs to clade together, and reviewing the cursorial characters (the Revised Data Set), then adding more characters and taxa (the Updated Data Set).  One thing I enjoyed about the paper is the speaking style, where Bennett goes against convention and speaks in the first person.  I also like the amount of discussion about coding choice and miscoding, which makes things more transparent.  As an example of both-

"I recently determined that the data set used in the analyses described in that paper differed from that in the published data matrix in that Scleromochlus was coded as 0 for Char. 43, whereas it was coded as missing in the published data matrix. From my present perspective, 14 years later, I cannot determine whether this was a typographical error or an intentional change during revision that was incompletely propagated through the manuscript, but here the published coding (i.e. – for missing) is used."

To cut to the chase, Bennett found the 14 cursorial characters were incongruent with other body areas and responsible for pterosaurs being avemetatarsalians.  Thus, "9 of 14 characters are found to be non-independent of other characters, functioning as inappropriate additional weighting of the underlying characters, and so are subsumed into the remaining characters as they are reformulated."  Once this was done, pterosaurs ended up as basal archosauriforms, with or without the new taxa and characters.

On the surface, this sounds great.  I was just complaining about correlated characters earlier.  But closer examination shows reason to worry.  Let's look at an example, character 112 from the 1996 analysis- "Bird-like distal end of femur – prominent anterior and posterior intercondylar grooves with latter constricted by prominent external tibial condyle. States: 0 = absent; 1 = present".  Well, that's pretty terrible in itself.  If I were to try to code Herrerasaurus for instance, it has a prominent posterior groove, but no anterior groove, and the lateral condyle doesn't constrict the posterior groove.  So we have a composite character that should be split into three.  Let's see how Bennett handles it.  He says-

"Comparison of the knees of ornithodirans sensu Gauthier reveals that they fall into two discrete types. [snip] Because of the presence of two discrete types of double condyle knees, the character needs to be reformulated:
Double condyle knee. States:
0 = absent;
1 = distal femur suboval, somewhat less than twice as broad transversely as long anteroposteriorly, with medial, lateral, and fibular condyles, and the posterior intercondylar groove constricted by the prominent external tibial condyle, proximal tibia and fibula not fused, and proximal tibia subtriangular and its anteroposterior length exceeds its transverse breadth;
2 = distal femur roughly D-shaped, roughly twice as broad transversely as long anteroposteriorly, with only two condyles and medial condyle considerably larger than lateral, posterior intercondylar groove not constricted, and the proximal tibia and fibula fused to form a suboval to subrectangular articular surface roughly twice as broad transversely as long anteroposteriorly,
with the coding as before except that the Pterosauria are coded 2. Because there is no evidence that one state evolved from the other, the character should be unordered for analysis."

That sound you just heard was the cladist in me choking and dying.  Bennett just made the character MORE composite.  In fact, I don't think I've ever seen such a composite character in my entire life.  I don't even know where to begin.  Herrerasaurus again, I suppose.  I guess the distal femur is kind of oval, but the front is flat.  Is that D-shaped as in 2, or does Bennett mean another side is flat in D-shaped femora?  It's 18% wider than deep, which is closer to "somewhat less than twice" than "roughly twice", but that state still doesn't sound right, nor are they quantified to help me if coding a femur e.g. 90% wider than deep.  It does have a fibular condyle, so that's like 1.  The posterior groove is unconstricted though, so that's like 2.  Also note state 1 doesn't define the comparative sizes of the medial and lateral condyles, though state 2 does.  The tibia and fibula are unfused, but what does that have to do with the femur?  It's quite the assumption that pterosaur tibiofibular fusion evolved at the same time as these other features.  The tibia is triangular because it has a cnemial crest.  It's longer than wide proximally, but state 2 compares that proportion in the tibia+fibula, so is not measuring the same thing.  It's not just that Herrerasaurus is some outlier either.  Heterodontosaurus lacks a posterior groove, but has a fibular condyle.  Scleromochlus lacks a cnemial crest, but also lacks tibiofibular fusion. Dromomeron romeri has a femur 71% wider than deep, but a tibia much longer than wide proximally.  This is why composite characters are terrible, and Bennett goes on to make equally horrible characters for the ankle and foot.  Note too that states 1 and 2 each contain plesiomorphic states that are shared with state 0, like the lack of tibiofibular fusion in state 1. 

