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.

Martyniuk's "A Field Guide to Mesozoic Birds and Other Winged Dinosaurs" is out, and while most of it is in the form of a popular field guide, it's also filled with a ton of new phylogenetic definitions and some new taxa.  A review of the entire book is in the pipeline, but let's look at this one section of it today.

Aviremigia is officially proposed (note Gauthier and de Quieroz only conditionally proposed it), though contra Martyniuk, the latter would near certainly have used Vultur not Passer, as in all of their bird-based clades.  Since we still don't know how far towards the base of Maniraptoriformes remiges and retrices extend due to possible taphonomic effects, proposing this apomorphy-based clade still seems premature.

We get a definition for Chuniaoae as the oviraptorosaur+paravian group (in most topologies), so we finally have a name for that.  I can't help but think my discussion of this name on the Database is responsible, which I regret a bit as it is such a terrible name and wasn't intended to be so inclusive (it was named as an avialan clade including Caudipteryx+birds).

Caenagnathiformes is defined, and while it is older than Oviraptorosauria, there are no rules saying it must have precedence, and Oviraptorosauria has had basically universal acceptance.  I can't see this being adopted, so I have to wonder why it was proposed.

Caenagnathinae is defined as (Caenagnathus collinsi< Oviraptor philoceratops, Avimimus portentosus), but is rather useless in a topology like mine where Avimimus is a caenagnathid. Ditto for Avimimidae being (Avimimus portentosus< Oviraptor philoceratops, Elmisaurus rarus, Caenagnathus collinsi). Elmisaurinae is used in the next section as sister to Caenagnathinae, but is never defined.  Note that position would make Elmisaurus a caenagnathine in Martyniuk's phylogeny.

Ornithes is proposed for Aves sensu Chiappe- (Archaeopteryx lithographica + Passer domesticus), which is nice to have.

We get a definition for Nicholson's 1878 name Saurornithes (Archaeopteryx lithographica< Passer domesticus), but I pretty strongly disagree with this. It's a synonym of the earlier named Archaeopterygidae (1871; using Xu et al.'s 2011 definition) if Archaeopteryx is avialan or basal to Eumaniraptora; or if Archaeopteryx is deinonychosaurian, it's a synonym of that clade. Though named far before Deinonychosauria, it's not nearly as widely used or well known, and if priority is what matters, why not use the even earlier Sauriurae (1866), which is also better known and used due to BANDITs?

Ornithodesmiformes (Ornithodesmus cluniculus, Dromaeosaurus albertensis, Troodon formosus< Archaeopteryx lithographica) is another name I'm unhappy with.  While I agree Ornithodesmus is probably a dromaeosaurid and Ornithodesmidae has priority over Dromaeosauridae, the need for linked subclades doesn't exist in Phylocode and the ICZN doesn't cover taxa higher than family level.  It's potentially useful when we have basal deinonychosaurs, and Ornithodesmus probably is a member, but there are more secure names that could have been chosen.

I DO like Troodontinae (Troodon formosus + Saurornithoides mongoliensis) though, which has been needed for a while.  Problematically, Saurornithoidinae is listed as a taxon of equal rank in the next section, though it would be a synonym and has never been proposed before.

Ornithodesmidae is used in place of Dromaeosauridae as it was named earlier and defined as (Ornithodesmus cluniculus< Archaeopteryx lithographica, Passer domesticus, Paronychodon lacustris, Pterodactylus antiquus). I'd guess Paronychodon stands in for Troodon as the latter was not named in 1913 when Ornithodesmidae was proposed. The ICZN does give Ornithodesmidae priority, but as it is never used (and not everyone accepts Ornithodesmus is a dromaeosaurid, though their published reasons have been invalid) I would rather the ICZN be petitioned to sink it.

Microraptorinae is defined as a less inclusive microraptorian clade- (Microraptor zhaoianus< Sinornithosaurus millenii, Dromaeosaurus albertensis).  It's useful if Cryptovolans is separate, but otherwise not so much until microraptorian phylogeny is better understood. Also note Turner et al. (2012) already defined this clade as a junior synonym of Microraptoria.

Itemiridae (1976) is defined as (Itemirus medullaris< Dromaeosaurus albertensis, Stenonychosaurus inequalis, Tyrannosaurus rex), which is seemingly to replace Velociraptorinae from 1983. Indeed, it is only referred to in the text as 'itemerine', and Itemirinae is proposed in the next section (which makes that a new name). I'm at a loss why Stenonychosaurus was used this time, as Troodon was named long beforehand and the fact the Stenonychosaurus holotype preserves a braincase wouldn't seem to matter for any part of Phylocode. I think using Itemiridae/inae is a bad choice, as only one analysis has placed Itemirus in Velociraptorinae, and this was only based on one character (basioccipital tubera with distinct, ovoid depressions on the caudal surface).  There are other characters that contradict this, and Miyashita (2011) even found it as a tyrannosauroid in his analysis.

Kudos to Martyniuk for recognizing Omnivoropterygidae/-iformes has priority over Sapeornithidae/-iformes.  Yet his solution puts us in an awkward situation, as he defines Omnivoropteryiformes, but ignores the family (though only the family is used in his taxonomic table).  And yet the family (as Sapeornithidae) is used more often than the order by authors, the ICZN doesn't recognize priority of order-level taxa (so really only the family's priority is mandated), and this is the first definition ever applied to any of these groups AFAIK. So if we want to follow the defined clade name, we have to use a synonym which is barely used AND non-mandated, and not of the same level as the term most authors use. Ack.

I like Martyniuk defining Confuciusornithiformes as (Confuciusornis sanctus< Enantiornis leali, Passer domesticus), since Confuciusornithidae has been defined as (Confuciusornis sanctus + Changchengornis hengdaoziensis) by Chiappe et al. (1999). Other authors (e.g. Zhang et al., 2008) have largely ignored the definition.

Martyniuk defines a LOT of enantiornithine clades, though I don't think our understanding of enantiornithine phylogeny justifies this yet.  For instance, using O'Connor and Zhou's (in press) topology, Iberomesornithiformes, Eoenantiornithiformes and Eoenantiornithidae are all monotypic, Longipterygiformes includes Longipteryx and the probably synonymous Boluochia, and Cathayornithiformes includes Neuquenornis, Eoenantiornis, Conornis, Eocathayornis, Liaoningornis and Eoalulavis in addition to Cathayornis.  I do like that he uses Cau and Anduini's definition of Avisauridae for Avisauroidea, since Avisauridae had been previously defined differently.

Patagopterygiformes is defined, which isn't too useful as no taxa have been found in published analyses to clade with Patagopteryx.  Sure Alamitornis, Kuszholia and Gargantuavis have been proposed, but surely it's better to need a clade before you define it.

Defining Chaoyangiformes is about as useful as those enantiornithine clades, since Chaoyangia's position among 'euornithines' hasn't been established.

Defining Songlingornithidae as (Songlingornis linghensis< Chaoyangia beishanensis, Passer domesticus) works as long as Chaoyangia isn't one, which it seems not to be.  However, defining Yanornithiformes as (Yanornis martini< Passer domesticus) seems like it should be a low priority until there's good evidence Yanornis isn't a songlingornithid.

Similarly, defining Ambiortiformes is nice (Ambiortus dementjevi< Passer domesticus), but then defining Apsaraviformes as a junior synonym in his own topology (Apsaravis ukhaana< Passer domesticus) is just odd.

Martyniuk defines a misspelled Odontolcae (as Odontoclae) as (teeth set in grooves as in Hesperornis regalis). Well, enantiornithines, Yanornis and outgroup avialans have teeth set in sockets (as may Gansus), but Hesperornis and Ichthyornis have them set in grooves.  Aves lack teeth so are inapplicable, which leaves us uncertain where to apply the name, even if we knew the relationships between Hesperornithes, Ichthyornis and Aves, which we don't.  So why ressurrect a name originally idealized as what we call Hesperornithes (Ichthyornis was in Odontormae) and give it a definition which can't be applied to a specific node given our current information?

He defines Odontornithes as (Ichthyornis anceps, Hesperornis regalis< Passer domesticus), but doesn't actually support the clade.  Hmm.  As a nitpick, if Martyniuk's goal was to choose taxa known when the clade was named, I. anceps was still placed in Graculavus in 1873 when Odontodornithes was named, and was not recognized as an odontornithine at the time, so I would have chosen I. dispar.

Hesperornithiformes is defined as (Hesperornis regalis + Enaliornis barretti), which is basically identical in composition to the stem-based Hesperornithes in most(every?) published phylogeny.  Even worse, we don't know how Potamornis and Pasquaornis relate to Enaliornis, nor if the three species of Enaliornis form a clade exclusive of Hesperornis.  So Hesperornithiformes is quite unecessary at the moment.  The same could be said of Enaliornithidae (Enaliornis barretti< Hesperornis regalis).

Based on my phylogeny for hesperornithines, Brodavis (if it includes varneri) falls within Hesperornithidae, so Martyniuk's definition for Brodavidae (Brodavis americanus< Hesperornis regalis) is not only redundant with Brodavis but inside another family.

I like Hesperornithoidea for the (Baptornis advenus + Hesperornis regalis) clade, but I should note Schufeldt (1903) originally named it for more inclusive clade also including Enaliornis.

A definition for Baptornithidae is nice I suppose, but there are no definite members besides Baptornis advenus, so it's redundant currently.

A definition for Gansuiformes is also redundant at the moment.

We already have the older clade Ichthyornithes defined as (Ichthyornis dispar< Struthio camelus, Tinamus major, Vultur gryphus), why define the newer Ichthyornithiformes as (Ichthyornis anceps< Hesperornis regalis, Gansus yumenensis, Passer domesticus)?  I agree including Hesperornis as an external specifier is good, but why not just ammend the definition of Ichthyornithes?  Also, the type species Ichthyornis dispar should be used in a definition based on Ichthyornis, even if I. anceps is a senior synonym.

I have no issue with his new definition for Anseriformes.  Anatoidea should be based on Anas platyrhynchos though, not Anser anser.

The suggested definition for Gaviiformes (crown Gavia immer< Podiceps cristatus, Passer domesticus) would include all of Natatores, Gruiformes, Cuculidae, etc. under molecular phylogenies.

The definition for Charadriiformes (crown Charadrius hiaticula< Passer domesticus) might work, but might also include Natatores, Gruiformes, etc. as well.

So overall, we have some useful definitions (Chuniaoae, Ornithes, Troodontinae, Confuciusornithiformes, Songlingornithidae, Ambiortiformes, Hesperornithoidea), but a large number are currently redundant and some don't even define clades he thinks are valid or are synonyms of other clades he defines.  Others don't have a clear use, as phylogenies of relevent taxa are still in flux.  The emphasis on oldest names is admirable in a way (and I fully support action to either use or officially suppress them for family level taxa), but when not mandated by the ICZN it just causes confusion (following Martyniuk's logic, we would use Goniopoda for Theropoda, Opisthocoelia for Saurischia, etc.).  Martyniuk does do a good job defining most clades though, using eponymous genera and type species for most.

Stay tuned for my feelings on the rest of the book.

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

We all know Martyniuk published his field guide of Mesozoic oviraptorosaurs and paravians last month.  How does it hold up?  I was happily surprised to see I was listed (second!) in the acknowledgements and that my Theropod Database is referenced and extensively consulted (though as the website address will change soon, that was unfortunate timing).  I'll try not to let that affect the amount of scathe expected in one of my reviews. ;)

When I was little, I would read field guides instead of story books, and loved the Peterson guides due to their completeness and illustrations.  More than once I started drawing my own, but I don't think I ever got past the grebes (second only to loons in all American field guides, which I now know goes back to Gaddow [1893] and Wetmore and Miller [1926]).  Similarly, I loved Sattler's (1983) "The Illustrated Dinosaur Dictionary", which while not quite in field guide format, did have detailed sequential entries for every dinosaur genus and illustrations of most.  So this book is appealing on a nostalgic level, despite [mostly] not being something I would return to for new technical details.  It's also hot on the heels of Paul's "The Princeton Field Guide to Dinosaurs", which I reviewed and will ellicit comparison.

If any word describes this book, it's 'progressive'.  Ideas are all completely up to date (e.g. the ornithomimid feather paper is used) and the phylogeny is quite good (I don't agree with it all, but it's all well referenced), but it's more than that.  Clades are italicized as if Phylocode were standard already.  Unpublished references are used, and many details which are probably correct but not in the literature yet are used without comment.  Combined with the field guide format, it really does seems like a book written from some enlightened future where we know much more than now.


As a field guide, this is very good.  The restorations are beautiful and extremely believable.  These are some of the only dinosaur illustrations I've seen that seem like real animals.  The coloration and plumage differences between taxa are all just what I'd expect based on recent birds.  If I didn't know better, I'd figure a time machine were involved.  More importantly, the details given to distinguish each species are numerous and accurate.  They almost always reflect what could actually be seen in life.  The habits are almost always stated with the proper amount of uncertainty, and usually explicitly supported by some anatomical detail.  I found these very interesting, as I normally don't think much about the functional reason for differences between taxa.  The use of common names for each species also adds to the illusion these are living creatures and not just objects of scientific study, though as expected of a field guide, scientific names are also provided along with habitat and distribution (both temporal and geographic).

I do have a few issues with it as a field guide.  As in Peterson's guides, arrows point to some distinctive features in the illustrations.  But in Peterson's, these features are italicized in the text and the arrows can overlap the illustration to point out a particular point, so you know exactly what to look for and where it is.  Martyniuk doesn't distinguish arrowed features in the text, and the arrows end a ways from the illustration.  This results in the arrows being almost useless ("so its wing... or maybe chest... is distinctive in some way... hmmm").  Also, sometimes (at least 21 times to be exact) internal anatomy is mentioned as distinctive, but while the details are correct, they aren't things any paleo bird watcher would be able to see ("Is this an Elmisaurus or a Chirostenotes? Time to shoot it and break out the hack saw to check the metatarsal III cross section").  So this takes one out of the feeling this is a field guide instead of an encyclopedia/dictionary.  Another problem is that when more than one individual is shown, it's not immediately obvious what each is representing.  The text usually clears it up, but Peterson's guides contain handy sex symbols, "imm.", "juv.", "adult", etc. so that you immediately know what's shown.  The situation is uncommon in Martyniuk's guide since this kind of variation is known in so few Mesozoic maniraptorans, but it's still an issue.  Finally, it's not always stated when species are based on young individuals (e.g. Microvenator, Eoconfuciusornis), which at least affects size and often other characters.


Scientifically, the book is highly accurate and is probably the best general text on bird origins that exists.  Paul's DoA is more detailed, but also older, more heterodox and a bit daunting to the casual reader.  One way in which Martyniuk's book is heterodox is its use of certain older yet not currently used clade names.  Some are correct according to ICZN rules (Deinodontoidea, Ornithodesmidae, possibly Itemirinae), and these I fully support either using or petitioning the ICZN to officially suppress them.  I should note though, that the ICZN also says if a family contains subfamilies, one has to be eponymous.  Martyniuk doesn't use an Ornithodesminae (and indeed it would be difficult given the uncertain position of Ornithodesmus within Eudromaeosauria), but why stick to one inconvenient rule if you don't follow another?  Other names (Ornithosuchia for avemetatarsalians, Segnosauria, Caenagnathiformes, Saurornithes, Odontoclae) aren't covered by the ICZN, and while I like Martyniuk's sentiment in wanting older names to retain priority, I think these are a lost cause.  If we're going back to 1800's names, we should be calling Theropoda Goniopoda.  I'm not for an Ornithosuchia which does not contain Ornithosuchus, so would reject that name.  I do regret Segnosauria's loss to Therizinosauria.  But Clarke (2004) brought Ichthyornithes back for Ichthyornithiformes, so maybe there's some hope?  Other names used are not standard, like Metatheropoda, Aviremigia and Chuniaoae.  Ditto for his new combination Saurornitholestes explanatus, which is based on and credited to me.  Yet as I state on the Database, while I do think Laelaps explanatus is probably synonymous with Saurornitholestes langstoni, I don't formally synonymize them "because from the limited description, explanatus is indistinguishable from not only Saurornitholestes, but Bambiraptor and Velociraptor as well. It is only referred to Saurornitholestes due to provenance."  I like being credited for the idea, it just hasn't been shown to be correct yet.  Overall, these heterodox names are just an odd thing to include in a field guide.  They add to the impression the book is from a different time where new standards are followed, but will not be good for unfamiliar readers who don't realize this area of the book represents Martyniuk's hopes instead of current thoughts (whereas while the Database uses e.g. Chiniaoae, I also explain its obscure origin).  The fact Martyniuk erects a few new taxa (Ornithes, Ornithodesmiformes) and provides new definitions for many is also odd for a field guide, which are generally popular works where no new science is presented.  The taxa and definitions are a mixed bag, with some being quite good but others quite bad, and my earlier post goes into those details.  Above I mentioned that many unpublished ideas are used without comment, and quite a few of these are mine (Dromiceiomimus brevitertius being the right name for Ornithomimus edmontonicus, Zhongornis as a juvenile confuciusornithid, Omnivoropterygiformes having priority over Sapeornithiformes, Ichthyornis anceps being the correct name instead of I. dispar, possibly oviraptorosaurian Kuszholia, microraptorian Richardoestesia, dromaeosaurine Zapsalis, lithornithid Limenavis, etc.).  On the one hand it's nice to have these out there and know people are listening to my ideas, and at least they aren't presented with arguments in technical papers.  Still I would have liked credit for the more certain, creative ones, though I was acknowledged extensively in the book (my hesperornithine phylogeny which predated O'Connor and Zhou's, my idea on Dapingfangornis' supposed horn, my belief Yungavolucris may be synonymous with Elbretornis based on size).  Jaime will be happy with some common names used for oviraptorids, like mitre-crested egg seizer and big-beaked shell thief.


While most of the information is accurate, there are some details I think are incorrect or unknown, mistakes, etc. in addition to the uncommon misspellings and such.  Yet these issues are rare considering the vast amount of information in the book.
Martyniuk states "the snout of T. formosus would be more pointed at the tip as seen from above [than Saurornitholestes]", which I think was just a mistake, since the Troodon entry states it has a broad snout.

Not an error per se, but I notice Yixianosaurus is still in the basal oviraptorosaur cladogram but not mentioned in the text.  No doubt it was accidentally left there after Martyniuk removed its entry, based on his blog post.
Incisivosaurus gauthieri is stated to be a probable synonym of Protarchaeopteryx robusta, but I don't think this has ever been suggested.
Skull details are given for Caudipteryx dongi, but it only preserves a frontal and pterygoid.
Microvenator is stated to be found in Oklahoma and Wyoming in addition to Montana (where the holotype was found), but only the holotype is known. It's also said to have a short tarsus, but only metatarsal I is preserved.
Chirostenotes elegans is presented as being a sexual variation of C. pergracilis.  I'm not sure why recent authors are trying so hard to dissociate elegans from Elmisaurus, but they really do share characters.  Note for example elegans doesn't have the diamond-shaped metatarsal III proximal section of C. pergracilis, which is even listed as a characteristic of the latter species by Martyniuk.  Instead, the section is triangular as in E. rarus.
Paul's (2010) ideas on oviraptorid synonymy are given credence (though not followed), but are highly unlikely, even moreso given the recent osteology of Khaan (Balanoff and Norell, 2012) which details numerous differences from the Citipati holotype.

Cryptovolans' habitat and distribution are obviously supposed to be those of Hesperonychus, which was seemingly cut from the main section and accidentally not added to the end list of poorly known taxa.
Dromaeosaurus is described as having "Legs relatively long compared to contemporary S. explanatus. Tail more flexible than most other eudromaeosaurians.", but these areas are unknown.  Indeed, Currie (2005) states some RTMP postcrania might be referrable to the genus because it is more robust than Saurornitholestes.
"Sickle claw very small" is listed as a feature of Adasaurus, but it turns out this is wrong (Kubota pers. comm. to Senter, 2010).
Timimus is listed as an unenlagiine, but was more recently determined to be a tyrannosauroid (Benson et al., 2012).
Buitreraptor was listed as having "wing claws short & digits nearly equal in length. Hand unusually short relative to very long humerus & radius/ulna." Yet this is based on the mount, which inaccurately restored the known fragments, which don't indicate any such morphology (Gianechini pers. comm.).
The tiny troodontid skulls from the Citipati nest are referred to Byronosaurus, but I believe the TWG team currently believes they belong to a more basal taxon like the Zos Canyon ?jinfengopterygiine (I'm sure I read this, but can't recall the source; they've gone back and forth so much on this).
"Legs long & slender." was listed as a trait of Zanabazar, but the preserved distal tibiotarsus and proximal tarsometatarsus leave this unknown.
Regarding Philovenator, "Additional specimens from the same time & general area, known as the “Zos Canyon Troodontid”, are probably the same species (Mortimer 2010)." It is nice to be credited, but I actually only "tentatively referred" them to the same species.  Since 2010, Philovenator has been redescribed and we have info on IGM 100/1280 (Zos Canyon specimen) and 100/1323 (both in Turner et al., 2012).  So the idea could use reevaluation.
Euronychodon is in quotes, as is the genus of Paronychodon caperatus.  I'm note sure of the rationale here.