But besides their terrible, terrible formation, what's really worrying about these characters is how they affect the analysis.  Bennett's basically taking characters that support avemetatarsalian pterosaurs (and in the case of ankle and foot characters, reducing their number), then combining them with perhaps functionally related but indepedent characters that differ between dinosaurs and pterosaurs, so that they can't group pterosaurs with avemetatarsalians.  You could do this with any character or set of characters.  Sure both caenagnathids and oviraptorids have a sliding mandible that lacks teeth and has a coronoid process, but oviraptorids have a mandible that's shorter, lacks symphyseal fusion, lacks the ASC complex, and has a surangular prong.  And I'm sure the sliding glenoid worked in conjunction with the coronoid process somehow and that it's related to their toothlessness.  Time to make that into two unordered states of a single character.  Ugh.  So Bennett eliminated most characters supporting avemetatarsalian pterosaurs and *gasp* didn't recover avemetatarsalian pterosaurs.

Just to round out my complaints, the characters were all ran unordered although many should be ordered (e.g. Parietal foramen. States: 0 = large; 1 = small; 2 = absent.).  Well, actually he states he ran the bistate characters as ordered, despite the fact ordering has no affect on bistate characters.  Also "most loss characters and a few gain characters (Char. 6, 14, 19, 20, 23–26, 28, 36, 41, 53–55, 68, 97, 118, 135, 136) were defined as irreversible".  I guess the humerus can never surround the median nerve and branchial artery again once the entepicondylar foramen is lost (24).  And hey, the antorbital fenestra can never be lost (41).  Who knew alligators were impossible?  In his Discussion, Bennett frankly admits his philosophical differences from most cladists-

"The general trend in phylogenetic analyses of diapsids has been towards analyses with more taxa and more
characters, as if more necessarily equated to better, and Nesbitt’s (2011) analysis is but the most recent. Unfortunately, the usual way to get more characters is to atomise the morphology of structures, coding for more and more insignificant features of structures, which leads to multiple unintentional weightings of the underlying character. Nesbitt’s analysis has 30 characters from the astragalus and calcaneum including, for example the shape of the anteromedial corner of the astragalus: acute or obtuse. It is absurd that the angle of the corner, a few degrees this way or that has the same weight in an analysis as the presence of an antorbital fenestra, a calcaneal tuber or a pteroid bone. I reject such atomisation of morphology, and point out again that most effort should go into formulation and testing of characters, rather than the analysis of the data and manipulation of trees and that one should use characters only if the ‘hypotheses of homology cannot be refuted’ (Gaffney et al. 1991)."

I wholeheartedly agree that we need to spend more time formulating and testing characters, but find the rest laughable.  First, there have been numerous papers showing adding taxa and characters usually results in a more accurate tree, though there are eventual limits to the payoff for both.  Bennett's 19 taxa and 144 characters is nowhere near those limits, needless to say.  What's truly absurd is that Bennett thinks he knows the angle of the anteromedial astragalar corner is less likely to change than the presence of an antorbital fenestra.  How would you even determine that?  Homoplasy?  Well, the corner character never converges or reverses in Nesbitt's matrix, so that can't be the reason.  The number of mutations it takes?  We have no clue about that, and given recent studies showing single genes can have huge phenotypic effects, I think it would be foolish to equate the apparent significance of a character with its phylogenetic worth.  The same issue surrounds his choice to make some characters irreversable.  How does he know which reversals are impossible genetically?  What Bennett is advocating is a return to the good ol' days of "key characters", or in this case key character complexes, which are even worse.

Oh, and Bennett doesn't include Longisquama, Cosesaurus or Sharovipteryx, instead adding two drepanosaurs and splitting Prolacertiformes into Prolacerta and Tanystropheus.  So he doesn't even really test Peters idea, since Peters has been saying since 2000 that those taxa are important for getting pterosaur affinities correct.  And of course he keeps Lepidosauromorpha as the outgroup, so Peters' new idea of lepidosauromorph pterosaurs isn't tested either.  Nor does it include important taxa like lagerpetids, silesaurids and Doswellia.  Bennett's analysis was fine in 1996, but doesn't cut it 16 years later.

So basically Bennett uses an outdated analysis, unfairly eliminates most characters supporting avemetatarsalian pterosaurs, doesn't include the best candidates for non-archosaurian pterosaurs, and espouses a horrible, subjective cladistic philosophy.  I'm still waiting for that good test of pterosaur relationships.

References- Peters, 2000. A reexamination of four prolacertiforms with implications for pterosaur phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia. 106(3), 293-336.

Bennett, 2012. The phylogenetic position of the Pterosauria within the Archosauromorpha re-examined.  Historical Biology. iFirst article, 19 pp.

Wednesday, August 29, 2012

Having your ideas published without attribution, and having your names with priority ignored

Gao et al. (2012) provide an excellent description of DNHM-D3078, a new Sapeornis specimen.  While the illustrations and photos are of high quality and I agree with their main conclusion all "sapeornithids" are synonymous, I'm calling the authors out on two issues.

First, I agree Sapeornis angustis, Didactylornis and Shenshiornis are synonymous with Sapeornis chaoyangensis because it's MY idea.  Gao et al. took it without acknowledgement. 

Compare my blog post from August 2010 to their discussion of Shenshiornis-
"Likewise, the differences between Shenshiornis primita and S. chaoyangensis proposed by Hu et al. (2010) are either mistaken or questionable in light of the holotype’s preservation (LPM B00018). We do not observe the proposed differences in the length of either the prenarial portion of the premaxilla or the maxillary process of the premaxilla (compare with Zhou and Zhang, 2003:fig. 3), the morphology of the teeth (Fig. 3), the number of sacral vertebrae (compare with Zhou and Zhang, 2003:fig. 4), or the length of metatarsals I and V (approximately 25% the length of the metatarsus; contra Hu et al., 2010); in all these respects, the morphology of these characters is the same as in specimens assigned to S. chaoyangensis. Additionally, the degree of tapering of the anterior margin of the ilium of the holotype of S. primita does not differ significantly from that of specimens of S. chaoyangensis. This margin is not preserved in the holotype of S. chaoyangensis and was incorrectly reconstructed as broad and rounded by Zhou and Zhang (2002, 2003). Our examination of other specimens of S. chaoyangensis (e.g., DNHMD1197, DNHM-D2523) indicates that the anterior margin of the ilium of this taxon is thinner and more tapering than that figured by Zhou and Zhang (2002, 2003) and, presumably, the reference used for comparisons by Hu et al. (2010). Furthermore, the caudal series of the holotype of S. primita is so poorly preserved that the alleged presence of 10 free caudal vertebrae cannot be verified. Morphologically, the holotype of S. primita cannot be discriminated from the holotype (or referred specimens) of S. chaoyangensis; the only significant difference between these two specimens is that the former is approximately 28% smaller than the latter."

Or my entry discussing Sapeornis angustiis posted on October 2009 to their discussion of that species-
"Sapeornis angustis was identified as a species different from the larger S. chaoyangensis on the basis of having fewer sacral vertebrae (six instead of the seven described for S. chaoyangensis) and rather subtle quantitative differences (i.e., narrower humeral deltopectoral crest, narrower furcular rami, shorter hypocledium, longer metacarpal I, and shorter pubic symphysis). Nonetheless, considering that the holotype of S. angustis (IVPP V13396) is likely a subadult (as noted by Provini et al., 2009), these differences can be explained as ontogenetic or intraspecific variability. We also interpret other differences to be the result of preservational biases or errors in measurements. For example, the deltopectoral crest of the holotype of S. angustis is comparable to that of the similarly sized DNHM-D3078 in being narrower than that of larger specimens of S. chaoyangensis, and in having a less abrupt distal angle. Such a difference is likely ontogenetic, because juvenile birds tend to have less developed humeral deltopectoral crests (L.M.C., pers. observ.). The proposed narrowness of the furcula is also questionable, because in the holotype of S. angustis this bone is poorly preserved and partially obscured by the right coracoid; therefore, this apparent
difference cannot be ascertained with confidence. In addition, Provini et al. (2009) correctly noted that some sacral vertebrae might be overlapped by the ilium and ischia; therefore, the smaller number of synsacral vertebrae may well be preservational. Perhaps the most striking difference noted by Provini et al. (2009) is the presence of a proportionally longer metacarpal I in S. angustis. However, our observations of the manus of IVPP V13396 indicate that the measurements provided by Provini et al. (2009) are incorrect. Based on our measurements (Table 2), the length of metacarpal I in S. angustis is 25% that of metacarpal II, exactly the same ratio as in the holotype of S. chaoyangensis."