Martyniuk states the "Diet is unknown in [Confuciusornis sanctus]" but consumed fish are preserved in one specimen (Dalsatt et al., 2006).  It could be argued this is a different species as it is from a younger formation and shares a mandibular similarity with C. dui (as I state on my blog), but this is not elaborated in the book.
An "upturned bill tip" is stated as distinctive for C. dui, but is a keratinous bill actually known in C. sanctus?  Even C. dui's premaxilla lacks an upcurved tip, after all.
Shenquiornis "Lacked procoracoid bones".  Oops!  Clearly just a typo.
Piksi, Palaeocursornis and Eurolimnornis are apparently pterosaurs (Agnolin and Varrichio, 2012), but this is forgivable as it was not published until after the book.


So overall this is an interesting book.  As a field guide, it is quite good, far better than Paul's, but still falling short of Peterson's.  It's so up to date it could be from the future, but the illustrations will make you think the author had access to the past.  As a popular reference to bird origins, it is perhaps unmatched in quality, from feathers, to beaks to wings.  It's even pretty good as an encyclopedia of maniraptorans for non-experts, since those rarely use internal details anyway.  More questionable are its attempts to add to the repository of science.  Some of the suggestions are good, others I dislike, but a field guide feels like the wrong place to publish them regardless.  The price of the physical book ($36.99) is quite steep considering Peterson's field guides are $20-26, larger, and far more useful since Martyniuk's species will never actually be seen in the field.  Similarly, though Paul's field guide is worse content-wise, it does contain skeletals, the whole range of Mesozoic non-pygostylian dinosaurs, and is hardcover at $35.  But as a fun and educational introduction to the species of Mesozoic oviraptorosaurs and paravians, I can easily recommend the pdf version at its low price of $9.99.  Thanks to Matt for trying this fascinating format!


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

As several of you noticed, my old Comcast account finally died and the Database went with it.  Nick Gardner was nice enough to provide me space on his domain, which sounds much cooler- http://archosaur.us/theropoddatabase/ .  The site there has been updated over the last year as well-

Megalosaurus? monasterii, Camarillasaurus, Ostafrikasaurus, Eoabelisaurus, Ichthyovenator, Piatnitzkysauridae, Sauroniops, Bicentenaria, Sciurumimus, Hexing, Alnashetri, Martharaptor, Philovenator, Sulcavis, Brodavis americanus, B? baileyi and B? mongoliensis were added. "Megalosaurus" woodwardi, "Dilophosaurus" sinensis, "Megalosaurus" insignis, "Megalosaurus" pombali, Ozraptor, Walgettosuchus, Kryptops, Kaijiangosaurus, "Megalosaurus" pannoniensis, Marshosaurus, Streptospondylus? cuvieri, "Tyrannosaurus" "lanpingensis", Erectopus, Yangchuanosaurus, Iliosuchus, "Allosaurus" sibiricus, Rapator, Scipionyx, Timimus, Sinovenator, Sinornithosaurus, Microraptor (including the immediately synonymized M. hanqingi) and Adasaurus were updated significantly. Carrano et al.'s (2012) HUGE Tetanurae paper was incorporated, which revised numerous non-coelurosaurian tetanurines and changed their phylogeny. It also added phylogenetic commentary and many unnamed specimens, though I have yet to finish the latter section. Turner et al.'s (2012) dromaeosaurid information was incorporated, as was Martyniuk's (2012) nomenclature and definitions.

Check it out.  Thanks for everyone's interest and support!

As we discussed before, David Peters' amniote analysis finds an odd topology for dinosauriformes.

--Theropoda including Marasuchus, Herrerasaurus and Trialestes
--- Panphagia+Pampadromaeus
---- a clade of Pisanosaurus, poposaurs and silesaurids
----- Sauropodomorpha including Saturnalia, Thecodontosaurus and Massospondylus
------ Daemonosaurus + standard Ornithischia

Why is this?  I set out to determine the reason.  First, I deleted most taxa Peters finds outside Dinosauria, leaving Turfanosuchus and Gracilisuchus as outgroups, as they are close to the base of Avemetatarsalia's sister group in both his and Nesbitt's phylogenies.  This way I don't have to deal with all the unrelated taxa I'm unfamiliar with.  I also kept in Arizonasaurus, to see if poposaurs would group by it instead.  His same topology resulted when I ran this in PAUP, so my deletions didn't affect that.  Enforcing traditional Dinosauria and Saurischia took 28 more steps.

I added the 15 saurischian and 11 dinosaurian characters from Nesbitt's analysis missing in Peters' (and also one I thought was coded for- the subnarial foramen, but it turns out Peters only codes for a subnarial fenestra).  I used Nesbitt's codings for these, also coding Massospondylus kaalae, Pampadromaeus, Panphagia and Daemonosaurus myself.  The new phylogeny excluded Marasuchus from Dinosauria but was otherwise largely the same.  It took only 5 more steps to make traditional Dinosauria and Saurischia.  A reduction in 23 steps isn't a bad start.

Then I started going through Peters' characters, making them ordered when needed (which sometimes involved rearranging states), and making sure each was only coding for one variable.  Luckily, with the non-dinosauriforms mostly deleted, a lot of Peters' characters had far less states in included taxa, so this was much easier than if I were to try it for his whole analysis.  Still, it's mighty tedious, so I stopped after doing the 115 cranial and dental characters.  During this process of fixing characters, I found 32 miscodings.  Being the first taxon in the list, I decided to code Turfanosuchus for these first 115 characters, plus the three extra characters I had spun off of them to keep each one only coding for one variable.  Turfanosuchus was miscoded for 33 characters, or 28%, which is pretty terrible.  Running the analysis found..... traditional Dinosauria and Saurischia. 

-- outgroups
--- Arizonasaurus
---- poposaurs
----- silesaurs
------ Marasuchus
------- Pisanosaurus
-------- Ornithischia
--------- Sauropodomorpha including Saturnalia, Thecodontosaurus and Massospondylus
------------ Daemonosaurus
------------ Panphagia+Pampadromaeus
--------------- Theropoda including Herrerasaurus and Trialestes

It doesn't perfectly match the consensus, but I didn't add any characters for e.g. Crurotarsi, Ornithischia including Pisanosaurus, Sauropodomorpha including Panphagia and Pampadromaeus, silesaurs+dinosaurs, so the fact I didn't get these clades is hardly surprising.  What was surprising was how soon this happened.  Adding 26 characters and changing 65 cranial states, half of the latter in the basalmost outgroup, and the traditional phylogeny shines through.  So why does Peters' analysis find odd topologies- it lacks enough characters, has poorly formed characters, and has numerous miscodings.  Fix even a fraction of those issues, and it resembles the traditional consensus.

Below are the gritty details of my alterations, for those who want to slog through them.

As we've discussed a few times before here, Peters finds an odd topology for dinosaurs in his Big Reptile Tree (bottom right in http://www.reptileevolution.com/reptile-tree.htm).  Marasuchus and probable 'sphenosuchian' SMNS 12352 are theropods (so was Trialestes until last month- I assume he changed some of its codings in response to my comments).  All herbivorous dinosaurs, silesaurs and poposaurs are in a Phytodinosauria clade.  Daemonosaurus is a basal ornithischian, Pisanosaurus is a basal poposaur+silesaur, sauropodomorphs are polyphyletic, etc..  It's quite a mess.

Avemetatarsalia in Peters' most recent cladogram, taken from his website.

I've attacked Peters' analysis from a number of angles.  Noting it lacks characters that support traditional clades, noting its characters are poorly formed, noting numerous miscodings, but Peters remains unconvinced by these small assaults on portions of the data.  He says "You missed the point, Mickey. What I am asking you to do is adjust my tree topology to suit your hypothesis. Then we can compare your changes to the large reptile tree. I’ll put up your figures and compare them with mine. Then we’ll look at synapomorphies. The list of characters is infinite for any taxon, as you can get down to individual chemistry and DNA if you like. So, merely listing a few to a dozen characters is not a solution. Rearrange the tree topology like you want to, then we’ll talk."  And "You have your assignment: Nest Daemonosaurus with theropods while including Heterodontosaurus and Massospondylus. That’s a half-dozen to a dozen taxa at most to deal with. Then we’ll compare answers."

So nothing less than a total review of his data will do, it seems.  And that's what I've done.  Recoded all of the taxa he includes in Dinosauria in addition to some outgroups, gone through the characters and ordered/divided them when appropriate, and determined what Peters' characters and taxa actually show.  What I've found is worse than I expected, but before we get into the results, I have a number of observations as to why his analysis is so bad.

First, Peters' codings are often not based on the preserved material at all.  I'm not even talking about his Digital Graphical Segregation, i.e. overzealous tracing.  No, I mean things like coding much of Turfanosuchus' postcrania from the Wikipedia photo of the specimen.  So all of the manual and pedal characters are coded, just like you can see the bones restored at his website.  But if he would have read Nesbitt (2011), he would know "only the proximal portions of the metatarsals are preserved, whereas the manus and most of the pes are sculpted", and indeed you can see the color difference of proximal metatarsals II-IV and phalanges IV-2 and IV-3 in the photo.  Similarly, he codes much of Lotosaurus from mounts, when parts of these are fake and e.g. the pubis is actually unknown.  Then there's the hand of Scelidosaurus, based on the specimen privately owned by Sole.  But this is fake as the actual fossil does not preserve the manus (or most of the pes, or the tip of the snout...).  Even worse is when he codes characters from areas not preserved or physically reconstructed.  Like Pisanosaurus (whose skull is known from a posterior maxillary fragment), being coded for premaxilla-maxilla articulation, snout depth, lacrimal-naris contact, lacrimal height, squamosal extent, skull roof fusion, vomeral and parasphenoid teeth, premaxillary tooth size, etc..  Even his own skull reconstruction doesn't show these as known.  Examples like this are common.

Most preserved skull elements of Pantydraco, from Galton and Kermack (2011).  Note combining these into a skull will not necessarily get you the result of Yates (2003) in every detail.

Peters also seems to code a LOT from reconstructions, without actually checking to see if the character can be determined from the material itself.  Marasuchus restored with gastralia?  Guess it had them, despite the fact it doesn't preserve any.  Another good example is the skull of Pantydraco, where Yates (2003) provided a nice reconstruction, but most elements are incomplete with uncertain articulations with each other, and preserved with only one surface exposed (see figure above).  A lot of reconstructions contain a good amount of plausible guesswork, but Peters treats it all as hard data to code. This is quite ironic considering that his own reconstructions often vary so much from published ones.

Connected to this flaw is Peters' overzealousness in coding characters that are based on the presence of small and easily lost elements.  Since Peters' tree goes back to Ichthyostega, there are many characters coding for the loss of all of the fishy skull roof bones (supratemporal, postfrontal, intertemporal, postparietal, tabular, etc.).  But taxa known from partial and disarticulated skulls are coded as lacking these, like Panphagia.  The other big area affected by this are the small pectoral elements.  Only preserve a disarticulated scapula and coracoid?  Guess I'll code you as lacking clavicles, an interclavicle, sternal plates and cleithrum...  Now sure all archosaurs probably did lack a cleithrum and most of the skull elements noted above, but it's just sloppy to code them that way when it's actually unknown.  And sometimes the elements really are present, contra Peters' coding.  Like Coelophysis having clavicles, or Heterodontosaurus and Scelidosaurus having ossified sterna.  I wonder how much this kind of coding is affecting his tree down in areas where taxa actually do commonly have these elements.

All known skull elements of Panphagia (from Martinez and Alcober, 2009).  Oh yeah, it definitely lacked supratemporals, tabulars, intertemporals and a postparietal....

The sheer amount of miscodings is appalling.  91 in the first 10 characters, from 28 taxa, so out of 280 possible codings.  91/280 = 32.5%.  93/280 for the middle 10 characters, or 33.2%.  87/280 for the last 10 characters, or 31.1%.  So basically one out of three characters is coded wrong by Peters.  Some of these are instances where it could be subjective regarding how complete a specimen has to be before a character is coded or how schematic reconstructions are when ratios are close, but there are a TON of blatant unjustifiable mistakes too.  Marasuchus coded as having osteoderms and phalanges on metatarsal V, Gracilisuchus coded as being mesotarsal (see below figure for how that happened) and having a tibia longer than its femur, Heterodontosaurus coded as lacking a parietal sagittal crest and parietal fusion... I could go on. 

Peters' comparison between supposed Gracilisuchus holotype (left) and Gracilisuchus specimen PVL 4597 (right).  In actuality, the left is a composite between the holotype and PVL 4597, though the ilium and hindlimb of the holotype don't belong to Gracilisuchus.  Note the "alternate" interpretation of Gracilisuchus as mesotarsal by Peters, which is a coded difference between the OTUs in his matrix.  Not only is the illustrated tarsus based on (wait for it...) PVL 4597, but his alternate illustration flips the calcaneum horizontally!  Sorry Peters, one side of that bone has a facet and the other doesn't, and it was quite clearly crurotarsal.  Bones aren't just shapes that can be rearranged.  But then, he jams the ischia in upside down against the pubes, though the latter were explicitly said to lack articular surfaces for the ischia.  Sigh.

In general, the coding suggests an unfamiliarity with the literature.  For instance, Peters codes PVL 4597 (a specimen whose pelvis and hindlimb were recently described by Lecuona and Desojo) separately from Gracilisuchus as he believes it differs from the holotype.  In the blog post, he compares the pelvis and hindlimb to figures 8 and 9 from Romer (1972), with the only noted difference being "Gracilisuchus has a metatarsal 4 shorter than 3. In the PVL specimen these two metatarsals were subequal."  Yet that pes in Romer's paper is not the holotype, it's a composite between the holotype and what Romer called the Tucuman specimen.  And what is the Tucuman specimen?  None other than PVL 4597.  Romer's text indicates the holotype doesn't preserve a complete metatarsal IV so the figure's IV/III ratio is based on PVL 4597.  Peters was comparing the specimen to itself and finding it belonged elsewhere!  The IV/III ratios of the left side as reported by Romer vs. L&D are 97% vs. 95%.  A 2% difference, and the right side Romer hadn't prepared yet has a ratio of 105%.  The other differences in his matrix are basically all due to miscodings.
This is just one example.  There's the fact he doesn't code any skull characters for Poposaurus, when jaw elements are known.  Sure, Parker and Nesbitt (2013) came out too late, but there's Gauthier et al.'s (2011) specimen which was coded into Nesbitt's matrix.  Or that he codes Pisanosaurus for both cervical and caudal characters, when the vertebrae in question are a series that have been assigned to the neck or to the tail, but you can't have it both ways!  Or that none of Hexinlusaurus' postcrania is coded, I can only assume because he was working with Barrett et al.'s (2005) brief discussion of the skull and lacked He and Cai's (1984) original osteology.  Ditto for not having Padian and Rosenbaum's (2000) description of new Scutellosaurus material.
Yes it's hard to keep up with the literature, but it's necessary if you're going to proclaim sweeping heterodox conclusions as the truth.

As for the characters used, there are simply far too few, as I've always said.  228 sounds like a lot, but 96 of these only vary in taxa not examined here (e.g. cleithrum presence), and another 31 only vary in a single examined taxon, making them useless in this analysis (phylogenetically uninformative, to use the technical term).  Which leaves us with 101 characters deciding dinosaur phylogeny.  If we only use this same set of taxa in Nesbitt's (2011) analysis, it still has 199 informative characters.  Even Cabreira et al.'s (2011) version of Yates' big sauropodomorph analysis (which has single OTUs for Crurotarsi and Ornithischia) has 159 informative characters, and Brusatte et al.'s (2010) archosaur analysis (which has two ornithischians and no sauropodomorphs shared with Peters') has 120.  The characters that do vary are often basic proportions and shapes, with relatively few structural details (foramina, fossae, processes, laminae, etc.) coded.  Thus it caters toward complete and articulated specimens, while more fragmentary taxa won't be able to be coded for much.  For instance, Diodorus (known from partial dentary, teeth, humeri, femur and metatarsal III) can be coded for 34 characters in Nesbitt's analysis, but only 11 in Peters'.  There's a huge emphasis on the skull (58% of the informative characters), and almost nothing on the main limb bones and tarsus.  The latter could go a ways toward explaining why Peters doesn't recover pterosaurs close to dinosaurs.  While usually we think of too few characters as being bad merely because taxa will be placed incorrectly without of the evidence being brought to bear, there are also more subtle consequences.  For instance, if only relatively complete and articulated specimens preserve enough characters to code, then more fragmentary taxa that are important for being basal or having novel character combinations won't be able to be included.  

Because most of the characters used are general proportions, they can more easily vary due to ontogeny and taphonomy.  This is fine in larger analyses that will have more detail characters that can overcome them, but in Peters' analysis taxa often end up related due to comparative sizes of cranial fenestrae or limb proportions without regard to detailed anatomy.  This probably explains in large part why Peters doesn't find standard clades in so many places.

What Peters' character 117 was intended to code.  Mandibles in dorsal view of Captorhinus (left) and Proganochelys (right), showing surangular ridge in the latter highlighted in blue.  Figure from Gaffney (1990).

Several times Peters uses characters from standard amniote analyses, but misunderstands or misuses them.  A few examples follow.
- Character 117 (Surangular lateral shelf: (0) absent; (1) present) refers to a laterally placed ridge in dorsal view- i.e. a narrow dorsal edge to the surangular, as described by Laurin and Reisz (1995- ch. 73).  They used it to group procolophonids with turtles, and it can be seen clearly in e.g. Proganochelys (Gaffney, 1990- fig. 55, 56, 57B), while the lateral surface lacks a ridge (fig. 58, 59).   Yet Peters codes it as if it refers to a ridge on the lateral surface that can be seen in lateral view, missing only in Pisanosaurus and poposaurs.  In actuality, all scorable taxa have it, which is unsurprising as it is supposedly a eureptilian character as well.
- Character 45 is defined as "Frontal shape: (0) without a posterior process; (1) posterior process present. [deBraga & Rieppel 1997, Rieppel 1998]."  Peters codes it as present basally but lacking in phytodinosaurs.  Yet deBraga and Rieppel define the frontal lateral process as "a distinct lateral lappet (process) that projects out from the frontal margins at an abrupt 70° to 90° angle."  This isn't present in any examined taxon.
- Peters defines character 50 as "Temporal ledge (distinct overhang at upper temporal area): (0) no ledge; (1) made from squamosal; (2) made from supratemporal and tabular. [Gauthier et al. 1988, Laurin & Reisz 1995, Hill 2005]."  Yet none of those references include such a character.  If he meant Gauthier et al.'s character 10 " Temporal musculature originates ventrally (0), or dorsally (1), on the parietal table" and Hill's character 91 "Temporal muscles on parietal table: (0) originate ventrolaterally – parietal margin straight; (1) originate dorsolaterally – parietal lateral margin embayed", that involves the medial edge of the supratemporal fenestra, not the lateral edge. The ledge is made from the parietal, not the squamosal, supratemporal or tabular.
While none of these actually vary in the examined taxa, I wonder what effect Peters' miscoding has deeper toward the tree base where they really do vary.  

Another type of problematic coding involves classic characters Peters adds states to, which end up hiding homology.  Imagine if we used the classic tetanurine character "less than X caudal vertebrae with transverse processes" but then added the state "caudals with elongated prezygapophyseal and chevron rods" and coded dromaeosaurids as having the rods.  This would hide the fact they also share the low number of transverse processes with other tetanurines, so that it couldn't help group them together.  A few examples from Peters' matrix follow.
- For character 187, taxa are coded either as having diverging pubic and ischial aprons (as opposed to a solid puboischiadic plate or a thyroid fenestra) or retroverted rods (in ornithischians).  Yet ornithischians still have elongated pubic and ischial shafts instead of a solid plate or thyroid fenestra, regardless of whether the pubis is retroverted or missing an apron (both also covered by other characters anyway).  
- Peters describes character 138 as swollen neural spines, and cites several authors.  Yet those authors instead code swollen neural arches- Evans (1988- ch. B1), Laurin and Reisz (1995- ch. 86), deBraga and Rieppel (1997- ch. 106), Hill (2005- ch. 220), which means the width of the zygapophyseal portion of the neural arch.  All of the taxa in this reduced matrix are coded a different state- transverse processes present.  Yet the taxa the previous authors coded for their states have transverse processes too (e.g. Ophiacodon, Seymouria), so this distinction is invalid.
- For character 93, every scored taxon is coded as state 4- "large choana that virtually fill that portion of the palate."  Oddly, the other states do not involve choana size.  States 0 and 1 ("Choanae orientation: (0) parallel the maxilla; (1) posteriorly deflected medially") were taken from Laurin and Reisz (1995- ch. 40), deBraga and Rieppel (1997- ch. 8) and Hill (2005- ch. 113)- choana "(0) parallel to maxilla, palatine forms its posterior edge only; (1) curved posteromedially, palatine forms its posterior and part of its lateral edge."  The scorable taxa actually have state 1 regardless of how big their choanae are.
As with the previous issue, this could really be affecting the phylogeny closer to the base of Peters' tree where the characters were designed to work.