At the same time, I wrote on Didactylornis.  Compare with their discussion-
"The differences used to distinguish Didactylornis jii from S. chaoyangensis are not much clearer. This species was diagnosed as having only two manual digits (i.e., a completely reduced digit III), an elongated first phalanx of manual digit I, and four, instead of five, phalanges in pedal digit IV (Yuan, 2008). However, the manus and pes of the holotype (CDPC-02-08-001) are poorly preserved (Yuan, 2008) and it is reasonable to assume that these apparent differences are taphonomic, particularly when considering the minute size of the digit III of sapeornithids, and the fact that the proximal phalanges of the digit IV of the holotype appear partially overlapped with the distal end of the metatarsals and other pedal digits. In fact, if one were to argue that the first phalanx of manual digit I is as long as claimed by Yuan (2008), this bone would leave no space for metacarpal I (see Yuan, 2008:fig. 1); thus, such argument would lead to the rather startling conclusion that CDPC-02-08-001 retains a digit I when its metacarpal has been completely reduced."

Incidentally, Li et al. (2010) also proposed Didactylornis was a probable synonym, but merely stated "these apparent differences may easily result from poor preservation or damage" without going into detail.  This was received in May 2010, seven months after my posting, but at least it wasn't a major conclusion of the paper or argued with the same points.  Note Gao et al. don't cite Li et al. either (and that the Zhang in each paper are different, so no authors were shared).

Now, I'm aware my writing was not published in a journal, so someone could reply that I have no claim to the idea, since blogs and websites are not "official" literature.  Thus Gao, Chiappe, Chinsamy et al. were free to use my idea without attribution.  But is that really the standard we want in our field?  If a hypothesis and its support are not written in paper peer-reviewed journals, it's up for grabs for anyone else who wants to put it in the latter venue?  Here's an idea- what if workers have the professional courtesy to ask the originator of an idea to be a coauthor?  Or link to their website.  Chiappe used a "pers. obs." in this paper after all, which is even less verifiable.  Or a worse but still more ethical idea- just list the person in the acknowledgements for coming up with that idea.  Speaking of the acknowledgements, I suppose no one in peer review noticed this?  Am I to believe none of the eleven workers responsible for this paper's publication were aware of my writings?  My post is the third result on Google for "Sapeornis Shenshiornis" and the second for "Sapeornis Didactylornis", after all.  My website and the DML aren't exactly obscure among Mesozoic dinosaur workers.

The second issue I have with Gao et al. is even worse in a way, since here they are ignoring published literature.  You know what a discussion of "sapeornithid" taxonomy should include?  Omnivoropteryx.  Can you guess what genus wasn't even mentioned in this paper?  Omnivoropteryx.  Gao et al. use Sapeornithidae when Omnivoropterygidae was named four years earlier.  What ever happened to the ICZN and priority?  Are Gao et al. really immature enough to be spiteful against Czerkas for his terrible ideas and in house journal/book?  We know Chiappe and such are aware of Omnivoropteryx.  The funny thing is that the latter genus actually helps the synonymy arguments since it shows the same proportional trends.  I'll note that the authors of other omnivoropterygids are also guilty of ignoring Omnivoropteryx, and that Provini et al.'s (2009) silence is particularly troubling, as Omnivoropteryx's holotype shares all the supposedly diagnostic characters of S. angustis where they can be observed (small size, short forelimb, low deltopectoral crest with unprojected distal edge, short pubis).  If any of you reviewers ever see sapeornithid or Sapeornithidae in a paper, make sure to do the right thing.

References- Czerkas and Ji, 2002. A preliminary report on an omnivorous volant bird from Northeast China. Feathered Dinosaurs and the Origin of Flight. The Dinosaur Museum Journal. 1, 127-135.

Provini, Zhou and Zhang, 2009. A new species of the basal bird Sapeornis from the Early Cretaceous of Liaoning, China. Vertebrata PalAsiatica. 47(3), 194-207.

Li, Sullivan, Zhou and Zhang, 2010. Basal birds from China: A brief review. Chinese Birds. 1(2), 83-96.

Gao, Chiappe, Zhang, Pomeroy, Shen, Chinsamy and Walsh, 2012. A subadult specimen of the Early Cretaceous bird Sapeornis chaoyangensis and a taxonomic reassessment of sapeornithids. Journal of Vertebrate Paleontology. 32(5), 1103-1112.

Friday, August 24, 2012

Turner et al. 2012- great review, sloppy analysis

Back in October 2011, Turner et al. redescribed Mahakala and included a phylogenetic analysis which basically combined the TWG matrix with Clarke's bird matrix.  This analysis of 102 taxa and 472 characters was not backed up with a matrix or character list in the paper.  However, Turner et al. did state "The character list, data matrix, and supplemental analysis data are available at and at"  Following links from the first page leads to , which didn't and still doesn't have the dataset.  The second page doesn't seem to have links to any datasets.  Emailing Turner resulted in no reply.  I'm very grateful for Norell's help and hospitality during my AMNH visits, but it's concerning to have not only an unavailable dataset, but also false statements in a paper about a dataset's availibility.

Regardless, Turner et al. (2011) stated their dataset was "developed by Turner et al. (in press).", a paper on dromaeosaurid systematics and paravian phylogeny, and theropod workers have been waiting ever since.  Eleven months later, the paper has been published, and this post will contain my thoughts on it.  Having a matrix of 111 taxa and 474 characters, it's actually different than the Mahakala analysis, meaning the latter has STILL not been published.

First of all, it's useful to know the paper is an updated version of parts of Turner's 2008 thesis.  Besides this, the thesis contains the Mahakala redescription noted above, a redescription of Jinfengopteryx's skull, and a description of "Ichabodcraniosaurus" IGM 100/980 (though Turner doesn't name it).  Unfortunately, the thesis has several major issues and these were not altered for the published version.

But before my usual scathing critique, let's look at the good.  The paper provides updated diagnoses for many dromaeosaurids (notable exceptions are Pamparaptor, Itemirus, Luanchuanraptor, Ornithodesmus and Dromaeosauroides among taxa generally thought to belong to the family).  Even better, there are numerous useful photos, including Adasaurus(!!!!) and new material of Utahraptor.  Though why they felt the need to waste 4 of 7 Utahraptor photos on the previously well described and illustrated premaxilla is a mystery.  Now that Adasaurus holotype photos have finally been published, I'm free to distribute mine, so those will be strewn throughout this review.  One juicy fact is "The only description of [Achillobator] is nefarious in that it was published without the knowledge of any of the junior authors based on a preliminary draft left in Mongolia in 1997."  Like Senter (2011), Turner et al. synonymize Tsaagan and Linheraptor, though they do this properly by evaluating the latter's supposed diagnosis.  Overall, this section is excellent.

Skull of Adasaurus mongoliensis IGM 100/20 in posterolateral view.

The phylogenetic analysis is where things start to fall apart.  The good news is it's better than most TWG analyses in ordering most of the characters that need it and having explicit state definitions for the 0 state.  Also, he's improved on the Turner et al. (2007) analysis that added Daspletosaurus in that he now codes its postcranium.  Another good thing is that the crown birds seem genuinely coded and not just assumed to be the same in regard to states usually diagnosing deeper branches.  In general, combining Clarke's bird matrix into the TWG matrix is a great way to quickly and easily give a better look at Mesozoic paravian phylogeny.  But here, it seems to have been done hastily and inconsistently. 

Take the taxon sampling for instance.  Numerous taxa are excluded supposedly because they could not be examined firsthand (Borogovia, Urbacodon, Tochisaurus, Geminiraptor, Sinusonasus, Gansus, Ambiortus, Archaeorhynchus).  Yet other taxa are admitted to be coded based only on literature (Xiaotingia, Xixiasaurus, Liaoningornis, Pengornis, Cathayornis, Concornis, Songlingornis, Baptornis, Hesperornis, Iaceornis, Ichthyornis; 35 included taxa if you trust Appendix 1).  Yet surely a basalmost "euornithine" like Archaeorhynchus is more important to include than a fragmentary possible crown bird like Iaceornis.  Similarly, if the goal is to test paravian relationships, why add taxa like Albertosaurus, Proceratosaurus and Albinykus, but not Yandangornis, Zhongjianornis, Protarchaeopteryx or Falcarius?  The latter is explained in Turner's thesis, where he says since Zanno is examining therizinosaurs, he didn't want to scoop her, but Zanno's papers are all out now and Falcarius was already coded for TWG matrices like Li et al. (2009). 

I mentioned Appendix 1 earlier, which is a list of which references and specimen numbers the authors used and examined firsthand.  But it's clearly wrong.  Daspletosaurus is coded completely, but the two provided references don't allow coding for most of it.  Harpymimus and Garudimimus both have Kobayashi and Barsbold (2005a, b) listed, but those were not used for most of the characters since the TWG codings were taken directly from Norell et al. (2001).  Many taxa have listings which are contradicted in the main text.  I note "Neuquenraptor sp." (near certainly Pamparaptor) is listed here too and was included in the thesis analysis, but not the published analysis.  Oops.  More distressing is that Citipati osmolskae is said to be based on IGM 100/978 and 100/979, but actually the TWG portion of its codings are directly from the IGM 100/42 OTU of Norell et al. (2001).  So that OTU is actually a chimaera.