Hypothetical example of two hands which would be coded the same by Peters' character 174 because in each a line intersecting the ends of metacarpals II and III intersects the end of manual phalanx I-1 as well.  Lateral digits and phalanges on digits II and III left out for simplicity.

The final kind of problematic character I'll outline here are those dealing with so-called interphalangeal lines.  Peters (2000) published this idea, and it was well refuted by Hone et al. (2009).  Quoting the latter authors, "interphalangeal (IP) lines connect sets of adjacent metatarsophalangeal (MP) or IP joints, and/or the tips of ungual phalanges. Peters (2000a) suggested that IP lines act as 'hinge lines' about which flexion and extension of the manus or pes can occur, that the lines might be helpful in matching fossil tracks to trackmakers and elucidating phylogenetic relationships, and that they might represent a powerful tool for vertebrate palaeontologists because the lines could be used to predict the lengths of missing phalanges."  Even if Peters were right that interphalangeal lines could be objectively identified and were functionally useful, they would make terrible characters for phylogenetic analyses due to the multiple ways of achieving the same state.  For example, in his analysis character 174 codes for where in manual digit I a line intersecting the ends of metacarpals II and III would go.  But the angle of that line depends on the comparative lengths of metacarpals II and III (if II is longer the line angles distomedially, if III is longer it angles proximomedially), and where in digit I it intersects depends on the lengths of metacarpal I, phalanx I-1 and manual ungual I.  Note the figure above.  They would be coded the same, but that sameness isn't anything that could be accounted for by an inherited mutation.  Hands and feet don't develop in a way that the lengths of metacarpals II and III could be connected to the lengths of I and phalanx I-1 at a certain angle.  This goes to show not every objective feature should be used as a character in a phylogenetic analysis.  An equivalent would be the hypothetical character "number of presacral vertebrae divided by number of sacral vertebrae, answer rounds to an - even number (0); odd number (1)."  You'll get a definite answer, but the same state could be arrived at in many unrelated ways and is nothing a shared mutation could account for.

But hey, all of this is missing the point.  What's the result of evaluating all of Peters' data for dinosaurs?  Does it support his phylogeny?  Stay tuned, as that's coming next time.

The last post covered many of the problems with Peters' amniote analysis- codings based on sculpted or nonexistent material, codings based on reconstructions, an unfamiliarity with the literature, coding small and easily lost elements as truly absent, using too few characters which mostly involve general proportions and shapes, mis-applying characters, making new states so that homology is hidden, using interphalangeal lines for characters, and basically having a third of all scores miscoded.  This in addition to issues I've covered before like not ordering character states, having correlated characters, having poorly formed characters that combine different kinds of changes, and leaving out characters that support certain clades.  But as I said before, Peters doesn't find these kinds of critiques to be especially harmful to his conclusions.  Requoting him-

He says "You missed the point, Mickey. What I am asking you to do is adjust my tree topology to suit your hypothesis. Then we can compare your changes to the large reptile tree. I’ll put up your figures and compare them with mine. Then we’ll look at synapomorphies. The list of characters is infinite for any taxon, as you can get down to individual chemistry and DNA if you like. So, merely listing a few to a dozen characters is not a solution. Rearrange the tree topology like you want to, then we’ll talk."  And "You have your assignment: Nest Daemonosaurus with theropods while including Heterodontosaurus and Massospondylus. That’s a half-dozen to a dozen taxa at most to deal with. Then we’ll compare answers."

So that's what we're doing today.  Taking the dinosaur portion of his tree, adjusting the codings to be correct and the character states to be well-formed, less correlated, ordered when appropriate, and seeing the results.  Then looking at what synapomorphies support clades in Peters' tree.

For those of you who don't want to wade through the minutia below, here's the short answer.  Peters'dinosaurian topology is completely due to miscodings and lack of characters/taxa.  When coded right, poposaurs fall outside Dinosauria, and Trialestes and SMNS go next to Terrestrisuchus once it's added, but we get new odd things like poposaurian Daemonosaurus, and theropodan Pseudolagosuchus, Silesaurus and Saturnalia.  As we add taxa one at a time, the phylogeny changes constantly so that sauropodomorphs are variously paraphyletic to theropods and/or ornithischians in different configurations, Saurischia is para- or monophyletic, silesaurs are polyphyletic in different ways, etc..  Simply put, there aren't enough characters to to stabilize topology, and it's only stable in Peters' matrix because he miscodes a ton.  If we add the saurischian and dinosaurian characters I noted long ago on this blog, the topology is fairly standard, and if we add the character evidence for Daemonosaurus being a theropod, it becomes a theropod.  I have no reason to believe the rest of his matrix isn't miscoded to a similar extent in similar ways, and that even if it were corrected, would lack the characters and taxa needed to be useful.

Methods

This evaluation uses Peters' amniote matrix from January 22, 2013.  He has since updated it (I assume in part due to my comments on his site about miscodings in some of his 'theropod' OTUs), but the only difference is that Trialestes is now sister to Dinosauria instead of the most basal theropod.  His matrix includes 228 characters, and this evaluation uses all of the taxa Peters recovers as avemetatarsalians (closer to birds than crocs).  For outgroups, I chose Gracilisuchus and Turfanosuchus.  Gracilisuchus is one of the most basal pseudosuchians (closer to crocs than birds) in Peters' tree, while Turfanosuchus is sister to Pseudosuchia+Avemetatarsalia.  Both are also well described and known from articulated skulls.  Note this is favoring Peters, as better outgroups in traditional phylogenies like Nesbitt's (2011) would be lagerpetids, pterosaurs and ornithosuchids.  But Peters finds those taxa to be more distantly related, so they are ignored here.  Similarly, Peters recovers Saltopus and Scleromochlus as pseudosuchians, so they are ignored.  Another important point is that he finds Lewisuchus to be outside Archosauria, so it is ignored here though traditionally it is considered close to and probably synonymous with the included taxon Pseudolagosuchus.  If we run this reduced analysis of Avemetatarsalia plus two outgroups, we get the same result as running the entire analysis of 328 taxa, so we know any changes in topology aren't due to only analyzing this area of the tree.

Running Peters' data results in one MPT of 354 steps.  90 characters don't vary in included taxa, and 18 variable characters can't affect the topology, so the number of useful characters is 120.  It has a consistency index of .52, so on average each character reverses or converges once.

So let's start fixing it.  Besides the Pseudolagosuchus note above, a few clarifications are necessary.
- For Turfanosuchus, only the type species was coded.  The more fragmentary T. shageduensis is no longer thought to be congeneric.  I lack the original description of Turfanosuchus, so this is the single instance where my codings do not reflect the total published knowledge of a taxon, but Peters lacks it too, so this shouldn't matter for our test.  Nesbitt says it's not great anyway, and as it's in Chinese only the figures would be useful to me if I had it.
- For Gracilisuchus, I included all specimens generally attributed to it (the holotype PULR 08, MCZ 4116, MCZ 4117, MCZ 4118, PVL 4597 which is the Tucumen specimen, and PVL 4612).  Romer (1972) used all of these when describing and illustrating the taxon, Brinkman (1981) reinterpreted the skull based on MCZ 4116 and 4118, and Lecuona and Desojo (2012) described the pelvis and hindlimb of PVL 4597 in depth.  Peters did not realize Romer used these latter three specimens too, and coded PVL 4597's pelvis and hindlimb and most recently MCZ 4116+4118's skulls and cervicals as separate OTUs from Romer's composite description/drawings. 
- For Trialestes, I only included the holotype, as Ezcurra et al. (2008) found the referred specimens to be a mix of dinosaur and indeterminate suchian bones (PVL 2559) and an indeterminate crocodylomorph (PVL 3889).  This is important because Peters' codings are almost entirely the crocodylomorph holotype skull and the dinosaurian and possibly herrerasaurid pes of PVL 2559.  So it's not surprising it falls out between crocodylomorphs and dinosaurs in his tree, since it's a composite.
- SMNS 12352 includes both a skull and a manus (these are the specimens originally referred to Procompsognathus that Sereno and Wild referred to Saltoposuchus in 1992), though Peters ignores the latter.
- Coelophysis is only coded based on C. bauri, which I think is what Peters did too.
- Massospondylus k is M. kaalae, shortened due to PAUP's display.  This species is based on a partial skull.
- On Peters' Thecodontosaurus page, he illustrates both the type species T. antiquus and what was originally named T. caducus, which is now known as Pantydraco caducus.  T. antiquus is based on a large number of generally disarticulated and unassociated bones, with a dentary as the holotype.  Most recently, Galton (2007) redescribed them and found them to belong to at least three different taxa based on humeral morphologies.  He named Asylosaurus based on the one articulated partial skeleton there, retained Thecodontosaurus for the dentaries and one kind of humerus, and kept most of the material unassigned.  The codings for Thecodontosaurus in Yates' matrices are apparently based mostly on a bonebed that remains undescribed, though he and Benton are working on it.  Given this mess, I've coded "Thecodontosaurus" based solely on Pantydraco and refer to it with the latter name.  It includes the only described skull and pes, and Peters' clearly used it when coding his OTU.  Later I add the chimaerical "Thecodontosaurus antiquus" as a separate OTU as a test.
- I included Stormbergia in the Lesothosaurus OTU, as I agree with Knoll et al. (2009) that their differences are ontogenetic.

Many of Peters' characters are composites, in that they code for multiple variables.  "Serrations large and tooth roots constricted" as a state, for example.  These had to be split into multiple characters to remain valid, which led to ten "new" characters being made.  This brings the total number to 238.  It would need to be much higher if the inappropriate states describing the anatomy of non-dinosaurs were examined as well.
Characters that have states which follow an objective sequence (e.g. "2 sacrals" "4 sacrals" "3 sacrals", or "humerus longer than femur" "humerus subequal to femur" "humerus shorter than femur") were set to be ordered in PAUP.  Thus, the program knows that e.g. a short humerus is more similar to a subequal humerus than it is to a long humerus.  It's implicit in many of Peters' states such as "more than 4 premaxillary teeth", since under unordered assumptions, 5 teeth is just as similar to 2 teeth as it to 6 teeth.  Ordering characters sometimes meant I had to rearrange the states, so state 2 in my matrix will not always be the same as state 2 in Peters' matrix.
Many of Peters' characters are correlated with each other.  Often this is due to one character coding for the presence/absence of a feature, then another character coding for attributes of that feature and also including a state coding for its presence/absence.  This weights the presence/absence compared to other characters, and is easily solved by making taxa without the feature coded inapplicable for characters about that feature.  Unfortunately, several correlated characters were retained, as altering them would lead to effectively using different characters than Peters, so it would be less fair of a test.  For example, there's a character comparing each cranial fenestra size to orbit size.  So if two taxa are exactly the same except one has larger orbits, they could be coded differently for "orbit compared to naris", "orbit compared to aof", "orbit compared to stf", "orbit compared to itf", and probably "orbit enters anterior half of skull" too.  Similarly, there are several characters coding for the length of metatarsal V, separate characters for which digit is longest and which digit+metapodial is longest, and other such things.  By not changing these, I'm giving Peters another advantage.

Results-

When those changes are made, we get one MPT of 458 steps.  95 characters don't vary in included taxa, and 31 variable characters can't affect the topology, so the number of useful characters is 122.  It has a consistency index of .39, so has more homoplasy than Peters' codings.  Differences include Daemonosaurus being a poposaur, poposaurs being outside Dinosauria, Silesaurus, Pseudolagosuchus and Saturnalia being theropods, Pantydraco being by Panphagia and Pampadromaeus, and Pisanosaurus being an ornithischian.  But like Peters' original tree, Marasuchus, Trialestes and SMNS 12352 are still theropods, and Phytodinosauria still exists with some sauropodomorphs basal in it.


Let's try substituting the probably chimaerical Thecodontosaurus (including Thecodontosaurus, Asylosaurus at at least one other sauropodomorph as well) for Pantydraco.  We get 95 MPTs of 453 steps.  Thecodontosaurus clades with Massospondylus (due to massopod elements?), Herrerasaurus with Saturnalia, and there's much less resolution overall. 

Adding taxa

As Thecodontosaurus is problematic, let's switch back to Pantydraco for the rest of the tests.  Since Trialestes and SMNS 12352 are generally thought to be basal crocodylomorphs, let's add well known crocodylomorph Terrestrisuchus.  It's thought by some to be a juvenile Saltoposuchus (which is poorly described), which is in turn thought by Sereno and Wild to be what SMNS 12352 belongs to.  That gives us 180 MPTs of 490 steps.

Well, that changed things considerably.  Trialestes and SMNS 12352 are now outside Dinosauria, Poposaurus and Silesaurus are successive sisters to Dinosauria, the Pan+Pan+Pam clade is within Theropoda, and lots of resolution has been lost.  Let's add Arizonasaurus as a basal poposaur.

And now Poposaurus and Daemonosaurus are back to Poposauridae, and all the crocodylomorphs are near the base.  What if we add the basal silesaurid Asilisaurus, since Pseudolagosuchus and Silesaurus are still separated.
Far less resolution (seemingly due to Daemonosaurus falling out in multiple possible positions), though Asilisaurus falls out with Pseudolagosuchus and Marasuchus.  So let's try adding another silesaurid- Sacisaurus.
Now Daemonosaurus moves to Theropoda, though most structure in non-theropod Dinosauria is lacking.  So let's try adding a complete sauropodomorph, since the four Peters uses are only partially known.  We add Plateosaurus to find...
Daemonosaurus goes back to Poposauridae, and we get sauropodomorphs (and Sacisaurus) as a grade leading to Ornithischia.  Why not add Massospondylus carinatus, to see if that affects M. kaalae's placement near/in Ornithischia.
Indeed, the Massospondylus species group together, and are sister to Plateosaurus.  But the clade's still closer to ornithischians, so let's try to add an intermediate sauropodomorph.  Efraasia usually lies between Plateosauria and Pantydraco in Yates' trees.
Well, it grouped with Pantydraco.  How about we add Guaibasaurus, as a largely complete (except for the head and neck) basal sauropodomorph.
That helped resolution quite a bit.  Silesaurus is back to being a theropod, so at least is closer to other silesaurids.  We still have sauropodomorphs forming a pre-ornithischian grade, except Saturnalia which is a basal theropod.  How about adding Eoraptor, variously claimed to be a theropod, sauropodomorph, or basal to both.  The result had a polytomy at the base of Poposauridae+Dinosauria, due to Daemonosaurus being able to go in several positions.  When we exclude it from the tree (but not the analysis), we get-
The blue area shows where Daemonosaurus can go.  Note Eoraptor is resolved as the basalmost theropod.  Maybe adding Eodromaeus will help things, since it's another basal theropod.
Here another polytomy results, mostly due to Trialestes (which can go in the blue spaces above) and Pisanosaurus (which can go in the pink spaces).  Daemonosaurus is restricted again to outside Dinosauria, but note things have changed in that basal sauropodomorphs are a grade leading to theropods again, while Silesaurus and Sacisaurus are now just outside Dinosauria.  Saturnalia's still odd being so deep within Theropoda, so let's add the fragmentary saturnaliine Chromogisaurus.
Oddly, this stabilizes the whole tree and changes the topology so that Saurischia and Sauropodomorpha exist.  Panphagia is now sister to Dinosauria, while Sacisaurus is a basal ornithischian.  Both Saturnalia and Chromogisaurus are theropods though.  What about adding the other named herrerasaurids, Staurikosaurus and Sanjuansaurus, to see if that affects Herrerasaurus' position.
This brings things back to generally how they were before Chromogisaurus was added.  Let's add three more basal ornithischians- Emausaurus to potentially connect Scutellosaurus and Scelidosaurus, Tianyulong as a basal heterodontosaurid, and Eocursor.
This is the tree with Chromogisaurus deleted a posteriori, with the pink area showing where it can go.  Here Trialestes is a theropod, though the other crocodylomorphs group together, and Poposaurus is with other poposaurs again.  Most of the tree matches the last one, but note Ornithischia is completely rearranged compared to previous trees with the addition of these three taxa.  Scelidosaurus is still most basal, and Agilisaurus is with Hexinlusaurus, but besides that things are different.  As a final test for Peters' characters, let's add a few fragmentary but potentially important taxa to see if they affect topology- silesaurids Eucoelophysis and Diodorus, and controversial saurischian Chindesaurus. 
With all taxa added, there are 54703 MPTs of length 636 (up from 458) with 139 informative characters (up from 122).  Trialestes is back down by crocodylomorphs, but there's a big polytomy in Dinosauria.  Deleting Eucoelophysis, Diodorus, Chindesaurus and Chromogisaurus a posteriori from the MPTs gives us a more resolved tree.
Notable here is that Saurischia occurs again, with the exception of Efraasia being by ornithischians and Panphagia being sister to dinosaurs.  Also, ornithischian topology is rearranged again, this time with all thyreophorans the basal grade. 

Adding characters

Before we finish this, recall one of my posts criticized Peters analysis for leaving out 16 unambiguous synapomorphies of Saurischia and 11 such synapomorphies of Dinosauria (from Nesbitt, 2011).  We've already seen that depending on the taxa you include, Peters' characters already can support a Saurischia containing all to most sauropodomorphs, but let's see what happens when we add those 16 saurischian synapomorphies.  For those curious, I checked Nesbitt's accuracy too and found only 8% of the entries were miscoded, which is a fourth of Peters' total.
Again, Eucoelophysis, Diodorus, Chindesaurus and Chromogisaurus were deleted a posteriori from the MPTs to give better resolution.  Note the saurischian characters got Panphagia and Efraasia back in the clade, and even made Sauropodomorpha monophyletic (potentially, as Saturnalia is still in a polytomy).  Crocodylomorphs are monophyletic too, though Daemonosaurus is still very basally placed.  There were also the 11 unambiguous dinosaurian characters of Nesbitt I commented on.  Adding those leads to-
Only Eucoelophysis and Daemonosaurus had to be deleted a posteriori from trees to give good resolution here.  Eucoelophysis can go anywhere in the pink area, which covers silesaurids so makes sense.  Daemonosaurus can go anywhere in the blue area, which includes Peters' preferred position (basal ornithischian), the position of its describers (basal theropod), and the position Peters' characters seem to be suggesting (basal near poposaurs).  Since Daemonosaurus is a sticking point with Peters (recall his assignment was "Nest Daemonosaurus with theropods while including Heterodontosaurus and Massospondylus"), let's test Sues et al.'s hypothesis.  We'll add all of the characters (18 total) Daemonosaurus was scored for in their analysis that are also synapomorphies of nodes which include it (namely Avemetatarsalia/Dinosauriformes, Silesauridae+Dinosauria, Saurischia, Theropoda, and two theropod subclades).  These are all cranial and cervical of course, as those are the only areas preserved in the genus.  Other taxa were scored when possible, with codings corrected when necessary, and we get the following tree (when Diodorus is excluded a posteriori).
So there you go, Daemonosaurus is a theropod, and everything else is generally traditional too.  Trialestes and SMNS 12352 are down by Terrestrisuchus, poposaurs aren't dinosaurian, Marasuchus and silesaurids form sister taxa to Dinosauria (except for possibly Sacisaurus), Saurischia exists.  There are some oddities, like Pampadromaeus and Saturnalia being theropods, silesaurids not being monophyletic, and ornithischian phylogeny being wrong, but just like the Daemonosaurus situation, these would probably be solved by adding the suggested sauropodomorph, silesaurid, genasaur, thyreophoran, cerapod, etc. characters to the mix (they only take 3, 6 and 3 more steps each respectively, so are only slightly-weakly rejected).  Just as I've told Peters innumerable times, (when coded correctly) phylogeny does not stabilize at a couple hundred characters.  Look at how much the last 18, 11 and 16 characters affected the entire topology each time, despite only being designed for one purpose each.

Comparing support for clades

Assignment completed, David.  Let's compare answers.  We'll compare the number of extra steps needed to find various groups in Peters' unaltered matrix, Peters' characters fixed and corrected by me using only the taxa he did, the fixed/corrected characters plus the 45 I added with all taxa added, and in Nesbitt's (2011; reduced to have only the taxa examined here that are shared) matrix.  Note all of the constraint trees only involve taxa Peters' included, so e.g. the Dinosauria constraint doesn't force Sacisaurus out of the clade, though it does force Silesaurus out.

First, we'll enforce Avemetatarsalia/Dinosauromorpha, to the exclusion of traditional pseudosuchians.
Peters original- 30
Peters fixed- 2
Peters with new added- 0
Nesbitt- 0
Result- Peters didn't recover this clade based almost entirely on miscodings.

Next, enforcing Silesauridae+Dinosauria.
Peters original- 41
Peters fixed- 10
Peters with new added- 4
Nesbitt- 0
Result- Peters didn't recover this clade mostly due to miscodings, but also due to lacking certain characters and taxa. 