Cervical vertebrae of Adasaurus mongoliensis IGM 100/20 in right lateral view.

But what about the coding?  First, it's obvious the TWG part of the matrix was just copied from all of the earlier iterations going back to Norell et al. (2001) for most taxa.  So Harpymimus is still woefully incompletely scored despite being well described for seven years now, and Tsaagan is still only coded for the holotype despite Turner synonymizing it with the very complete Linheraptor in this very paper.  Sadly, this paper is the first real TWG example of my favorite pet peeve.  See if you can tell what I mean based on Turner's codings for Tarbosaurus-


Now you don't even have to know what the characters are to see the problem.  Tarbosaurus is known from well described basically complete specimens, so nearly all of those question marks shouldn't be there.  Baptornis is uncoded for almost every non-Clarke-based character.  Patagopteryx is uncoded for many as well.  For the Clarke-based characters, Troodon, Jinfengopteryx, most of Saurornitholestes, the front half of his jinfengopterygine troodontids and the back half of Alxasaurus and Graciliraptor are uncoded.

Turner didn't recover Songlingornithidae, which seems odd since Clarke did.  Wanna know why?  He didn't notice Clarke et al. (2006) accidentally switched a few pectoral characters in their matrix, then partially recoded them himself.  It's just sloppy.

Dorsal vertebrae, sacrum, pelvis and femur of Adasaurus mongoliensis IGM 100/20.

When it comes to understanding Clarke's bird characters and applying them to non-birds, Turner makes some mistakes.  He codes all long-tailed theropods polymorphic for caudal transverse process length (some avians have very short processes on their free caudals, but instead of just comparing long-tailed theropod proximal caudals, I guess Turner coded all their free caudals, which of course start out with long processes that decrease to nothing distally).  Turner "rewords" the alvarezsaurid TWG character of a transversely convex distal ulna (visible in front/back view) with the ornithothoracine Clarke character of a posteriorly convex distal ulna (visible in side view), so that alvarezsaurids and ornithothoracines are both coded as having the same character.  Another example is how he codes the obturator tuber of birds as an obturator process, when birds lack an obturator process (see Hutchinson, 2001 for details).  But then he codes birds as lacking the obturator tuber, leaving it only known in some dromaeosaurids, when actually those dromaeosaurids share the obturator tuber with birds.

Turner's conclusions also seem inappropriate.  Try this one on for size- "On the other hand, only 1 additional step is required to place Troodontidae as the sister taxon to Avialae (fig. 73).  These only slightly less parsimonious topologies could be interpreted as an indication of weakness in deinonychosaurian monophyly. We are inclined to interpret (and think it is more readily borne out by the data) that this is instead a reflection of the overall morphological similarity of the basal members of each paravian clade (e.g., compare Mahakala to IGM 100/1126 or Archaeopteryx)."  But but... the refutation is too obvious to even state.  Interestingly, the quote is straight from his thesis (replacing I with we), so apparently adding Xiaotingia, Anchiornis and other taxa didn't change this number.  As those two genera are the basalmost troodontids in his topology and are very bird-like, it would be quite the coincidence for them to not affect this test, so I wonder if Turner truly did re-run the constraint analysis after the changes were made to his thesis' analysis.

Lower leg and pes of Adasaurus mongoliensis IGM 100/20.  Note the small pedal ungual II is incorrect (Kubota, pers. comm. to Senter, 2012).

Or "Constraining Rahonavis ostromi as a basal avialan requires seven additional steps beyond the most parsimonious topology, and constraining Rahonavis to a more derived placement within Avialae requires 11 additional steps (fig. 79). Taken together with the strong morphological support for the Unenlagiinae clade and strongly unparsimonious nature of an ‘‘avialan’’ Rahonavis, it has emerged that there is no reason to
consider Rahonavis as a problematic taxon."  So six steps is supposedly unambiguous enough to be non-controversial, but he finds Dilong to be closer to birds than tyrannosaurids and it takes twelve more steps to constrain as a tyrannosauroid (as stated in the thesis).  By that logic non-tyrannosauroid Dilong must be incredibly secure.  Ugh.

So my basic message is, the review section is excellent with tons of useful new information, but the phylogenetic analysis is more flawed than most TWG efforts.

References- Turner, 2008. Phylogenetic relationships of paravian Theropods. PhD Thesis. Columbia University. 666 pp.

Turner, Pol and Norell, 2011. Anatomy of Mahakala omnogovae (Theropoda: Dromaeosauridae), Togrogiin Shiree, Mongolia. American Museum Novitates. 3722, 1-66.

Turner, Makovicky and Norell, 2012. A review of dromaeosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History. 371, 1-206.

Thursday, August 23, 2012

Adasaurus' skull!

So Turner et al. (2012) has been published and FINALLY we can see Adasaurus a mere 29 years after it was described.  Was that so hard?  Here's a high resolution photo I haven't been allowed to share, but now that the same view has been published (figure 10A) I can't see the harm.

Skull of Adasaurus mongoliensis holotype IGM 100/20.
Look forward to a detailed review of Turner et al.'s paper tonight.

Reference- Turner, Makovicky and Norell, 2012. A review of dromaeosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History. 371, 1-206.

Thursday, August 16, 2012

When new data appears in creationism papers

Well that title ought to get the views.  You may recall a while back when I complained about Senter not stating his Tsaagan OTU included Linheraptor or his Parvicursor OTU included the Tugrik parvicursorine.  Well, I have to apologize for that because it turns out, Senter did state these things explicitly, but in a paper I didn't know about until this week.  While I'm ultimately responsible for my mistake, since Senter did reference his earlier paper in his Yurgovuchia one, let's look at the form of that reference-

"For this analysis we used the phylogenetic data matrix of a recent study [36], with the following improvements."

I had assumed reference 36 was his 2010 creation paper or maybe the Geminiraptor update, but no, it's a 2011 creation paper.  You know what would have made it obvious?  If PLoS ONE used normal author+date citations instead of numbers.  This part is not a criticism of Senter at all, but instead of PLoS ONE.  While I strongly support that journal and will no doubt submit there myself in the future, the citation system has got to go.

Another aspect of this situation is somewhat Senter's fault, which is that a paper designed to combat a creationist claim is the source of a major overhaul of an important dinosaur matrix.  In fact, it's worse than that.  Senter already included new information in his original 2010 anti-creation paper, yet this one is a response to Young Earth Creationist Todd Wood's critiques of the earlier paper, and completely overhauls the matrix.  I'm all for scientists engaging with creationists, but it's an odd venue to debut important scientific information.  The DML had never even noticed the paper, so I had to learn of it through a Tetrapod Zoology comment.  Again, I would have learned about the paper if I would have looked up reference 36 in the Yurgovuchia paper, so it is ultimately my fault.  But don't you think "Using creation science to demonstrate evolution 2: morphological continuity within Dinosauria" is an odd paper to propose the synonymy of two dromaeosaurids, or to add 38 new characters to your analysis and renumber every character?

Readers' thoughts?

Monday, July 23, 2012

Resolving why Confuciusornis has a modified wireframe nearly identical to juvenile Alligator

In my last post, I took Bhullar et al. (2012) to task for 1) their choice of Confuciusornis as being a close match in analyzed skull shape to juvenile Alligator; 2) Bhullar's own online statement it wouldn't matter which basal bird they used, since the Catalan enantiornithine embryo and others would come out very similarly; and 3) why their wireframes vary so much from the specimens themselves.  After communicating with Bhullar, we have answers to these issues.

Number three is easiest, and works to explain the rest.  As Bhullar explained (and Rodriguez noted on the DML), the wireframes in the paper are not actually the raw wireframes that result from placing landmarks on photos.  Instead, they are a combination of principal components.  Now morphometrics is not my thing, but as I understand it, Principal Component 1 is the horizontal variation in landmarks and Principal Component 2 is the vertical variation in landmarks, once the skulls have been resized and rotated to best agree with each other.  As their figure S6 below shows, each component has a hypothetical extreme on each end.  On each axis, a certain line will change from one extreme to another.  So on PC1, you can see the naris moving further back going left to right.  However, some features weren't common or consistent enough to show over those features that explain most of the variation.  So you'll notice nothing in any extreme has a large naris, since that didn't vary consistently with the main horizontal or vertical changes.  And that's why the Confuciusornis and juvenile Alligator both have modified wireframes with small, partially retracted nares- most of their horizontal measurements fall out to average a PCI of ~0.08-0.10, and at that (and every) point in the graph, skulls have small and partially retracted nares.  So you take the average wireframe of skulls on a certain point of the PC1 axis, and mix it with the average wireframe of skulls on a certain point of the PC2 axis, and ta-da!, you have your modified wireframe that doesn't really resemble the original much at all.