Next, Dinosauria itself.
Peters original- 30
Peters fixed- 8
Peters with new added- 0
Nesbitt- 0
Result- Peters not finding traditional Dinosauria is due mostly to miscodings, but partially due to missing character and taxon data.

Peters' Phytodinosauria including Daemonosaurus, silesaurids and poposaurs.
Peters original- 0
Peters fixed- 12
Peters with new added- 34
Nesbitt- 76 (not Daemonosaurus)
Result- Peters' support is entirely due to miscodings, as fixing these makes the clade rather improbable.  Adding characters and taxa makes this is extremely unlikely to be a real clade.  And lest Peters claims for the nth time it's our emphasis on the crurotarsal ankle that blinds us to placing poposaurs in Dinosauria, even when proximal tarsal characters are excluded, this still takes 59 more steps in Nesbitt's analysis. 

Saurischia.
Peters original-34
Peters fixed- 15
Peters with new added- 0
Nesbitt- 0
Result- Peters doesn't recover this due to half miscoding and half lack of included data.

Peters' Theropoda with Marasuchus and SMNS 12352.
Peters original- 0
Peters fixed- 2
Peters with new added- 19
Nesbitt- 34 (only Marasuchus)
Result- Peters recovered these as theropods due to miscodings, though adding taxa and characters makes them highly unlikely to be correct.

Peters' derived phytodinosaurs excluding Panphagia and Pampadromaeus.
Peters original- 0
Peters fixed- 16
Peters with new added- 35
*Cabreira et al.- 31
Cabreira et al.'s (2011) sauropodomorph analysis was used, as Nesbitt did not include Panphagia or Pampadromaeus.  All taxa were retained, as none are outside the scope of this analysis except the outgroup Euparkeria.
Result- Peters recovered this completely due to miscoding.  At 31-35 steps once other taxa and characters are added, it's highly unlikely to be correct.

'Paraornithischia' consisting of silesaurs, poposaurs and Pisanosaurus.
Peters original- 0
Peters fixed- 13
Peters with new added- 26
Nesbitt- 50
Result-  Again recovered entirely due to miscodings, this becomes rather unlikely once recoded and extremely unlikely with added taxa and characters.

Daemonosaurus sister to Ornithischia sensu lato (Pisanosaurus ignored).
Peters original- 0
Peters fixed- 9
Peters with new added- 10
*Sues et al.- 7
Sues et al.'s (2011) analysis was used, as Nesbitt's does not include Daemonosaurus.  Taxa outside the scope of this critique were deleted.
Result- Another grouping based entirely on miscodings, though in this case added taxa and characters don't affect its liklihood much.  It's always moderately rejected.

Daemonosaurus in derived Theropoda (by Tawa and Coelophysis).
Peters original-18
Peters fixed- 5
Peters with new added- 0
*Sues et al.- 0
Result- Peters' analysis rejected this mostly due to miscodings, but once correct it's only weakly rejected.  Adding taxa and characters makes it most parsimonious.

Sauropodomorpha+Ornithischia.
Peters original-14
Peters fixed- 2
Peters with new added- 8
Nesbitt- 13
Result- While Peters does not actually recover a traditional Phytodinosauria due to having Pisanosaurus, Pampadromaeus and Panphagia in the clade only if silesaurids and poposaurs are, the reduced version seems quite possible once his codings are fixed.  Yet once more taxa and characters are added it becomes unlikely.  In case you're wondering, making silesaurids phytodinosaurs is 28 steps less likely in both Nesbitt's matrix and the version of Peters with taxa and characters added.

Derived Sauropodomorpha+Ornithischia (Pisanosaurus ignored).
Peters original- 0
Peters fixed- 5
Peters with new added- 11
*Cabreira et al.- 25
Result- Peters has Saturnalia, Pantydraco/Thecodontosaurus and Massospondylus kaalae closer to ornithischians than Panphagia and Pampadromaeus.  This is due to miscodings, though it still seems possible once these are corrected.  More taxa and saurischian characters help make this unlikely, but what really kills it are the sauropodomorph charcters and intermediate taxa present in a large analysis like Cabreira et al.'s.

Sauropodomorpha.
Peters original-13
Peters fixed- 12
Peters with new added- 3
Nesbitt- 0
Result- Somewhat uniquely, Peters' characters and taxa really do reject Sauropodomorpha sensu lato (containing Panphagia and Pampadromaeus), even after correction.  Though in the corrected version this is due to Saturnalia and Pampadromaeus being theropods, and Panphagia being outside Eusaurischia in the corrected version.  Adding more taxa and characters makes Sauropodomorpha sensu lato only slightly unlikely, though Nesbitt's character selection makes it most parsimonious.   Though Peters' alternative to monophyly was rejected soundly above (25 more steps in Cabreira et al.'s matrix), you might wonder about "my" alternative.  This is also soundly rejected in Cabreira et al.'s matrix, taking 24 more steps.

Peters' arrangement of Ornithischia (Pis(Scel((Het+Hex)(Agi(Scut+Les))))).
Peters original- 0
Peters fixed- 8
Peters with new added- 14
*Butler- 12
The updated version of Butler et al.'s (2007) ornithischian analysis (from Coria et al., 2013) was used.  All taxa were retained, as none are outside the scope of this analysis except the outgroup Euparkeria.
Result- Peters' odd ornithischian topology with Scelidosaurus basal is due to miscodings.   Adding more data only increases its unliklihood, to a level similar to that in the most exhaustive published ornithischian analysis.

Butler's arrangement of Ornithischia (Pis(Het(Les(Agi+Hex)(Scut+Scel)))))
Peters original-18
Peters fixed- 9
Peters with new added- 3
*Butler- 0
Result-The current standard topology of Ornithischia is strongly rejected by Peters' original matrix, but still somewhat rejected after coding it correctly.  Adding more taxa makes it only weakly rejected, and adding the many ornithischians and applicable characters from Butler's analysis supports it.

Character support

Peters requested we look at synapomorphies, so let's check what characters support heterodox nodes in his unaltered analysis. Of course based on the above, we know these nodes are due almost entirely to miscodings, but just to make sure the thrashing is total and unambiguous, we'll go in for a closer look...

To be continued...

We interrupt our regularly scheduled dismantling of Peters' phylogeny to bring you a non-theropod paper.

Basal titanosauriforms and macronarians have one of the most contentious phylogenies among dinosaurs.  Mannion et al. redescribe Lusotitan, which used to be Brachiosaurus atalaiensis, finding it to be just basal to Titanosauriformes.  They also redescribe "Brachiosaurus" nougaredi, which I learned is known from unassociated elements, only one of which can be located (an indeterminate titanosauriform metacarpal III).  Just with this the paper would be great, as I love redescriptions of old taxa, but the authors went further and performed a large phylogenetic analysis (with continuous characters) centering on this part of the tree AND reviewed all previous records of basal titanosauriforms.  It's like the titanosauriform equivalent of Carrano et al.'s tetanurine paper.  I'm really not caught up on the lit for these things, as there were plenty of facts I didn't know.  For instance, Agustinia's "osteoderms" are actually rib fragments and ischia.

One thing I did disagree with is their take on Lapparentosaurus.  Bothriospondylus madagascariensis was named by Lydekker (1895) based on a dorsal and other material which Mannion believes to be indeterminate.  Bonaparte (1986) erected Lapparentosaurus madagascariensis for that material and what's subsequently been referred to the species, but made two dorsal neural arches described by Ogier (1975; part of a partial skeleton) the holotype.  You might think he was just naive and tried to reset the holotype, but he explicitly erects madagascariensis as a new species as opposed to crediting Lydekker, so it seems he was naively trying to ignore priority instead.  Of course by giving it the same species name, this has engendered confusion.
Mannion et al.'s take is that Bonaparte both referred Lydekker's madagascariensis to the new genus Lapparentosaurus AND erected Lapparentosaurus madagascariensis as a homonym, and thus Ogier's material should be renamed, except that it's what people today think of as being Lapparentosaurus, so the ICZN should be petitioned to conserve the genus for Ogier's material.
I think this is more work than needs to be done.  Bonaparte only says the remains studied by Lydekker "are considered here to represent a new genus, Lapparentosaurus, with the species name L. madagas-madagascariensis [sic]."  Then he goes on to formally erect Lapparentosaurus madagascariensis as a gen. et sp. nov. with his new holotype.  So he never formally refers Lydekker's species to his new genus, just the material it was based on.  Thus we have no homonym, only seemingly indeterminate Bothriospondylus madagascariensis and valid Lapparentosaurus madagascariensis.  If they were synonymous, we'd use Lydekker's madagascariensis for the species name, but since they aren't we don't have a problem.  Certainly not one requiring the ICZN.

If I have one general complaint about the paper, it's that some taxa are declared indeterminate without valid justification, like Pukongosaurus ("based on a lack of diagnostic features"), Agustinia ("The absence of diagnostic features"), Dinodocus, Macrurosaurus, Jiutaisaurus ("All of the features listed as diagnostic by Wu et al. (2006) are more widespread amongst sauropods"), Arkharavia ("The holotype specimen lacks any diagnostic features (all are more widespread – see the current analysis)"), Amargatitanis ("the proposed autapomorphies in Apesteguía (2007) are all more widespread or based on incompletely preserved elements") and Rugocaudia ("all of the characters used to diagnose Rugocaudia are more widespread amongst titanosauriforms and do not form an unusual character combination (see this analysis), or are of dubious diagnostic value (see also D’Emic & Foreman, 2012)").  Just saying something lacks diagnostic characters or character combinations, or that the proposed diagnostic characters/combinations are more widespread are both assertions.  Explicitly describing which two or more taxa share each proposed character or combinarion is better, but Mannion et al. usually don't even go that far.  What's really needed is to go over all the known characters of taxon, and show which two or more other taxa share them all, or indicate they aren't useful for distinguishing species.

Let's use Arkharavia as an example, since it's so simple (... I said before I wrote this paragraph).  It was based on a partial caudal and some referred caudals, the latter of which Mannion et al. identify as hadrosaurian.  I agree with this.  They go on to state all the proposed diagnostic features of the holotype are more widespread, and cite their current analysis as the reference.  Alifanov and Bolotsky (2010) really only propose two characters to diagnose Arkharavia that can be observed in the holotype.  The first is heterocoelous proximal caudal centra, and if we check Mannion et al.'s analysis, that's not a character used.  They do say the centrum is mildly procoelous in Arkharavia, which again I agree with, but never say this differs from the original description or that it nullifies a suggested autapomorphy.  So one of the two characters is not more widespread nor analyzed in their matrix, but is a misinterpretation by the original describers.  The second suggested autapomorphy is the shortness of the centrum compared to its height.  And here, Mannion et al. do use that as a character (C26), which could separate Arkharavia in the continuous character analysis.  Arkharavia has a value of 0.4 (kudos to Mannion et al. for describing their characters so well, btw), which is also scored that way in Camarasaurus and Tangvayosaurus (both the lowest values in the matrix).  So is Arkharavia indeterminate compared to these two genera?  Well no, because neither of these has procoelous centra which Mannion et al. just commented on.  Both are coded 0 for that character (C27), while Arkharavia would be a 1 (or a 0.1 in the continuous version).  Ironically, though they say it's an "indeterminate somphospondylan based on its mildly procoelous, anteroposteriorly short centrum", this is actually a unique character combination in their own matrix!  And based on these two characters alone, it would end up equally parsimonious as a camarasaurid or sister to Tangvayosaurus/Fusuisaurus, so would be Macronaria instead of definitely in Somphospondyli.  Now do I think this character combination means Arkharavia is valid?  No.  The degree of procoely can change in sauropod tails, and doesn't even always follow a simple progression.  Similarly, the elongation of centra changes between vertebrae, and several taxa are only 10% away in Mannion et al.'s matrix.  You would have to examine the degree of variation in each within taxa and see if the position of Arkharavia's holotype in its tail could be constrained.  But note you'd have to do this to support either option- validity or indeterminacy.  This is the start of the kind of work that would need to be done, and Mannion et al. don't come close or even get the summary of why they think it's invalid correct.  Then you'd need to look at the other morphologies preserved in the holotype, which probably also vary throughout the caudal series, and may be scorable in their matrix so that Macronaria incertae sedis isn't the most parsimonious placement, etc etc..  To their credit, the authors do assume indeterminacy less than most authors, and call several other taxa only provisionally indeterminate until they are studied in more depth.

Okay, I have another general complaint as well, and that's that no alternate positions for taxa were tested.  The authors do run a bootstrap-esque test, but those aren't useful for trees with incomplete taxa since they easily destabilize clades that are otherwise well supported.  They do have a handy Table 7 that lists alternative placements for taxa by different authors, which will make it easy for someone to check their homoplasy in the future though.  Furthermore, the analysis in general is well done, with ordered characters, various tests of how to work in continuous states, and well described characters.  Their phylogenetic definitions are also top notch, using eponymous type species.  Maybe with Giraffatitan falling closer to Cedarosaurus, Abydosaurus and Sonorasaurus than to Brachiosaurus, those refusing to use the new genus name will finally change their mind.

Oh, and I hate the continuation of the myth that "Titanosaurus is indeterminate and thus its co-ordinated rank-taxa must be abandoned (Wilson & Upchurch, 2003)."  Why oh why did Wilson and Upchurch start the legend that indeterminate taxa can't have eponymous ranks in the ICZN?

But besides these minor problems, the paper's excellent.  And it's open access, at the address below!  I highly recommend anyone interested in sauropods check it out, as while it doesn't solve all the problems with basal macronarians, it starts us on the right track for many of them.

Reference- Mannion, Upchurch, Barnes and Mateus, 2013. Osteology of the Late Jurassic Portuguese sauropod dinosaur Lusotitan atalaiensis (Macronaria) and the evolutionary history of basal titanosauriforms. Zoological Journal of the Linnean Society. advance online publication.
DOI: 10.1111/zoj.12029
http://onlinelibrary.wiley.com/doi/10.1111/zoj.12029/pdf

No, of course not, as we saw in my earlier post where correcting codings and adding data excludes them from the clade.  But Peters thinks they belong.  Let's go through his supporting characters below.

Figure 1. Trialestes holotype skull (left) modified after Reig (1963), and forelimb (right) after Bonaparte (1978).  Unknown portions of skull and hypothetical dotted sutures drawn by Reig removed, except around the external mandibular fenestra which is apparently present but of unknown shape.  Note these are the only illustrations available, and no photos or further information on the skull not obvious from Reig's drawing, so when Peters codes things like skull width or palatal characters, it's just his imagination.

Theropoda (Trialestes, Herrerasaurus, Marasuchus, SMNS 12352, Tawa, Coelophysis)
3. Skull less than 1.2 times wider than tall.  This was miscoded as present in Trialestes and Marasuchus (see figures 1 and 2), when they cannot actually be coded.  Also, this is present in all examined dinosaurs except Lesothosaurus, so many 'phytodinosaurs' were miscoded.
13. Snout convex and angled over external naris.  This was miscoded as present in Trialestes and Marasuchus, when they cannot actually be coded (see figures 1 and 2).  One side of Herrerasaurus' snout is smoothly curved instead of angled, so it can't be coded unambiguously.  As more derived theropods reverse this in Peters' tree, this completely eliminates the character's validity.
55. Posterior jugal process descends.  This was miscoded as missing in sauropodomorphs, Silesaurus and Lotosaurus.  In actuality, all examined dinosauriforms have it except Daemonosaurus, Heterodontosaurus and some Coelophysis individuals.
63. Jugal posterior process extends more than halfway down cheek.  This was miscoded as absent in Gracilisuchus, which would make it a symplesiomorphy lost in phytodinosaurs instead.
89. Maxilla palatal process present.  This is actually present in all examined taxa except seemingly Turfanosuchus, but Peters miscoded sauropodomorphs, ornithischians and Gracilisuchus as lacking it.  Amusingly, two of the three 'phytodinosaurs' he coded (Pisanosaurus and Pantydraco) actually can not be, and neither can Trialestes (see figure 1).
92. Choanae "medial rostral pinch", or as Peters has explained via pers. comm., choanae with posterior end angled medially due to the palatine lining some of the lateral margin, and maxillae anteriorly pinched instead of parallel.  You can see this is a composite character, and indeed the choanae are lined by the palatines laterally in their posterior part in all taxa examined here.  Ironically, Coelophysis and Herrerasaurus actually have more parallel maxillae than the other two taxa Peters codes that are actually scorable- Lesothosaurus and Silesaurus.  Trialestes cannot be coded from published data (see figure 1), while SMNS 12352 has more pinched maxillae.  Once all of the taxa Peters didn't code or include are scored, subparallel maxillae are present in Arizonasaurus and Dinosauria, except for ornithischians besides Heterodontosaurus (which works with heterodontosaurids being the basalmost ornithischians).
206. Metatarsus compact, which as Peters codes it seems to involve metatarsals II-IV contacting over most of their shafts.  Miscoded as absent in Silesaurus and Pisanosaurus, and given the wrong polarity in Ornithischia because he has Scelidosaurus most basal (when Pisanosaurus, heterodontosaurids and Lesothosaurus are most basal, a compact metatarsus is primitive for the clade).  This is actually primitive for dinosauriforms and lost in sauropodomorphs and thyreophorans.  Also, Trialestes was coded for it based on a dinosaurian foot.  Ironically, that metatarsus is not restored as being compact anyway.
216. Pedal phalanges of digit IV shorter than metatarsal IV.  Again, Trialestes was coded based on the wrongly referred foot.  Even that foot only preserves phalanx IV-4, part of IV-3 and part of ungual IV, and metatarsal IV is broken so its length is unknown.  So it couldn't be coded anyway.  Herrerasaurus was not coded but lacks the character, so it would actually support the Marasuchus+Coelophysis node in Peters' phylogeny.  But it's lacking in the next most derived scorable taxon, Dilophosaurus.  As Tawa cannot be coded yet, this makes it ambiguous.  It was also miscoded as absent in Saturnalia, though Pantydraco was left uncoded and lacks it.
Results- All of these only optimize to Theropoda due to miscodings.  Trialestes only has two, which are both primitive once taxa are coded correctly.  Marasuchus also only has two, one of which is primitive once taxa are correctly coded, though the other which would be valid for joining it with Coelophysis.  SMNS 12352 has two, but one is present in almost all taxa and the other is lacking in the actual theropods.

(Herrerasaurus, Marasuchus, SMNS 12352, Tawa, Coelophysis)
This is Theropoda in Peters' more recent tree.
161. Scapulocoracoid fused.  Miscoded in Tawa, while Coelophysis can have unfused bones too.  So if coded correctly, would only ambiguously support this clade.  Also miscoded as absent in Saturnalia.  Honestly, this near certainly varies with age, so related taxa like Pampadromeus, Panphagia and Pantydraco with unfused elements may just not be fully grown.
179. Manual digit IV reduced in width.  In Peters' tree, this is convergent with sauropodomorphs+ornithischians.  But that's only because he miscodes it as absent in Pisanosaurus (doesn't even preserve digit IV), Effigia and Poposaurus.  If coded correctly in his tree, it would diagnose Dinosauria and reverse in Lotosaurus.  Also note SMNS 12352 lacks it (see figure 3), though Peters doesn't code its hand.
180. Manual phalanx II-2 longer than II-1.  Peters again doesn't code SMNS 12352's manus, but it lacks the character.  While this is actually usually thought to be a theropod character, its presence in taxa Peters doesn't include like Guaibasaurus, Efraasia and Eocursor might suggest it's primitive to Dinosauria instead.
182. Metacarpal V absent.  This is miscoded, as both Herrerasaurus and Coelophysis have metacarpal V.  So does SMNS 13252 (see figure 3), which was again not coded for manual characters.
191. At least semiperforated acetabulum.  This is another character that is convergent in his tree with sauropodomorphs+ornithischians.  But that's only because he miscodes poposaurs, Pampadromaeus and Panphagia as lacking it.  It's actually present in all dinosaurs (and convergently poposaurs), while Marasuchus has at most a tiny slit that Silesaurus might also have (note the non-included Sacisaurus has it, but Asilisaurus does not, so the exact sequence of acquisition at the base of Dinosauriformes is uncertain).
194. Large pubic boot.  This was miscoded as present in Marasuchus, when the pubic apron of that taxon is actually only folded over to make it appear as if the bone expands distally.  As Coelophysis lacks it, this makes it shared between only Herrerasaurus and Tawa.  I have no issue with them being related, though its absence in the unincluded Eodromaeus complicates things.
Results- Marasuchus only has two, one of which is primitive for Dinosauria (at least) once it is coded correctly, and the other which is an ambiguous synapomorphy once coded correctly and may be ontogenetic.  It also lacks one.  SMNS 12352 has none and lacks two, though it was not even coded for them.

Figure 2. Skull material of Marasuchus specimen PVL 3870, modified after Bonaparte (1975). Maxilla in medial view, though Bonaparte thought the anterior fragment was the premaxilla and the posterior margin was the antorbital fenestra, this isn't true.  The postorbital was misidentified as a quadrate by Bonaparte and has been moved here.  These new interpretations are all from Sereno and Arcucci (1994).

(Marasuchus, SMNS 12352, Tawa, Coelophysis)
11. Nasals with parallel sides in dorsal view.  Marasuchus doesn't even preserve nasals so is miscoded (see figure 2), and their shape hasn't been reported in Tawa, so that's miscoded too.  Furthermore, SMNS 12352 and Coelophysis actually have posteriorly expanding nasals like Herrerasaurus, so every taxon was miscoded.  And lest you think posteriorly expanding nasals could be a theropod character of SMNS 12352, note the crocodylomorph Terrestrisuchus also has them.
146. Second sacral rib not bifurcated.  This is here because Peters miscodes all other scored taxa as having a bifurcate rib, but no archosaur actually has one.  Confusing.  Maybe he misunderstood the character?
147. Second caudal transverse process longer than centrum.  This is miscoded as present in the two scored taxa- Marasuchus and Coelophysis.  It's actually only present in Hexinlusaurus among included taxa, though Peters didn't score that.
152. Proximal caudal neural spines shorter than centrum height.  This was miscoded as being present in Coelophysis.  Thus it would only ambiguously support this clade.  Even then, the coding in Tawa is based on a schematic skeletal reconstruction, while the caudals of Marasuchus are preserved to show the ventrolateral faces and artificially shorten the spines due to perspective.
154. Mid caudal centra (here defined as vertebrae which reduce the transverse processes and spines but not to mere ridges) at least three times longer than tall.  *Gasp*  For once, a valid character.  Marasuchus does indeed share this with Tawa and avepods, as well as the non-included Chindesaurus and Eodromaeus.
208. Metatarsal I less than 50% of metatarsal III.  This is miscoded and is absent in Marasuchus.  Among included taxa, it's only present in Coelophysis and some Lesothosaurus individuals.
Results- Marasuchus has two, one of which is valid and the other which is present in all archosaurs.  It may have another, but that would only connect it with Tawa if THAT taxon's reconstruction is correct, not Coelophysis.  It also lacks two.  SMNS 12352 lacks one and doesn't have any.

Figure 3. SMNS 12352 snout in lateral view (C) and manus in extensor view (D), after Sereno and Wild (1992).

(SMNS 12352, Tawa, Coelophysis)
13. Snout triangular due to having only a slight convexity over the naris.  SMNS 12352 doesn't preserve the snout tip, but the low angled dorsal surface suggests it had a notable convexity if anything, so is miscoded.  This may be a useful synapomorphy for Tawa and Coelophysis, and the miscoded Daemonosaurus.
20. External naris angled 30 degrees or less from horizontal.  SMNS 12352 doesn't preserve any part of the external naris, so was miscoded (see figure 3).  This again actually does diagnose Tawa and Coelophysis, and is also found in the non-included Eoraptor.
23. External naris placed at snout tip.  This is contrasted with adjacent taxa being coded as having a naris "at snout tip but dorsal", which highlights its composite nature coding for both anteroposterior and dorsoventral placement.  But none of that matters here, as SMNS 12352 doesn't preserve any part of the external naris, so can't be coded regardless (see figure 3).
Results- SMNS 12352 can't be coded for two and probably lacks the third. 

Total Theropod Results- Of eight characters, Trialestes only has two, and both are primitive once miscodings are corrected.  Small wonder it's no longer a theropod in Peters' newest tree.  I would say the wrongly referred foot influenced it, but even that lacks Peters' theropod characters.
Of twenty characters, Marasuchus has five, might have two more, and lacks three.  Of the first seven, three are primitive for dinosaurs once coded correctly in other taxa, and three more are absent in a basal theropod so are ambiguous (one is also probably ontogenetic).  The one valid character is that it has elongate mid caudals, but as it lacks e.g. more than ten dinosauriform and saurischian characters neglected by Peters, this is hardly meaningful.
Of twenty-three characters, SMNS 12352 has two.  Maxillary palatal processes are present in all archosaurs, and a pinched palate is lacking in the actual theropods.  It lacks five, and while one of those is actually lacking in theropods as well, Terrestrisuchus has the same state.  I should note that Terrestrisuchus itself falls within Theropoda if only skull characters are coded, so Peters' characters cannot distinguish theropod and sphenosuchian skulls even when correctly coded.  This makes it even more problematic that Peters didn't code SMNS 12352's manus.

As you can see, Peters' characters provide no evidence Trialestes or SMNS 12352 are theropodan, and only a single character supporting Marasuchus as one, and that's vastly outweighed by the dinosaurian and saurischian characters he doesn't include that have been standard in the literature for two decades.

Jason Brougham has a post at his blog discussing Larry Martin, one of the BAND* leaders and later MANIAC** who passed away in March.  I met Larry at SVP 2002, where my reaction was-

"I had a good discussion with Martin. He's quite a nice guy, it's a shame he's so wrong about almost everything dinobird-related. Seems he officially believes that maniraptorans are birds, but that other coelurosaurs are unrelated. He terms this the "Paulian hypothesis", though it's only similar in thinking of maniraptorans as 2F and preferring the arboreal origin. In his mind, maniraptorans and other birds evolved from a Longisquama-like creature. And like Czerkas believes, some taxa (eg. Scansoriopteryx) are just too hard to place as birds or dinosaurs until a more in depth study is completed. The same old ABSRD arguments were brought up (digit homology, terrestrial theropods, Yixian feathers being collagen, etc.). He referred to both ichthyosaurs and Psittacosaurus as having structures like those found in Sinosauropteryx et al., which is just plain wrong of course. In any case, he does have an interesting eumaniraptoran that will be out soon."

That eumaniraptoran was later named Microraptor gui, btw.  As I recall, he said the leg remiges proved M. gui wasn't terrestrial, therefore birds evolved flight from trees, and therefore birds aren't dinosaurs.  I then said I have no issue with some dinosaurs being arboreal, which I think he was surprised by.
* Birds Are Not Dinosaurs, contrasted with BAD being Birds Are Dinosaurs
** Maniraptorans Are Not In Actuality Coelurosaurs

I feel Jason's post bends over backwards to seem fair, but also that it leaves out Martin's greatest positive influences on paleontology. 

He first writes about Martin being on "our side", which seems to be opposed to creationists, since "He spent his life studying evolution, observing fossils, and we all agreed that dinosaurs and birds were closely related archosaurs."  It seems trivially true that anyone will be on your side about some value or opinion.  Indeed, even evangelical creationists are on "our side" for wishing to teach people the truth, we just disagree on what that truth is.  In any case, as a scientist I think he would have been proud to be against "our side" when it came to heterodox ideas he strongly defended.

Jason believes Martin had a beneficial effect on bird origins research in that BADists "wrote some papers they would not have written unless they felt the need to answer Martin. In the process, progress was made on quantifying the ‘temporal paradox’ issue, and everyone’s hypotheses became more precise and explicit."  But I honestly can't think of many examples where Martin's criticisms directly led to science examining the issue more closely to result in more discoveries, they were mostly just pointed out to be based on fallaceous reasoning or inaccurate interpretation.  If we look at his classic (1983) arguments for BAND, the temporal gap problem had been answered perfectly years earlier by Ostrom (1976).  I don't see Brochu and Norell's (2001) quantification paper as doing more than telling us what we already knew, i.e. the gap between the Tithonian and Aptian is less than between the Tithonian and Triassic.  The arboreal vs. terrestrial rationale actually hindered our side in my estimation, as the BAD response was to double down on the terrestriality of Archaeopteryx and flight origins instead of accepting arboreal theropods could exist, which only occured decades later when scansoriopterygids and microraptorians were found.  These examples can be contrasted with e.g. Jones et al. (2000) instigating research on Longisquama's parafeathers or Burke and Feduccia (1997) instigating research on digital development.

The next argument is that some recent large morphological analyses (e.g. Livezey and Zusi, 2007) have shown Martin was right that convergent evolution could confound cladistic analyses.  I don't think anyone's ever doubted this in principle, as analyses do differ so some must be wrong.  Moreover, the ways such analyses were shown to be confounded were never used by Martin (more characters and taxa, molecular analyses, biogeography, etc.), with his naive falsification and evolutionary scenario alternatives ignored (Makovicky and Dyke, 2001).  Sure Martin (1997) was right(er) than Chiappe that alvarezsaurids are ornithomimosaurs instead of avialans, but it was for all the wrong reasons, so should that really count scientifically?

Finally, Jason says of Martin's 2005 transition to MANIAC that "I have heard few mention that, in this 2004 paper, Martin rather quietly gave up on that view [that dromaeosaurs were only distantly related to birds]."  "... this demonstrates that Martin was open-minded enough to be persuaded by the evidence and to reverse himself on a major part of his hypothesis."  While I do give credit to Martin for finally recognizing this relationship, the details make it look less noble.  First note Martin never actually admitted his quarter century of arguments against Archaeopteryx and Deinonychus being similar were fallaceous, or that this calls into question his entire methodology.  Indeed, he still uses most of them in that very paper, seemingly without realizing his new phylogeny cancels them out (e.g. if maniraptorans are all considered birds, then deriving this whole group from something standard like Ornitholestes eliminates any temporal paradox).  Second, he (as with Feduccia) framed neoflightless maniraptorans as a surprising compromise, when by that time most theropod workers considered it possible if less parsimonious.  The feeling from MANIAC papers is that taxa like Microraptor and Scansoriopteryx have sent everyone back to the drawing board, when BADists have actually been relatively unaffected besides the character distributions in our cladograms.  The impression is an attempt to save face while admitting as little error as possible, which seems distinctly unscientific to me.  Still, I'll say Martin's work was less polemical than Olson's or Feduccia's, the latter's 2013 paper being more unhinged than anything Martin wrote.

Well, that's a lot of criticism of a dead man, but I've never been one to follow the tradition of emphasizing the positive aspects of the deceased while downplaying the negatives.  Yet positives did exist, and I think his greatest legacies in science have yet to be articulated.  Foremost, Larry worked on a LOT besides bird origins.  While I'm not qualified to review e.g. his saber-tooth cat work, his hesperornithine work such as the 1976 osteology of Baptornis was quite good.  He continued such studies until the end of his life, such as his 2011 ornithuromorph predentary paper with Zhou that analysed an often ignored element.  Which brings us to Martin's other great legacy- his students.  I know at least Zhou and Witmer trained under Martin.  Zhou's been instrumental in expanding our knowledge of Jehol bird diversity.  As for Witmer, he has this touching summary on his institutional biography page, which shows my two favorite aspects of his excellent studies are due to Martin-

"I also owe a huge debt to Larry Martin, who got me interested in so many things.  He always encouraged me to look at modern animals along side extinct groups, and this has emerged as my major research paradigm, these nascent ideas later evolving into the extant phylogenetic bracket approach.  And of course it was Larry who introduced me to the previously under-appreciated anatomical system of cephalic pneumaticity, which became my major research focus for a decade and a half.  Although Larry and I are often now pitted as opponents in the fierce debate on avian origins, he has been one of the most important positive influences in my career."

So there are my criticisms and accolades.  But there's one more story I'd like to tell.  Back in October 2004, I decided to write Larry regarding bird origins.  It wasn't meant as a harsh debate, and I wasn't so naive as to think I could do what two decades of published professionals couldn't, but I was intrigued to see where he was coming from and how he would respond to questions and facts that aren't brought up in his papers.  Note this was before his 2005 paper declaring his MANIAC status, but I knew he thought that way due to SVP 2002.  I reproduce the content of this email exchange below, with changes in color and font between Mickey Mortimer and Larry Martin.  I've left out most of the pleasantries preceding and following each actual email, and have formatted them so that e.g. when Martin has four paragraphs, my four paragraphs are responding to them in that order.  While publishing email exchanges without explicit permission is of course frowned on in most instances, I'm hoping my own feelings this is ethical once one party is dead are shared by the community.  I think of Martin's words being like the personal letters of historical scientists that are now public, and it's all scientific exchange matching what he published as opposed to personal details.  So enjoy.  I don't think I've ever read a conversation between a BADist and BANDit, which makes this rather unique.  For all the criticisms I piled on Larry, I don't know many other scientists who would take the time to write such a long and detailed exchange with an unknown undergraduate amateur.  He'll be missed.

I'm an undergraduate at the University of Washington
currently investigating theropod and Mesozoic bird phylogeny.  I heard you
gave a talk the other day where you advanced the hypothesis that
maniraptorans are in actuality birds, and that they are unrelated to
theropods.  I wonder if you could answer a few of my questions.
1. What characters show oviraptorosaurs and dromaeosaurs are birds, while
leaving ornithomimosaurs and tyrannosaurs in Theropoda?
2. What is the sister group of birds + Longisquama in your hypothesis?
3. Do you believe homeotic shifts occur in nature?
Thank you for your time.

I suppose that we could define birds as animals who have or
give evidence of have having an avian wing (primary feathers attached to the
middle digit with the palm extending between the middle and outer digits and
a digit reduction pattern of 2-3-4) all animals with such a wing may
reasonably be supposed to have shared a common volant ancestor.  This brings
dromaeosaurs and oviraptosaurs into the avian fold.  The sister group of
birds and Longisquama (including Longisquama relatives) would probably be
dinosaurs plus many of the more conventional thecodonts.  I am not sure how
crocodilians fit in.  In any case the connection would be very basal within
archosaurs.  Please notice that if dromaeosaurs are secondarily terrestrial
we can expect many reversals of polarity from earlier analysis.  The
frameshift hypothesis was badly crunched by developmental types in a recent
conferance and is only being maintained to preserve a theropod hypothesis
that now fatally flawed.

Accepting your definition of 'bird', why are tyrannosaurs and
ornithomimosaurs excluded?  We have no embryological evidence to know if
they possess digits I-II-III or II-III-IV, and no preserved manual
integument that would tell us if they had primary feathers (no manual
integument has been reported for Pelecanimimus, Dilong, or tyrannosaurids,
though they each preserve integument elsewhere).
What characters do dinosaurs and these 'more conventional thecodonts' share
than Longisquama and birds lack?
Finally, do you mean the particular digital homeotic shift theorized for
theropods was questioned in this recent conference, or the reality of
homeotic shifts as a whole?  In either case, I'd be interested to know the
name of the conference, so that I can examine the references.

Thanks for the reply.  I agree dromaeosaurs and oviraptorosaurs were
secondarily flightless, which indeed leads to reversals of character
polarity from prior analyses.

Tyrannosaurs are excluded because their hand as restored is not avian,
(they are not maniraptoran), maybe evidence could be provided that they
were once that way, but why worry until there is some reason.  They also
lack a lot of the other cranial features, etc.  Recent description of so
called protofeathers on a tyrannosaurid would seem to be clearly muscle fibers 

or ligaments and is probably better seen as evidence for a lack of feathers.

Ornithomimosaurs (including Mononykus) have derived hands with enlarged
MTCI and a reduced wrist.  I can't see how it relates to the avian hand
and think that they are best compared to compsognathids. I think in terms
of the general story, it makes very little difference where these taxa go. 

If Tyrannosaurs are carnosaurs, we know that at least some carnosaurs have
typical dinosaur rosette scale patterns and this may be a dinosaur
synapomorphy.  They also have interdental plates covered by a 

superdentary bone and this would make them very unlikely birds.  They also
have a long postacetabular ilium, a derived feature found in the earliest dinosaurs and absent from
all of the very early birds.

The conference was the Society of Avian Paleontology and Evolution. 

Essently none of the developmental types thought much of frameshift
although one tried to preserve bird/theropod by postulating a presently 

unknown ancestral six fingered hand.  You have to ask yourself about 

the credibility of an idea that requires a lot of ad hoc new science
to keep it alive.

I accept your proposal tyrannosauroids lack some maniraptoran characters.
What prevents them from being maniraptoran relatives though?  Branching off
the bird line before maniraptorans developed all of their distinctive
traits?  They do share a lot of characters with maniraptorans, after all.
Regarding Dilong, what features do its supposed feathers have that would
make them less likely to be feathers than the identical structures in
Sinornithosaurus' holotype, or the plumulaceous body feathers of Caudipteryx
and Protarchaeopteryx (besides the fact you know these last three are
maniraptorans; that would be circular reasoning, after all)? 

Check out Ingenia for a maniraptoran example of enlarged mcI, though I admit
no maniraptoran reduces its carpals like ornithomimosaurs.  I agree with you
about Mononykus and other alvarezsaurids being closely related to
ornithomimosaurs.  I even wrote a post to the Dinosaur Mailing List in June
about how they were being put inside Maniraptora and Avialae due to flaws of
most cladistic analyses.  I also agree both groups are close to
compsognathids.  I think ornithomimosaurs+alvarezsaurids could be very
important for your hypothesis, since they show a number of characters you
think of as avian- no supradentary; serrationless teeth with basal
constriction; large sternum; ossified sternal ribs; costal facets on the
sternum; coracoid facets on the sternum; hollow keratinous integument.

Thanks for providing these specific characters.  Tyrannosauroids are almost
universally agreed to be coelurosaurs now, so we don't have to worry about
rosette scale patterns yet.  Velociraptor and Dromaeosaurus possess
supradentaries, so that can't bar tyrannosauroids from being on the bird
line.  If we use the ratio between postacetabular and preacetabular
processes to be an indicator of postacetabular length, the long
postacetabular processes of tyrannosauroids (~120-140%) are comparable to
some maniraptorans (Microvenator- 132%; Ingenia- 128%; Sinornithoides-
146%).  So that can't bar them from being on the bird line either.  Unless
you use a different ratio. 

I completely agree with the latter sentiment.  Unfortunately, the 2004 SAPE
abstracts aren't available yet, so I'll have to wait to see what new data
was presented.  It will be interesting to see how they deal with homeotic
shifts observed in human cervical number, which we can validate since we
know the geneology of the people in question.

please give citations for superdentaries in maniraptorans of any sort!

I think that the position of tyrannosaurs is quite controversal and it
doesn't make any difference to me how they fall out.

I am not convinced that any of the so called protofeathers are real.
Everybody has muscles and just because something is on a bird doesn't mean it's a feather.

Gladly.  If you ever want confirmation of my statements, just ask.
Dromaeosaurus-
Currie, 1995. New information on the anatomy and relationships of
Dromaeosaurus albertensis (Dinosauria: Theropoda). Journal of Vertebrate
Paleontology. 15, 576-591.
Velociraptor-
Barsbold, 1983. Carnivorous dinosaurs from the Cretaceous of Mongolia. Joint
Soviet-Mongolian Paleontol. Expedition Trans. 19, 5-120. 

If tyrannosauroids are stem-birds, they would help us understand bird
evolution a lot.  There's a big gap between Longisquama and dromaeosaurs,
but tyrannosauroids help fill it out.  Besides, if theropods and
maniraptorans are so distantly related, it should be easy to tell them
apart, right?  Even in famous cases of convergence like thylacines vs.
canids, Notoryctes vs. talpids or hesperornithines vs. gaviiformes, the
differences are easy to see if one looks at skeletal details and not gross
resemblence.

This is a very interesting stance I've not seen in the literature.  How do
you reconcile this with the fact Shuvuuia's hollow cylindrical structures
are made of keratin (Schweitzer et al., 1999), and not collagen, actin or
myosin?

I doubt that any keratin has survived since the Cretaceous.  At least the
mollecular types don't buy into Mary's results.  Evidence that any of these 

structures were hollow is hard to come by.  All of the morphological structure 

is best expained by other interpretations. 

Quite a lot of the anatomy of dinosaurs has been uncertain, for instance
the two decade struggle to get the hand and wrist of Deinonychus correctly
interpreted.

What are the citations for molecular biologists disputing Schweitzer et
al.'s paper, and/or keratin fragments being unable to survive since the
Cretaceous?  Schweitzer et al. state quite plainly "These fibers are seen to
be hollow, both grossly and in microscopic cross section," and photograph an
example in figure 2.  Which alternative explanation is better for clumps of
hollow fibers 200 micrometers in diameter which show smooth outer surfaces,
pithy inner surfaces, plate-like structures at one end, small filaments on
the outer surface, and consisting of microfilaments of 90-95 nanometers?

Agreed.  Even now, there are interesting new possibilities being raised,
like Gishlick's (2002) idea maniraptorans' distal carpal III is fused to the
base of metacarpal III.  As might be expected in e-mail discussions, it
seems a couple questions I'm curious about have got lost with all the
supradentary and keratin information.  Namely-
Why are some (which?) 'thecodonts' more closely related to dinosaurs than to
Longisquama+birds?
Given other examples of tetrapod convergence, shouldn't it be easy to tell
maniraptorans from theropods if they are so distantly related?

There has been quite a bit of rethinking of some of the earlier claims and
right at the mommentI think that real evidence of intact Tertiary proteins 

is pretty cutting edge.  Let's say for argumentation that she has keratin tubes, 

what feather structure could they be?  How would it form?
We should have some criteria for thinking something is a feather beyond
finding it on a dinosaur if we intend to show that dinosaurs have feathers.

I think that Roger Sawyer who provided the antigens is going to or has commented on the paper. 

Alan Feduccia probably could give you more commentary. 