Bhullar said he should have noted this in their paper (especially in the oft copied figure 4 which purported to show the "nearly identical skull configuration" of Confuciusornis and juvenile Alligator, with almost complete overlap of every line) and I said I shouldn't have called his data seriously flawed before confirming his methods.  We've both apologized and are happy with how things turned out.  Bhullar sent me his Confuciusornis and juvenile Alligator raw wireframes, and while I would place a few points differently, they're accurate overall.  The above discussion also shows what Bhullar meant when saying the choice of Confuciusornis over e.g. the Catalan nestling wouldn't matter, since it's very close in PCA morphospace.  The reduced antorbital area of Confuciusornis doesn't factor in, since on average, taxa in that area of the graph don't have such reduction, so the PCA average wireframe the computer uses for Confuciusornis doesn't either.

So then, despite their wildly varying anatomy, Confuciusornis and juvenile Alligator are getting similar PCAs.  What actual anatomy is controlling most of the variation?  We both hypothesized that most of the variation is simply due to the general skull outline.  You'll remember from before that the snout length and slope match almost perfectly, and the braincase is just a little more expanded in Confuciusornis (though perhaps due to crushing). 
To test this, I suggested Bhullar eliminate all but the major landmarks outlining the skull- 1, 2, 3, 4, 16, 23, 24, 25, 29, 40 and 43.  He ran this reduced analysis based purely on the skull outline and found very similar results.
PCA plot by Bhullar using only 11 landmarks, all defining the lateral skull outline.  Figure shown upside down to more easily compare to their figure S6 above.  Juvenile Alligator highlighted in blue, Confuciusornis in brown.  Other taxon-number correlates given below.
Note Confuciusornis and juvenile Alligator as about as close as they are when all 45 points are analyzed, showing Bhullar et al.'s analysis mostly compared gross skull shape.

And that's that.  As I said at the beginning on my first post, I agree with their main thesis- that bird skulls are paedomorphic.  Before ending, I'd like to thank Bhullar for how gracious he has been toward me and my critique.  As he said in an email, such criticisms and responses are how science should work.

Supplementary data- 

Numbers representing each skull in Bhullar's reduced PCA plot.
ID=01 Alligator adult
ID=02 Alligator embryo
ID=03 Allosaurus adult
ID=04 Anchiornis adult
ID=05 Archaeopteryx adult
ID=06 juv Archaeopteryx
ID=07 Bambiraptor
ID=08 Byronosaurus adult
ID=09 Ceratosaurus adult
ID=10 Citipati adult
ID=11 Citipati embryo
ID=12 Coelophysis juvenile
ID=13 Coelophysis adult
ID=14 Compsognathus adult
ID=15 Confuciusornis adult
ID=16 Dilong adult
ID=17 Dilophosaurus adult
ID=18 Dromaius adult
ID=19 Eoraptor
ID=20 Erlikosaurus adult
ID=21 Eudromia adult
ID=22 Euparkeria adult
ID=23 Gallus adult
ID=24 Gallus juvenile
ID=25 Garudimimus adult
ID=26 Gorgosaurus adult
ID=27 Guanlong adult
ID=28 Herrerasaurus adult
ID=29 Incisivosaurus adult
ID=30 Majungasaurus adult
ID=31 Monolophosaurus adult
ID=32 Scipionyx juvenile
ID=33 Suchomimus adult
ID=34 Tarbosaurus adult
ID=35 Tarbosaurus juvenile
ID=36 therizinosaurid embryo
ID=37 Tyrannosaurus adult
ID=38 Tyrannosaurus subadult
ID=39 Tyrannosaurus large adult
ID=40 Velociraptor adult
ID=41 Zanabazar adult
ID=42 Haplocheirus adult
ID=43 enantiornithine juvenile
ID=44 Pengornis adult
ID=45 Shenqiornis adult
ID=46 Struthio adult
ID=47 Struthio juvenile
ID=48 Yixianornis adult
ID=49 Pterocles adult
ID=50 Chauna adult
ID=51 Opisthocomus adult
ID=52 "Byronosaurus" perinate