Tyrannosaurs are so highly derived that I can't see that they would help much. 

Their wrists, hands, ankles. feet and skulls are all more derived and modified 

than the other tax we have discussed.

Well, these are only supposed to be keratin fragments, not intact keratin.
So that may make it more plausible to you.  If they are keratin tubes, the
feather structure represented would be the rachis and/or barbs.  Prum (1999)
goes into detail about how feathers form ontogenetically and perhaps
phylogenetically as well.
I agree with your statement we need non-circular reasoning if we wish to
show dinosaurs have feathers.  Prum has defined feathers in relation to the
feather follicle, making the first epidermal structure originating from a
follicle homologous to those in living birds the first feather.  I might
just be naive, but it seems to me any epidermal derivitive with a slender
cylindrical base necessitates a follicle to grow from.  So those of
stem-birds (like Confuciusornis and Sinornithosaurus), pterosaurs, and
Longisquama are are potential feathers, if we can establish homology with
birds' feathers.  This latter job is not easy, but is helped by phylogeny
and feather morphology.  As an example of the former, no non-feathered taxa
are closer to modern birds than Confuciusornis or Sinornithosaurus, so their
structures are phylogenetically congruent with homology.  An example of the
latter is the branching observed in the structures of Sinornithosaurus and
Dilong, which is unique to feathers.

Thanks.  I'll ask them. 

This doesn't appear to be true for basal taxa like Dilong.  Besides a few
characters (symmetrical premaxillary teeth in section; fused nasals; nasals
anteriorly convex in transverse section; pneumatic articular; preacetabular
notch on ilium), it looks like a good stem-bird.  Sure, it probably lacked a
true semilunate and other maniraptoran characters, but so did Longisquama.

If I understand Prum's model, his protofeather is none of the above.  It
does not claim homology with any part of a feather other than the collar 

and completely ignores the feather sheath.  It was created directly 

from the dinosaur protofeathers so there is no surprise that it looks like
them. 

I certainly don't believe the so called "feathers" in pterosaurs, and I am
amazed that nobody seems to to be upset with spreading feathers everywhere
especially when the majority of dinosaurs can be shown to be covered with scales. 

Why think that these things are feathers when they can't be distinguished
from fossilized muscles found in other organisms.

Notice that Mary's study comes from sediments where we might not expect
ancient preservation while they > are not duplicated where the opportunity
seems better.

Prum's (1999) stage I feather is homologous to the calamus of modern
feathers, in the sense that it is formed by an undifferentiated follicle
collar.  Sorry for not specifying the calamus last time, I was grouping it
with the rachis in my mind.  Prum and Dyck (2003) describe sheath morphogy
and development in detail.
Though I can't claim to know Prum's thought processes, Prum and Dyck
describe how the model is largely dictated by the developmental mechanisms
of feathers (hierarchical modules), not merely resemblence to
Sinosauropteryx and Beipiaosaurus feathers.  Barbs have to evolve before
rachis because the rachis is just a fusion of barb ridges; barbules have to
evolve after barbs because they are formed by the differentiation of cell
layers in barb ridges; the calamus has to evolve first because the barb
ridges are differentiations of the collar that forms the calamus.  How do
you explain the structure of Longisquama's parafeathers being primitive for
feathers if they have a rachis and a barbless vane (as shown by those
successive magnifications at SVP 2001), when the rachis forms from fused
barb ridges?

Basically every pterosaur worker believes pterosaurs had filamentous
integument.  Why would you doubt it?  I know Feduccia cites Unwin and
Bakhurina (1994) as a contrary view, but they specifically noted such
integument was present in later papers and online communications.  They were
merely saying that the supposed Sordes hairs _figured up till that point_
were internal fibers.  I personally don't think they are feathers, but
that's only because there are so many scaled taxa between pterosaurs and
birds.  Filamentous integument evolved at least twice anyway (birds,
mammals), why not a third time?  And given the standard phylogeny, diapsid
filamentous integument only shows up twice- pterosaurs and coelurosaurs.
Unless you count Longisquama's or Psittacosaurus' structures. 

What specimens would these fossilized muscles be in?  In any case, they can
be distinguished from muscles and collagen (Lingham-Soliar, 2003) in the
following ways.
1. Dinosaur feathers are too long to be collagen fibers.  Even if one were
to hypothesize axial frills on Sinosauropteryx, how do you explain elongate
filaments on left and right sides of dorsoventrally preserved animals (NGMC
91; many Confuciusornis; Eoenantiornis)?  Elongate filaments on areas not
expected to have thick skin or need elongate muscle fibers (skull of
Microraptor; middle of Bewipiaosaurus' ulna)?
2. Dinosaur feathers are mostly perpendicular to the body wall (along ulna,
shoulders, femur of NGMC 91; head and chest of Microraptor; tail and ilium
of Sinosauropteryx), which is compatable with collagen, but not with muscle.
3. Dinosaur feathers are not inside the body wall like the fibers of
ichthyosaurs.  Ichthyosaurs have a very thick body wall, analogous to
cetaceans.  But proposing the body wall of theropods extended as far away
from the bones as seen in NGMC 91 or Eoenantiornis is preposterous.
4. Dinosaur feathers are hollow, unlike collagen.  Even if ichthyosaur
fibers look hollow due to mineralization stages (and you doubt Yixian
dinosaur feathers based on this), the filaments of Shuvuuia are three
dimensional, so cannot be explained in this manner.
5. Dinosaur feathers are suspiciously distributed similar to bird feathers.
There are none on the feet or distal snout.  Elongate feathers are
conveniently on the ulnar side of the lower arm (Beipiaosaurus, NGMC 91) and
distal tail (NGMC 91).  In particular, if they were muscles, we would expect
long tibial fibers on at least some specimens.
6. Dinosaur feathers are sometimes intermixed with vaned feathers, such as
on the head of Microraptor.  This is fairly indisputable proof that whatever
the more simple structures are, they are integument.
7. Dinosaur feathers are made of beta keratin, not collagen, actin or
myosin.  At least in Shuvuuia's case.
8. Why are Yixian lizards, choristoderes, salamanders and psittacosaurs not
covered with these structures?  They should have muscles and collagen, after
all.
How do you explain all of these factors?  I admit they could also be
homologous to turkey bristles (Sawyer et al., 2003), but the data seem to
argue against muscle or collagen.

Specimens from the Djadockhta can preserve keratinous structures, in the
form of claw tips (e.g. Citipati in Clark et al., 1999).  On the other hand,
how many specimens with preserved internal soft tissues have been found
there?

The theory that the rachis is fused barb ridges was rejected some decades
ago and the problems that it had then still aren't resolved. 

Why would you have a calmus if you have nothing else and where does the
feather sheath come in?  

Does Prum actually say that the protofeather is a calamus.  I don't
remember his saying so in any presentation.  I asked him once what part of a 

feather he was talking about, but the collar was all that I got out of it. 

You might try Paul Maderson if you want a critque on his model
of feather development.

Have you read Harris et al. (2002), which shows barb ridges fusing to form a
rachis in figure 4F-J?  Indeed, barb ridges can be induced to fuse to form
rachis if the follicle is split into two (Prum and Dyck, 2003).  Any
explanation?
Harris MK, Fallon JF, Prum RO. 2002. A Shh-Bmp2 developmental module and the
evolutionary origin and
diversification of feathers. J Exp Zool (Mol Dev Evol) 294:160-176.

Among the more plausible theories is for insulation (it would be comparable
to having fur).  Since the sheath is subsumed by the calamus once the latter
starts developing, and becomes an indistinguishable part of it, one might
assume a feather which is formed completely from the undifferentiated
'calamus setting' of the follicle collar would lack a sheath.  Sheaths would
have evolved only once the follicle collar became differentiated into barb
ridges. 

Prum says stage 1 feathers were formed by an undifferentiated follicle
collar, which is the same way that modern birds form their calamus.
Portions of feathers are only homologous in the sense that homologous
genetic patterns are being expressed at the time they are formed.
Maderson's model seems to contradict the developmental and genetic evidence
in asserting scales and feathers are homologous past the placode stage and
that barbs are formed from frayed scale edges.

Do you have any explanation for why muscle or collagen would exhibit the
eight traits I noted last time in coelurosaur and bird filaments?  They're
listed below in the copy of that message.

Comparison with dinosaurs should be through the common ancestor of the

maniraptorians and birds which according to the cladograms would have an 

avian wing.  If anything else is included as closer to maniraptorians 

than to birds, it would share that ancestor and hence be uninformative. 

If microraptor is a good model the common ancestor would not be bipedal. 

Longisquama has many feather features while protofeathers have essently none.

It also has an avian shoulder girdle.

Yes, but tyrannosauroids and ornithomimosaurs would be outside the
maniraptoran+birds group, not necessarily have an avian wing (presence of
primaries unknown), and thus be informative.

Sure, but the stem leading to that common ancestor could be bipedal.  We
don't have Longisquama's hindlimbs, after all. 

I suppose I'll bite.  Like Longisquama's structures and bird feathers,
protofeathers are elongate, have a cylindrical base (hence, follicular
development), and a hollow shaft (Shuvuuia).  Pulp caps and sheaths are not
even seen in Yixian bird remiges or retrices, so their apparent absence in
protofeathers is meaningless.  The vanes of Longisquama's structures consist
of a two-layered sheet (since they were filled with sediment; Reisz and
Sues, 2001), so are only superficially similar to a feather vane (which
forms from barb ridges).  I fail to see any feather features parafeathers
have that are absent in protofeathers, let alone many.  Are there any I
missed?

Could you be more specific?  Coelurosaurs have slender scapulae and furculae
too, so those characters can't be used to place Longisquama closer to birds
than coelurosaurs.  I can't recall hearing of any other avian pectoral
characters in Longisquama.

Why you resist the one that has a lot of evidence for avian structure and
support the one that does not is more interesting to me than the debate. 

If you want to argue a bipedal ancestor and I would ask why you would even
care?  Than you must go quadrupedal to bipedal to quadrupedal to bipedal.  This seems to be
tedious and should only be pushed because of compelling evidence. 

If tyrannosaurs should turn out to be another secondarily terrestrial
lineage, I don't see how that advances the discussion.

It's exactly the same for me, though of course we have different views
regarding which specimens have a lot of evidence for avian structure and
which have less.  I don't expect to convince you my opinion is correct
(since it's been argued many times in the last couple decades by people with
far more experience) in this debate.  I'm mainly curious why you hold your
position and how you justify it.
But it's only fair I explain why I resist and support what I do too.  In
regards to Longisquama, here are the reasons I don't accept it as feathered.
Reisz and Sues (2000) have shown the supposed sheath is actually an
infilling of sediment.  This is proven by the fact that it covers the vane
corrugations on both part and counterpart, so must be internal.  I have not
heard a defense of why this is wrong from you or anyone else who supports a
feathered Longisquama.
The vane, being formed of two sheets, is unlike a feather vane in everything
except its expanded shape.  I've heard no developmental hypotheses for
changing this into a vane of barbs from you, Maderson or anyone else.  The
fact it can fold or is expanded distally has no relevence if it isn't
homologous.
Senter (2003) notes the supposed pulp caps are troughs between corrugations
on the middle vane.  He also describes the structures as being tripartite,
with anterior, middle and posterior vanes (the posterior vane narrows
distally until it disappears at midlength, while the middle and anterior
vanes expand to form the distal half.  I don't have the proper photos to
determine if these features are correct, but the fact multiple
interpretations exist certainly makes me weary of accepting Jones et al.'s
view (especially when the latter has proven incorrect in the ways described
above, and in regards to the supposedly separate barbs too- the successively
enlarged photos of the vane edge at SVP 2001 were convincing).
All this leaves in regards to featherlike characters is the narrow base,
which isn't too convincing since protofeathers exhibit it too, and the rest
of Longisquama's anatomy places it outside Sauria (Senter, 2003; 2004).
I've told you why I support protofeathers, with my eight ways they differ
from collagen and/or muscle.  Until you tell me why those are incorrect, we
can't progress on that topic.

When you said Microraptor was quadrupedal, I assumed you meant while
climbing.  While on the ground, you think Archaeopteryx and Confuciusornis
were bipedal, and since the former is so similar to Microraptor, I assumed
you thought it was bipedal on the ground too.  So if we are concerned about
terretrial locomotion only, birds are always bipedal, which is congruent
with ornithomimosaurs or tyrannosauroids being stem birds.  While climbing,
I don't see why small ornithomimosaurs or tyrannosauroids wouldn't use their
hands too.  Hell, with more arm/wrist mobility and perhaps no remiges, it
might have been easier for them than for maniraptorans. 

Here are my thoughts for how it could advance the discussion.
Foremost, I'm trying to understand how you justify separating maniraptorans
from theropods.  I know you'll use the homeotic shift for four-fingered
theropods, so I'm concentrating on the tridactyl ones.  You suggested
postacetabular length and supradentaries, but I showed those characters
don't work.  It's just such an odd concept to believe theropods and
maniraptorans are so distantly related, while being unable to assign some
taxa known from many complete skeletons to either group.  At least back when
you thought maniraptorans were dinosaurs, you had a list of characters that
could be used to separate dinosaurs from birds (hypopubic cup; expanded
tooth roots; four carpals; etc.).  So although you thought the groups were
superficially similar, these details could be used to differentiate them.
But that doesn't seem to be true for your new view.  This confuses me.
Secondly, your entire philosophy of 'not caring' about the relationships of
tyrannosauroids and ornithomimosaurs is confusing.  Finding that
maniraptorans are birds warrants a public talk, but what the next most
closely related group is seems unimportant to you.  There's a huge
morphological gap between Longisquama and birds, and you haven't been able
to give reasons tyrannosauroids and ornithomimosaurs don't fill that gap.
If they are stem birds, it would give us more evidence to use when deciding
what the next most closely related group is.  And I assume that question is
important to you.  This is analogous to my confusion regarding why you or
any other supporter of feathered Longisquama has never tried to figure out
where in Archosauria it goes.  The relationships between archosaurs have
been well resolved for over a decade, I would think such an important taxon
would be worth classifying more precisely.

No, of course not.  Phytodinosauria doesn't even exist.   But Peters doesn't believe that, due to the many issues discovered in my evaluationof his analysis.  Last time we looked at the characters he uses to support his heterodox Theropoda.  This time we'll look at the characters he uses to support his heterodox Phytodinosauria and internal clades.  A spoiler for those who don't want to read further- none of Peters' clades are even plausible except for ornithischian Daemonosaurus, which is rejected by "only" 7-10 more steps compared to 25-76 more steps for his other clades.

Phytodinosauria (Panphagia, Pampadromaeus, Sauropodomorpha, Daemonosaurus, Ornithischia, Silesauridae, Poposauridae)
8. Posterior maxilla not flared laterally to form constricted snout.  This was coded by Peters for way too many taxa, and actually has a very mixed distribution.  Effigia, Coelophysis (miscoded), Pantydraco and Heterodontosaurus (not coded) lack it, while Lotosaurus (miscoded), Herrerasaurus, possibly Pisanosaurus (not coded) and Lesothosaurus (miscoded) have it.  Daemonosaurus cannot be coded, contra Peters.
22. External naris faces dorsolaterally instead of laterally.  Peters again codes this for many more taxa than can be evaluated, and miscodes Heterodontosaurus and Silesaurus as dorsolateral when they are actually lateral.  In Peters' topology it's still recovered as supporting this clade, but barely.  Daemonosaurus cannot be coded, contra Peters.
45. Frontal without posterior process.  This was an example in my list of characters misunderstood by Peters.  No included taxon has such a process.
69. Squamosal and quadratojugal form a semicircular indentation in the infratemporal fenestra.  Peters codes this as present in Pampadromaeus (actually lacks it), Lotosaurus, Silesaurus (actually unknown) and Shuvosaurus (lacks it).  That already disqualifies it, but I'll also note that the not included Plateosaurus and Massospondylus carinatus can have a semicircular or pointed indentation, so it's quite a variable character.  Again Daemonosaurus cannot be coded, contra Peters.
119. Dentary decurved.  This is miscoded in Panphagia, Massospondylus kaalae and Daemonosaurus, and not coded in Saturnalia (actually absent).  So only Pampadromaeus and Pantydraco are correctly coded as having it, and I have no issue with this being a synapomorphy within Sauropodomorpha.
125. Posterior mandible deepest anteriorly.  This was miscoded as present in Pampadromaeus, Panphagia, Shuvosaurus (actually unknown) and Effigia.  So it would actually diagnose the sauropodomorph+ornithischian node in Peters tree, though its absence in the non-included Efraasia makes its convergent development in each group likely.  Again, this is miscoded in Daemonosaurus.
Results-  Of six characters, Daemonosaurus has one (which is found in all examined taxa) and lacks two.  Only the external naris being angled more dorsally even potentially supports the clade.

(Sauropodomorpha, Daemonosaurus, Ornithischia, Silesauridae, Poposauridae)
6. Premaxilla a third or more of preorbital length.  This is miscoded in Pantydraco and Silesaurus.  It actually distinguishes ornithischians and poposaurids, while also being present in Massospondylus kaalae (but not the non-included M. carinatus, Plateosaurus or Efraasia).  Yet again, it is miscoded in Daemonosaurus.
11. Nasals widest at midpoint.  This is also true in Panphagia (uncoded) and Pampadromaeus (miscoded).  This would leave it as a phytodinosaur character, except that Turfanosuchus (miscoded) has it has well, and among 'paraornithischians' only Effigia has it (Silesaurus, Shuvosaurus and Lotosaurus miscoded).  Daemonosaurus is correctly coded as having it.
37. Orbit enters anterior half of skull.  Within 'paraornithischians' this is only true in Lotosaurus, not Silesaurus (unknown, miscoded), Shuvosaurus (unknown, miscoded) or Effigia (miscoded).  Otherwise it would fit combining derived sauropodomorphs with ornithischians.  Though note Daemonosaurus lacks it and is again miscoded.
95. Interpterygoid vacuity tapers sharply anteriorly.  This was coded as absent in Turfanosuchus (present), Gracilisuchus and Herrerasaurus (unknown).   In reality, all examined taxa except Gracilisuchus have it or could have it.
113. Caniniform teeth absent in maxilla.  This is here mostly due to misunderstandings on Peters' part.  He codes the toothless scorable poposaurs as having it, but as they lack teeth of any sort, they should be coded inapplicable for whether those teeth are caniniform.  More importantly, the character is used by authors Peters' cites for it such as deBraga and Rieppel (1997- ch. 95) in the sense that a taxon has caniform teeth when their size is greatest near the middle of the maxillary tooth tow (as opposed to anteriorly, or all being equally large).  So we can code taxa for this character even when they lack elongate pointed teeth that are usually thought of as caniniform.  When we do so, we see that Silesaurus and Massospondylus kaalae truly do lack caniniform teeth, but that Pantydraco doesn't preserve the anterior maxilla and that ornithischians have teeth near the middle largest so actually have a caniniform region.  Expanding to taxa not included by Peters, Sacisaurus still has a caniniform region, as does Efraasia, while Plateosaurus is debatable (first tooth slightly smaller).  So it seems that Silesaurus and plateosaurs evolved this convergently.  Peters correctly codes Daemonosaurus has having caniniform teeth.
115. Lateral teeth blunt.  This is part of a composite character involving sharpness, serration size and crown base constriction.  It's a good example of why such characters are bad, because while Scelidosaurus is coded as blunt (state 1), its teeth are also multicusped with a constricted base (state 3).  In any case, we'll look past the technical errors here and check the distribution of teeth with large serrations and constricted bases, which is what makes the teeth in question blunt compared to a typical archosauriform tooth.
For serration size, Panphagia and Pampadromeus are miscoded as being different than e.g. Thecodontosaurus and Pantydraco.  Yet Peters leaves Saturnalia uncoded, when it actually has small serrations.  Another thing Peters leaves out is that the fangs of Heterodontosaurus have tiny serrations like carnivorous archosaur teeth, so it has both states.  He correctly codes Silesaurus and Daemonosaurus as lacking it, but leaves Poposaurus uncoded when it lacked it too.  All of this combines so that it is equally parsimonious being a phytodinosaur character or developing convergently in Pampadromaeus+Panphagia, sauropodomorphs, ornithischians and Pisanosaurus in his tree.
The situation is similar for constricted crown bases- Pampadromeus and Panphagia were miscoded as lacking them, Heterodontosaurus actually has both states due to its fangs, Daemonosaurus was correctly coded as lacking it, and Poposaurus lacks it too but was left uncoded.  Though because Saturnalia and Silesaurus both have this character, it's slightly more parsimonious as a phytodinosaur synapomorphy reversed in a few cases.
What complicates the situation are the silesaurids Peters didn't include.  Sacisaurus and Diodorus both have large serrations, but Asilisaurus has small ones like Silesaurus itself.  Sacisaurus and Diodorus also have constricted roots, but Asilisaurus is unique among silesaurids (ignoring Lewisuchus of course) in lacking them.  This leaves both characters changing 6.5 and 4.5 times respectively if they are phytodinosaurian synapomorphies that reversed in some members.  They're much simpler in the standard phylogeny, where they each evolve three times (in derived silesaurids, derived sauropodomorphs and derived ornithischians), and the basal members of each (Asilisaurus, Silesaurus, Saturnalia, heterodontosaurids) show intermediate conditions.
122. Dentary extends into coronoid process.  Back to simple problems.  Peters miscoded Pantydraco (unpreserved), Daemonosaurus, Lotosaurus and Effigia as having this.  He also didn't code Silesaurus and Shuvosaurus for it, but they lack it too.  It's actually only present in ornithischians and some anchisaurs like Massospondylus, but not more basal sauropodomorphs unexamined by Peters like Efraasia and Plateosaurus, or even some taxa closely related to Massospondylus like Adeopapposaurus and Mussaurus.
128. Mandible straight ventrally.  Another complicated character because Peters' divides this into several states, with the anterior and posterior mandible being straight, concave or convex.  It's full of homoplasy in Peters' codings, with Silesaurus+Lotosaurus and ornithischians reversing to the 'straight anterior convex posterior' state he codes Panphagia and Pampadromeus for.  But as with so many of these characters, Peters miscodes a large number of taxa.  Saturnalia, Pantydraco and Massospondylus kaalae actually have concave anterior mandibles, his basalmost ornithischian Scelidosaurus and Pisanosaurus have convex ones, and Lotosaurus' and Shuvosaurus' are concave.  Posteriorly, none of his sauropodomorphs can be coded, Silesaurus' is convex, Lotosaurus and Effigia have both straight and convex margins and his basalmost ornithischians have both straight and convex (Scelidosaurus), concave (Heterodontosaurus) or convex (Agilisaurus) margins.  There's a huge amount of homoplasy and numerous taxa vary simply between individuals or sides of the head.
131. Cervicals decrease in size anteriorly.  Besides the atlas and often the axis, this isn't true in any examined taxon.  Peters simply miscoded them.
137. Mid-cervical centra (here c5-7 are used) shorter than mid dorsal centra (here d7-9 used).  This was miscoded by Peters as true in sauropodomorphs (ironically famous for their long necks).  It's found in Poposaurus, Lotosaurus and ornithischians (for at least some vertebrae), and is more parsimonious even in his tree as being convergent in these groups than being a phytodinosaur character lost in sauropodomorphs, silesaurids and shuvosaurs.
142. Lumbar area ("shortened to missing dorsal ribs") absent.  This is a hard one to code due to preservation and definition.  Very few taxa preserve the posteriormost dorsal ribs, and they're shorter than others as a rule.  It might be easiest just to note that Peters' coded many taxa whose posteriormost ribs are unpreserved and/or present in reconstructions, which accounts for all six non-ornithischians coded as lacking a lumbar area by Peters.  Also Scelidosaurus, Peters' basalmost ornithischian, was described as having a lumbar vertebra by Owen, while Plateosaurus has one or two dorsals without ribs as well.
144. Three to four sacral vertebrae, which if ordered would be "three or more sacral vertebrae".  Herrerasaurus was miscoded as having less, while Pseudolagosuchus was miscoded as unknown, but has two.  This means it now takes 4 steps in Peters' tree, while it would take five for Dinosauria to start with three sacrals and reverse in Marasuchus, Tawa and silesaurid Pseudolagosuchus.  But also note basal silesaurid Asilisaurus only has two, while theropod Eodromaeus has three, as does Eoraptor which wherever it goes seems close to theropods or Panphagia and Pampadromeus.  This leaves it more likely three sacrals are primitive for dinosaurs in Peters' tree, and more likely Silesaurus got its large sacral count convergently in reality.
175. Metacarpal II longest.  This is actually a fine character for grouping Sauropodomorpha and Ornithischia (note the condition in Pampadromaeus and Panphagia aren't known, so it doesn't support them being basal to both; indeed, the similar but unincluded Guaibasaurus also has it).  Of Peters' coded 'paraornithischians' though, Poposaurus has it but Lotosaurus is miscoded as having it (based on a sculpted museum mount I assume).  So strict Phytodinosauria sure, but that plus poposaurs is ambiguous.
195. Tibia shorter than femur.  This also works in Peters' tree, helped by his placement of Scelidosaurus basally in Ornithischia, as others' have long tibiae.   But it takes the same number of steps in the standard tree, where dinosauriforms have long tibiae, and it reverses in Silesaurus, Herrerasaurus, sauropodomorphs and Scelidosaurus (+ eurypods).
199. Tibia less than twice ilial length.  Hey, didn't we just look at tibial length? *cough correlated cough*  But that doesn't even matter here, because this is also true in Pampadromaeus (left uncoded by Peters), Herrerasaurus (miscoded) and possibly Tawa (the schematic reconstruction suggests so, but I would leave it uncoded for now).  So of included taxa, it's only not true in Marasuchus, Silesaurus and Panphagia.  Invalid.
Results- Of fifteen characters, Daemonosaurus has one (nasals widest in middle; which would work for Sauropodomorpha+Ornithischia) and a half (anterior mandible straight ventrally), though the latter doesn't actually support any similar clade.  It lacks five.  Nasals widest at midpoint would support Sauropodomorpha+Ornithischia; orbit enters anterior half of skull would support derived sauropodomorphs plus ornithischians; metacarpal II longest would support either variant; premaxilla a third or more of preorbital length and (somwhat ambiguously) short mid cervical centra would support Poposauridae+Ornithischia.  Large serrations and constricted crown bases would indeed resolve at the previous node (Phytodinosauria) in Peters' tree, but requires less homoplasy in the standard tree.  A short tibia also resolves here, but is equally parsimonious in the standard phylogeny.

'Paraornithischia' (Pisanosaurus, Poposauridae, Silesauridae)
28. Maxilla ventrally straight.  Miscoded in Pisanosaurus (unknown), Silesaurus, Shuvosaurus (unknown) and Effigia, so only Lotosaurus is correctly coded.  Varies so much that either a straight or convex maxilla might be basal for Saurischia, Dinosauria, Silesauridae+Dinosauria or Dinosauriformes.
112. Maxillary teeth shorter than twice their FABL.  Note Peters wrongly codes the toothless poposaurs as having this when they should be inapplicable.  More generally, this true for some teeth in basically every taxon known from a good sample size, including standard carnivorous taxa like theropods.  It's only true for all maxillary teeth in some derived ornithischians.
117. Laterally placed surangular ridge in dorsal view.  This was an example of characters Peters misunderstood and thus coded inaccurately (see part 1 of my critique).  In actuality, all examined taxa have this ridge.
119. Dentary straight.  Pisanosaurus miscoded.  While true in poposaurs and silesaurids, this is also primitive for dinosaurs in general and found in Arizonasaurus.  Peters didn't find this due to miscodings (e.g. Scelidosaurus, Heterodontosaurus, Panphagia) and missing taxa.
167. Olecranon process absent.  Miscoded in Pisanosaurus (unknown), Lotosaurus (unreported), Poposaurus (unreported).  It's only true in Silesaurus, Effigia, Gracilisuchus and some ornithischians (Scutellosaurus and Agilisaurus+Hexinlusaurus).  Thus it fits with the silesaurid+poposaur clade in Peters tree, though in the standard tree the olecranon in basal rauisuchians sensu lato and crocodylomorphs indicate convergence.
178. Four phalanges in manual digit IV (up from three or less).  Miscoded in Pisanosaurus (unknown), Lotosaurus (five phalanges) and Effigia (unknown).  Correctly coded as absent in Poposaurus (three phalanges), and no other 'paraornithischians' can be coded.  This leaves the state untrue for any taxon.
205. (Preseumedly large) calcaneal tuber proximally oriented.  Miscoded in Pisanosaurus (absent) and correctly coded as absent in silesaurids.  Thus it's only present in poposaurs, which in standard trees is because they're outside Avemetatarsalia and doesn't require a reversal then.
Results- Only the absent olecranon would work for this clade in Peters' tree, which is only known in Silesaurus and Effigia.  Note Pisanosaurus was miscoded for all except one which is present in all examined taxa (and coded correctly by accident by Peters as he was looking at the wrong structure), and another which actually varies in almost all taxa (and may vary in Pisanosaurus if anterior maxillary teeth were preserved, as these are the elongate ones in basal ornithischians).  Thus there's no evidence Pisanosaurus is closer to poposaurs and silesaurs than to ornithischians.

(Poposauridae+Silesauridae)
84. Postorbital extends posteriorly less than halfway through the parietal.  This was only coded as true in Lotosaurus and Effigia and is miscoded in both anyway.  It's actually not found in any included taxon except Terrestrisuchus.
115. Maxilla toothless.  Poposaurus was miscoded as unknown when it has maxillary teeth.  Being absent in silesaurids, it's only present in Lotosaurus and shuvosaurs, which I have no issue with and takes less steps in the standard phylogeny than Peters'.
118. Paired predentary.  A fictional element found in no animal I know of. Peters just imagines predentaries are fused to dentaries in these taxa.
135. Cervical ribs of average width and at high angle to neck.  Both width and orientation miscoded in Lotosaurus, Silesaurus and Effigia (unknown).  Only Gracilisuchus, some Lotosaurus ribs and some Hexinlusaurus ribs are not slender, and no examined taxon has high-angled ribs.
140. Cervicals 6-9 without offset central faces.  Miscoded in Silesaurus, and I have no issue with poposaurs having it, since it's generally considered the primitive condition modified in dinosauriforms.
160. Clavicle present (and shorter than scapula, as if that needed to be said).  This is only here because Peters miscoded a ton of taxa as lacking clavicles when they're just incompletely preserved (also note no silesaurid can be coded).  In actuality, only some crocodylomorphs and ornithischians have good evidence for missing clavicles, while saurischians retain them.
181. Manual unguals blunt.  Only known in poposaurs (though Effigia was miscoded).
Results- Not a single character is even present in silesaurids.  Perhaps the biggest fail of any Peters clade examined here.

(Lotosaurus+Silesauridae)
14. Premaxilla-maxilla notch over 45 degrees.  This entire character is miscoded by Peters.  In actuality, all examined taxa lack a notch except Tawa+Coelophysis, Pampadromaeus and heterodontosaurids (with Eoraptor and Daemonosaurus being intermediate).
15. Premaxilla ventral surface angled anteroventrally.  This is untrue in silesaurids and, contra Peters, present in Effigia and probably Poposaurus.
31. Orbit shorter than postorbital skull length.  This is unknown in silesaurids.
44. Frontal not wider posteriorly than anteriorly.  This is widely miscoded by Peters and actually only present in Gracilisuchus among examined taxa.
125. Posterior mandible of even depth anteriorly and posteriorly.  Intrue, both Silesaurus and Lotosaurus have mandibles deepest in the middle, which is true for most taxa.
128. Ventral mandible edge straight anteriorly and convex posteriorly (as opposed to completely straight).  Lotosaurus actually has a concave anterior mandible, with a (sometimes) convex posterior mandible is typical of all but some herbivorous dinosaurs and is also found in some specimens of the only other scorable poposaur, Effigia.
145. Sacral neural spines taller than acetabulum.  True in Lotosaurus and Silesaurus, but unknown in Pseudolagosuchus (unknown), and absent in the unexamined silesaurid Asilisaurus.  This makes the character ambiguous. 
149. Gastralia absent.  Peters miscoded Silesaurus (absent), Pseudolagosuchus (unknown) and Lotosaurus (unknown).  Another instance of Peters assuming partially preserved skeletons or mounted specimens include all originally present elements.
170. Forelimb between 55 and 100 percent of hindlimb length (instead of being shorter).   The ratio in Lotosaurus is unreported and was guessed at by Peters from mounts of uncertain completeness.
183. Preacetabular process truncated.  The condition in Lotosaurus is unreported and was guessed at by Peters from mounts of uncertain completeness.
200. Iliofibularis tubercle a 'spot'.   Silesaurus, Pseudolagosuchus and Lotosaurus all actually have a crest-like tubercle, so are miscoded.
210. Metatarsus less than half of tibial length.  Miscoded in Silesaurus, Poposaurus and Effigia, so only untrue in Effigia among these taxa. 
Results- Only the long sacral neural spines even ambiguously link Silesaurus and Lotosaurus.  The rest of the characters are highly miscoded.

(Sauropodomorpha, Daemonosaurus, Ornithischia)
33. Naris larger than antorbital fenestra.  This was miscoded for Daemonosaurus, Saturnalia (unknown) and Pantydraco.  It's actually only present in ornithischians and some plateosaurs, as even taxa like the unincluded Riojasaurus, Sellosaurus, Lufengosaurus and Jingshanosaurus lack it.
41. Frontoparietal suture straight and longer than frontonasal suture.  Another composite character, the length aspect of which is true for basically all examined taxa.  Straightness does indeed work as a character for this clade though.
69. Squamosal and quadratojugal do not contact.  This is only here because Peters miscoded theropods as having contact and sauropodomorphs, Heterodontosaurus and Lesothosaurus as lacking contact.  It's actually only true in theropods and some ornithischians (Scelidosaurus, Agilisaurus+Hexinlusaurus).  Miscoded in Daemonosaurus as it is actually not known.
127. Retroarticular process angles ventrally.  Widely miscoded and only actually present in Hexinlusaurus among included taxa.
179. Manual digit IV reduced in width.  This is true in almost all dinosaurs and was actually miscoded by Peters as absent in Pisanosaurus (actually unknown), Poposaurus and Effigia.  So in his tree it would actually diagnose Dinosauria and reverse in Lotosaurus and (miscoded) Lesothosaurus.  Note it is equally parsimonious for it to converge in derived poposaurids and dinosaurs as in the standard phylogeny.
191.  Acetabulum at least partly perforated.  Similar to the previous character, this is true in all dinosaurs and was miscoded by Peters as being absent in the examined poposaurs.  It was also miscoded as lacking in Pampadromaeus and Panphagia, and may even be present in Silesaurus (though lacking in the unincluded Asilisaurus and probably Sacisaurus). 
216. Phalanges of pedal digit IV subequal to metatarsal IV.  Here's an example of how not ordering your characters can lead to problems.  In Peters' data, the outgroup and 'paraornithischians' have long phalanges, sauropodomorphs and ornithischians have subequal phalanges and theropods have short phalanges.  PAUP doesn't realize which of these are most similar, but if it were ordered PAUP would know this means theropods are most like sauropodomorphs and ornithischians.  In any case, Peters miscoded Herrerasaurus which has subequal phalanges too, and Saturnalia, Lesothosaurus and Hexinlusaurus (left uncoded) which all have shorter phalanges.  The latter examples, along with Pisanosaurus and unexamined Tianyulong having short phalanges, means this is probably the basal state for ornithischians and sauropodomorphs.  Yes Peters has Scelidosaurus basal in Ornithischia, but also miscoded it as subequal when it actually has long phalanges, so doesn't fit with subequal being basal for sauropodomorphs+ornithischians anyway.  As theropods are subequal (Herrerasaurus, Dilophosaurus) or short (Coelophysis, Liliensternus, Procompsognathus), this leaves it ambiguous whether short phalanges are a phytodinosaurian character.
Results- Daemonosaurus has one of these (straight frontoparietal suture), which is indeed valid for this clade.  It lacks two, neither of which really diagnoses the clade anyway.  Besides the straight frontoparietal suture, only the short pedal digit IV phalanges even ambiguously works for this clade.

(Daemonosaurus, Ornithischia)
114. Last maxillary tooth placed at mid orbit (instead of anterior orbit).  This works, though note it's also present in Eoraptor, wherever that taxon goes (Peters seems to think Theropoda).
Results- Yes, this single character is valid for this clade.


Total Results- There are several heterodox aspects that should be evaluated.

First is that 'paraornithischians' are closer to phytodinosaurs than to theropods.  This is supported by external naris being angled more dorsally, which takes one more step in the standard phylogeny.  A short tibia takes equal steps, and while large serrations and constricted crown bases work for this node in Peters' tree, they are better explained by the standard tree.  Even if we just correct Peters' characters, this grouping takes 12 more steps in his trees.  When I added new characters and taxa, it took 34 more steps.  In Nesbitt's analysis with far more anatomical data (even excluding taxa Peters doesn't see as avemetatarsalians, like pterosaurs and lagerpetonids), it takes an astounding 76 more steps.  Utterly rejected.

Regarding Paraornithischia itself, no characters support placing Pisanosaurus in it, and this is 13 (Peters' characters corrected), 26 (Peters' corrected matrix with more data added) and 50 (Nesbitt's reduced matrix) steps longer than the most parsimonious tree.  Pisanosaurus being a paraornithischian is very strongly rejected.

For a more reduced Paraornithischia containing only silesaurids and poposaurs, only two characters could  plausibly support this in Peters' matrix.  Silesaurus could share an absent olecranon with poposaurs (only known in Effigia), then ambigiously share long sacral neural spines with Lotosaurus (unknown in Poposaurus and Arizonosaurus, though probable in both considering other neural spines; absent in shuvosaurs).  This is incredibly weak support compared to the numerous characters placing Silesaurus close to dinosaurs and poposaurs in Pseudosuchia.  Enforcing poposaurs and silesaurids as a monophyletic group takes 8 more steps in Peters' matrix both with corrected codings and once the extra characters and taxa are added (in both cases they are sister to Dinosauria and Pisanosaurus is ornithischian), and 41 more steps in Nesbitt's reduced matrix (where they are sister to Dinosauriformes and Pisanosaurus again is ornithischian).  So strongly rejected again, though at least leaving Pisanosaurus out made it a tad less homoplasious.

Peters places Lotosaurus closer to silesaurids than to poposaurs.  Given the liklihood Poposaurus has tall sacral neural spines noted above, even this one remaining possibly applicable character is questionable.  This grouping takes 15 more steps using Peters' matrix with corrected codings, where the Lotosaurus+silesaurid clade ends up in Crocodylomorpha.  It takes 19 more steps once the extra characters and taxa are added, where the clade falls out between Crocodylotarsi and poposaurs on the grade leading to dinosauriforms.  No other silesaurids follow.  Finally, it takes 45 more steps in Nesbitt's reduced matrix, where it's apparently easiest just to let Lotosaurus be placed as the basalmost silesaurid.  Another strongly rejected concept, which when taken together with the previous two paragraphs shows all parts of 'Paraornithischia' besides Silesauridae and Poposauridae each being real is unlikely in the extreme.

Back to actual dinosaurs, there is Peters' idea derived sauropodomorphs are closer to ornithischians than to Panphagia and Pampadromeus.  This is supported by orbit enters anterior half of skull, a straight frontoparietal suture, (ambiguously) posterior mandible deepest anteriorly and (ambiguously) tibia shorter than femur, which are outweighed by the sauropodomorph characters not included by Peters.  Just fixing Peters' characters leaves this 5 steps less likely than sauropodomorph monophyly, and adding taxa and characters brings it to 11 steps less likely.  But if you try this in a dedicated sauropodomorph matrix like Cabreira et al. (2011), it's a whopping 25 steps less parsimonious.  Very unlikely to be true.

Then there's Sauropodomorpha+Ornithischia itself.  This has actually been suggested by other workers before, unlike most of Peters' unusual ideas (technically, Peters doesn't support the standard version since Pisanosaurus, Pampadromaeus and Panphagia are excluded, and Daemonosaurus is included).  This is supported by nasals widest at midlength, (ambiguously due to Saturnalia) enlarged serrations, teeth constricted at base, metacarpal II longest and (ambiguously) short phalanges of pedal digit IV.  But these are outweighed even in his own matrix, where correcting codings makes it 2 steps less parsimonious.  Adding characters and taxa brings this up to 8 steps.  In Nesbitt's matrix (again only using taxa Peters did in this part of his tree), it takes 13 more steps.  So this non-Petersian Phytodinosauria isn't completely rejected, but does seem quite unlikely.

Finally, there's the idea Daemonosaurus is a member of any of the above clades instead of being a theropod.  Of all of the above valid characters, it only has nasals widest at midpoint (sauropodomorphs+ornithischians), straight frontoparietal suture (derived sauropodomorphs+ornithischians) and last maxillary tooth placed at mid orbit (ornithischians).  But it lacks large serrations, constricted tooth crown bases, orbit enters anterior half of skull, and posterior mandible deepest anteriorly, and the above clades are probably not real anyway.  We saw before forcing Daemonosaurus to be ornithischian took 7-10 more steps depending on the matrix used.  Forcing it to be phytodinosaurian takes 2 (sister to remaining phytodinosaurs), 10 (it's sister to Eodromaeus with both sister to other phytodinosaurs, and theropods are paraphyletic to the latter) or 20 (herrerasaurids become basalmost phytodinosaurs, followed by Daemonosaurus+Eoraptor) more steps in Peters' corrected, Peters' corrected with added data, and Sues et al.'s reduced analyses respectively.  So far from helping Phytodinosauria, placing Daemonosaurus in that clade makes it 0, 2 or 4 steps less likely to exist.  The most you can say for Peters' idea is that in the quite unlikely chance Phytodinosauria is real, making Daemonosaurus the basalmost member is only slightly more problematic, though taxa he considers theropods such as herrerasaurids, Eoraptor and/or Eodromaeus would follow.

As Daemonosaurus is so emphasized by Peters, which characters suggest it is a theropod instead of an ornithischian?  We previously saw it took ten more steps to place Daemonosaurus in Ornithischia in the full matrix used here, and seven more in Sues et al.'s (2011) original matrix.  Some of the characters suggested by Sues et al. have more homoplasy when examined in the larger matrix, but several have relatively clear distributions.  Remember despite the homoplasy noted below, these were still found to diagnose the clades when all of Peters' characters were included too.  Characters that could also work for an ornithischian placement aren't noted.

Saurischia
- Ventral ramus of the opisthotic not covered by the lateralmost edge of exoccipital in posterior view. Reverses in Massospondylus kaalae and avepods.  Not used by Peters.

Saurischia/Theropoda
- Maxilla ventrally convex.  Exactly which node this belongs to is uncertain as Eoraptor and Pampadromaeus have it, but other sauropodomorphs don't.  Tawa is miscoded by Peters.

Theropoda
- Snout roughly triangular. As in Tawa and Coelophysis, which are more derived than Eoraptor, Herrerasaurus and Eodromaeus in this tree.  Miscoded in Daemonosaurus by Peters.
- Sharp jugal ridge. In all examined theropods including Eoraptor, also in some Scelidosaurus specimens.  Not used by Peters.
- Deep pneumatic fossae in cervical centra. Also in sauropods.  Not used by Peters.

Sister to Tawa
- Less than four premaxillary teeth.  Also in heterodontosaurids, but as they're not sister to Daemonosaurus or even basal in Ornithischia in Peters' trees, this doesn't matter.  Miscoded in Daemonosaurus and Tawa by Peters.
- Jugal, anterior extent of the slot for the quadratojugal: at or anterior to the posterior edge of the dorsal process of the jugal.  Also in Pampadromaeus, some Scelidosaurus and Massospondylus carinatus specimens.  Not used by Peters.
- Exoccipital, lateral surface: without subvertical crest (metotic strut). Unique among dinosauriforms.  Not used by Peters.

"You have your assignment: Nest Daemonosaurus with theropods while including Heterodontosaurus and Massospondylus. That’s a half-dozen to a dozen taxa at most to deal with. Then we’ll compare answers."

Assignment complete, Peters.  Comparison indicates massive miscoding by you, a lack of included taxa and characters, and in this particular case using a largely fictional skull for Daemonosaurus.  Almost like what I figured out by just looking at a portion of your dataset without reanalyzing the entire thing...


And that wraps things up as far as Peters' Dinosauria goes.  Unfortunately, despite my utter demolishing of his analysis, he's unlikely to fix it.  So many of the problems are due to a third of the characters being miscoded, but while he seems willing to fix a few, for most he remains stubbornly convinced that his tracing is better than what's indicated by the actual experts who saw and studied the material.  Sure you can tell Peters where he gets things wrong, but he'll consider that worthless.  Sometimes he requests you take the time to trace your interpretation for him, but his errors are so numerous and his understanding of anatomy so poor that it would be a full time job for anyone to educate him.  He also remains intransigent regarding how he should fix his character formulation and ordering.  Just doesn't care.  Similarly, Peters is blase about his potential for miscoding by using reconstructions and sculpted mounts.  It will balance out he says, because his terribly miscoded analysis has falsely assured him that most nodes are strongly supported, making noise unimportant.  He's unconcerned with adding more characters because he just wants to see what his 228 will find, apparently not realizing limiting it to such a small amount makes the result almost worthless.  It's like my coding new taxa into small older analyses on the Database- it's fun and interesting to see how taxa fall out using classic data, but I would never claim e.g. segnosaurs are closer to caenagnathids than to oviraptorids just because that's where they ended up when added to Gauthier's 1986 matrix.  Even if his whole topology is shown to be based on erroneous data, he'll get things backwards and compare the resulting trees to see how subjectively similar related taxa seem to him.  As if the result matters when the data used to get it are wrong.  So what point is there in trying to educate someone who refuses to learn?  While I was naive in thinking a detailed critique just might show Peters how much more work he needs to do before his analysis is useful, I hope this will at least help those amateurs who think Peters' ideas have merit and fall for his "I'm a rebel underdog whose ideas are disliked by the experts because they're blinded by tradition and conformity" schtick.  All of the information in this series of posts (and more) will be uploaded to the Database in the Evaluating Phylogenetic Analyses section.  Until Peters shows willingness to do more than correct a few scores, it's just a time sink to engage him in detail.  Hope you all enjoyed the series.

Jaime Headden, Lord and Master of All Oviraptorosaurian, just wrote a detailed commentary on this work, but my commentary is limited to the phylogenetic analysis and Elmisaurus monophyly.  Just so everyone's up to speed, Longrich et al. (2013) describe some new caenagnathid remains from Texas, revise the taxonomy of the whole clade, and present a phylogenetic analysis of oviraptorosaurs.  Among their actions is to create the genus Leptorhynchos for Elmisaurus elegans and their new species gaddisi. 

The analysis in the paper is represented as an Adams consensus that leaves out two included oviraptorosaurs- Epichirostenotes and Nomingia.  For those of you who don't know, Adams consensus' can be misleading.  What they do is move unstable taxa to the base of the smallest clade they definitely belong to.  So if e.g. segnosaurs were most parsimoniously either plateosaurs like Sereno thought or oviraptorosaurs like Russell and Dong thought, an Adams consensus would move them to the base of Saurischia where no one was advocating they go.  Which is fine in an incertae sedis sort of way, except that PAUP doesn't tell you when any taxon actually is basal in a clade or is just being displayed basally because it can occupy multiple more derived positions.  Also, Longrich et al. excluded Nomingia and Epichirostenotes a priori instead of a posteriori, which meant none of their information affected the topology.

Analyzing every taxon, but only leaving those in which preserve mandibles results in-
(Microv(Gigant(Caenagnathasia(elegans,gaddisi(pergracilis(collinsi,sp.))))))

The Adams consensus places Elmisaurus rarus out by Caenagnathasia, making it seem like the analysis supports creating a new genus for elegans.  But that's just an illusion caused by E. rarus not preserving mandibles, so it can go many places in Caenagnathidae and is placed basally due to the Adams consensus artifact noted above.  Indeed, if we delete taxa which don't preserve feet a posteriori, we get-

(Microv(Gigant(elegans,pergracilis,rarus)))

So it seems rarus isn't separated from elegans. Trees constrained to place elegans in Elmisaurus are equal length to trees which don't.  How many Elmisaurus apomorphies were included?

1. tarsometatarsal fusion- included, but E. rarus miscoded as lacking metatarsal fusion.

2. posterior surface of metatarsus deeply concave- not included.

3. metatarsals II and IV subequal in length to III (>93%)- not included.

4. distal end of metatarsal II curves anteriorly away from the longitudinal axis of the metatarsus- not included.

5. proximolateral process on metatarsal IV- not included.

6. more extensive proximodistal contact between metatarsals II and IV- not included.

Longrich et al. do claim elegans is more similar to Chirostenotes in one way though.  They state "Longrich (2008a) tentatively placed [elegans] in Chirostenotes, because the third metatarsal has an anteroposteriorly flattened shaft that is concave and broadly exposed on the posterior of the metatarsus (Currie 1989). This is a derived feature found in Chirostenotes (Currie and Russell 1988) but not Elmisaurus (Osmólska 1981)."  This seems related to their new character 205- "Metatarsal III with an ovoid or subtriangular cross section (0) or anteroposteriorly flattened, with a concave posterior surface (1). Primitively in theropods the third metatarsal has an ovoid cross section, or a triangular cross section in arctometatarsalian forms. This condition is retained in most oviraptorosaurs, including the basal caenagnathid Elmisaurus rarus. In Caenagnathinae, the third metatarsal is anteroposteriorly compressed."

Posterior view of proximal left caenagnathid tarsometatarsi, metatarsal III colored blue.  Left- Elmisaurus/Leptorhynchos elegans holotype ROM 781 (after Currie, 1989); Middle- Elmisaurus rarus holotype ZPAL MgD-I/172 (after Osmolska, 1981); Right- Elmisaurus/Leptorhynchos elegans referred RTMP 92.39.4 (after Currie, 1989).

Yet the posterior transverse exposure of proximal metatarsal III proximally seems intermediate in E. rarus' holotype compared to the two specimens of elegans (see figure above).  More distally, Currie's (1989) figure 2P section indicates the posterior exposure is narrow as in E. rarus (see lower left section below).  Currie's (1989) figure 2Q shows E. rarus has a concave posterior metatarsal III surface as well (see middle left section below, outlined in blue). 

Left- cross sections of caenagnathid metatarsi after Currie (1989), anterior/extensor to top, anterior and posterior surfaces lined with red and blue respectively; Top- Elmisaurus/Leptorhynchos elegans referred RTMP 92.39.4; Middle- Elmisaurus rarus holotype ZPAL MgD-I/172; Bottom- Elmisaurus/Leptorhynchos elegans holotype ROM 781.  Green lines indicate region of sectioning.  Right- Holotype of Elmisaurus rarus in anterior (left) and posterior (right) views (after Olsmolska, 1981).

As for shape, the main issue seems to be we're dealing with different proximodistal points along the bone.  Currie and Russell (1988) state in Chirostenotes pergracilis "The proximal end, viewed dorsally, is diamond shaped, tapering both anteriorly (between the contact of metatarsals 11 and IV) and posteriorly. Its major horizontal axis, 17.5 mm long, is anteroposterior in orientation and thins backwards."  Sternberg (1932) also states the Macrophalangia holotype (possibly Caenagnathus collinsi according to Longrich et al.) has a transversely compressed proximal end.  The proximal ends of E. rarus' and elegans' metatarsal III are fused too well with surrounding bones to compare.  Once C. pergracilis' anterior surface is exposed, "the bone twists until the medial surface is facing anteriorly" and "the anterior edge has broadened out to 7.5 mm to separate the adjacent metatarsals and is triangular in section" (Currie and Russell, 1988).  elegans' holotype is broken at about this same point and also shows a triangular section (upper section left above).  Note a triangular section is what Longrich et al. are claiming caenagnathines don't have, though it exists in both pergracilis and elegans.  Currie (1989) was also wrong in comparing the proximal diamond shape of Chirostenotes pergracilis with the more distal triangular shape of elegans, and none of these areas have been described in E. rarus (thus I need to fix that on the Database).  At two-thirds down in Chirostenotes, "In section, a shallow concave surface faces posteriorly at this level, while slightly concave surfaces face posteromedially and posterolaterally for contact with the adjacent metatarsals."  This appears similar to E. rarus from what the anterior and posterior views suggest (right above), and matches how Snively (2000) described an RTMP "Elmisaurus sp." metatarsus that is probably elegans.  It also matches the cross section of elegans illustrated by Currie (1989- fig. 2P; lower left section above).  While Currie's figure 2Q of Elmisaurus rarus (middle left section above) would suggest a slightly different shape where the articular surfaces are smaller and that for metatarsal IV doesn't angle posteromedially, the narrow anterior exposure of metatarsal III means it must have been taken more proximally, probably about halfway down considering the ratio between anterior and posterior exposure of metatarsal III.  This leaves anteroposterior compression, which varies throughout the bone in elegans at least.  Distally it's transversely compressed but proximally it's anteroposteriorly compressed.  The E. rarus section which is probably intermediate in position is also intermediate in compression, being slightly transversely compressed.  If Chirostenotes/Caenagnathus specimens are any indication, the bone switches back to transversely compressed at its proximal tip.  So there are actually no valid described differences in metatarsal III sectional shape between Chirostenotes and any Elmisaurus species in the primary literature.

Correcting the coding for Elmisaurus rarus having fused metatarsals and adding the 5 other characters (one as an additional ordered state of the arctometatarsaly character) results in elegans and gaddisi being in a trichotomy with E. rarus.  This elmisaur clade is sister to a caenagnath clade containing Chirostenotes, Hagryphus, Caenagnathus collinsi and C. sp. from Hell Creek.  Nomingia and Epichirostenotes both have uncertain positions in the elmisaur-caenagnath clade, which is sister to Caenagnathasia, then Gigantoraptor as in Longrich et al.'s trees.

Given this result, I wonder why Longrich et al. didn't include the Elmisaurus characters suggested by Currie.  Also, making elegans the type of Leptorhynchos puts us in a confusing situation, as the only elements described in all three species are distal metatarsal III and proximal metatarsal IV.  Neither of these seem particularly distinctive in any of the species, and rarus' limited illustrations and description makes them difficult to compare in depth.  Thus there's no obvious reason to refer gaddisi to either Elmisaurus or Leptorhynchos, so it would have been easier and more accurate to just keep elegans in Elmisaurus and not name a new genus.  Longrich et al.'s diagnoses for Leptorhynchos and each of its species are purely mandibular, so we can't even evaluate Elmisaurus rarus or the elegans holotype for them.  But if elegans' diagnosis is based only on characters not observable in the holotype metatarsus, then doesn't that make the species indeterminate?  If the holotype can't actually be distinguished from the two metatarsal fragments referred to gaddisi, we have a problem.  Luckily, it seems Longrich et al. never assigned a type species to Leptorhynchos, making it unavailable (thanks to Cay on Jaime's blog).  I really think it should just be dropped and gaddisi assigned to Elmisaurus, though even then it might only be distinguishable from referred specimens of E. elegans, and perhaps not at all from E. rarus.  Ugh, caenagnathids.

References- Osmolska, 1981. Coossified tarsometatarsi in theropod dinosaurs and their bearing on the problem of bird origins. Palaeontologia Polonica. 42, 79-95.

Currie and Russell, 1988. Osteology and relationships of Chirostenotes pergracilis (Saurischia, Theropoda) from the Judith River (Oldman) Formation of Alberta, Canada. Canadian Journal of Earth Sciences. 25, 972-986.

Currie, 1989. The first records of Elmisaurus (Saurischia, Theropoda) from North America. Canadian Journal of Earth Sciences. 26, 1319-1324.

Snively, 2000. Functional morphology of the tyrannosaund arctometatarsus. Unpublished Masters Thesis. 273 pp.

Longrich, Barnes, Clark and Millar, 2013. Caenagnathidae from the Upper Campanian Aguja Formation of west Texas, and a revision of the Caenagnathinae. Bulletin of the Peabody Museum of Natural History. 54(1), 23-49.

Hi all.  It's been a while, but I've been finishing the Lori matrix and earning money.  This post is based on Carr's excellent Tyrannosauroidea blog, which will be added to my blogroll once I update it.  Carr wrote a post arguing Nanotyrannus are juvenile Tyrannosaurus, and while I provisionally agree with this, I felt his reasons were partly flawed and that any modern defender of the genus wouldn't be convinced.  Arguing as Devil's Advocate, I commented about this, and Carr has since replied.  As my own reply to that is so long, I felt I would post it here and link here from his blog.  The points are numbered to correspond to Carr's, though this is rather messy as some points are made in multiple places.  Enjoy.

Thanks for the detailed reply, Tom!  As with before, I write as Devil's Advocate, as I do provisionally agree with you Nanotyrannus are juvenile Tyrannosaurus.  That said, it seems we do actually have some philosophical differences.

#1/#6- You seem to have a double standard here.  For Nanotyrannus you write "Instead, they have just heaped on new characters as if that’ll do the job of rescuing the taxon" but for Tyrannosaurus you say "there is no reason to think that T. rex is invalid, given the quality of specimens (including the type) and sample size that has been amassed. Certainly, the time has come to bring the diagnoses for T. rex and many other taxa up to date..."  So we can heap on new characters for Tyrannosaurus, but not for Nanotyrannus?  What's ironic here is that Bakker et al.'s (1988) diagnosis was itself heaping on new/all characters to the original diagnosis of lancensis by Gilmore (1946).  That original diagnosis was completely stratigraphic, as Gilmore viewed the few differences he saw between lancensis and sternbergi as potentially individual variation.  Thus he wrote "in view of the great interval of time that has elapsed between Belly River and Lance, one appears justified in believing that it is too great a span in time for a species to pass unchanged from one to the other, and that with the discovery of additional materials characters will eventually be found that will adequately distinguish them."

"In my mind, there is no reason not to accept the diagnosis of Nanotyrannus (or any other taxon) as, prima facie, the best argument for establishing a scientific name."  The reason is that diagnoses are a product of their time, both in the sense of less material being known and available, and the philosophy being outdated.  Original diagnoses are often terrible for this reason, though the taxa are still valid.

In my view, an original diagnosis is just a starting point for assessing validity.  If it fails, you then check subsequently suggested diagnostic characters.  If that fails, you then look yourself for unpublished diagnostic characters.  If that fails, synonymy or indeterminacy is reasonable.

#1/#2/#3- Now you do have a point that if Jane were diagnostic but the Cleveland skull were not, then Jane could not easily be called Nanotyrannus lancensis.  But this isn't true of all of the characters suggested by Larson.  According to him, the Cleveland skull has a large number of maxillary teeth, strongly labiolingually compressed lateral teeth, a narrow vomer, posteriorly located maxillary fenestra, shallow antorbital fossa, posterodorsal quadratojugal notch, subnarial foramen enclosed by maxilla, quadratojugal foramen, and dorsally opening jugal foramen.  Now I agree with you that most of these are ontogenetic (though even younger Tarbosaurus MPC-D 107/7 lacks the high maxillary tooth count, enclosed subnarial foramen, pneumatic quadratojugal and jugal foramen orientation, so on the surface those look potentially valid), but you can't write off new Nanotyrannus diagnoses as being only based on Jane.  And given that the Cleveland skull and Jane share some apparent apomorphies, it's perfectly valid to use the additional apparent apomorphies from Jane to support Nanotyrannus.

#X- I understand your not wanting to discuss Larson's (2013) proposed Nanotyrannus characters or those only preserved in Jane, due to your work on those topics being in prep..  In a sense, that stalls the issue on your blog for now and makes it so we really can't have a good modern defense of synonymy. 

But there is one character we can tackle, preserved in the Cleveland skull and presented as an autapomorphy prior to Larson's work- the high maxillary and dentary tooth count.  You say "I did propose a hypothesis to account for the difference in tooth count (Carr, 1999)" and that's true- that libratus and some modern crocodilians also show a reduction.  But since then Currie (2003- fig. 5) have graphed out both libratus and Tarbosaurus to show no decrease, and Tsuihiji et al.'s (2011) new tiny Tarbosaurus has an adult count too.  As a stable or increasing count is also seen in Coelophysis, Ceratosaurus, Majungasaurus and therizinosauroids, this makes the apparent condition in crocodilians irrelevent and argues against your hypothesis.  It's always possible Tyrannosaurus was unusual among theropods in reducing tooth count with age, or that the Cleveland skull is an outlier independent of age (though Jane strains the probability of this), but either rationale is ad hoc instead of fitting with expected trends.  This was always the strongest pre-Jane argument for Nanotyrannus in my opinion, and it remains so.  If the toothy Alioramus are Tarbosaurus, this would give some precedent (for the jugal foramen orientation too), but see below for that.

#4- "In the table I present (implicitly) the hypothesis that Daspletosaurus is peramorphic relative to A. libratus, in that the growth trends are carried further in the tyrannosaurine. That is why Daspletosaurus is under the heading “Stage 4”."  But in 1996, you explicitly said- "Four ontogenetic stages are defined ...  These morphotypes have been misinterpreted by previous workers as distinct taxa. Daspletosaurus torosus ... are found to be invalid taxa, representing the adult morphotype of Albertosaurus libratus ...".  So Daspletosaurus was explicitly thought to be a a stage 4 Albertosaurus by you at first, based on these stages.  Like I said, you changed your mind by 1998, but this indicates the list/table itself is not capable of distinguishing ontogeny from peadomorphy/peramorphy. 

"The salient point you make is the suggestion that the Cleveland skull is an adult, but it does not grow past stage 1. I think it is reasonable to expect that an adult of a true ‘pygmy’ tyrannosaurid would have all of the adult characters seen in its closest relatives."
Wouldn't a paedomorphic taxon by definition not have all of the adult characters seen in its closest relatives?  More importantly for our actual argument, you showed the Cleveland skull has juvenile bone grain.  This seals the deal on its age for me, so I agree with you its a juvenile regardless of any other ontogenetically variable characters.  Unless paedomorphic vertebrates can have juvenile bone grain?  Does that happen?

#5- "With regard to Bakker et al.’s (1988) tyrannosaurid phylogeny, I do think that context matters. Their arrangement complements what they say in the text, together showing the deductions that led to their taxonomic decision. It is an excellent article in that the data are absolutely clear."  Not really important to our debate, but this further illustrates a difference in our philosophy.  Put basically, if a taxon is conceived in an inaccurate context (be it diagnosis or phylogenetic hypothesis), it's invalid.

#7- So put less obscurely, you disagree with your coauthors and think Alioramus is a juvenile Tarbosaurus?

#8- "Yes, it is fair because sufficient data was at hand (e.g., Rozhdestvensky, 1965), and there were two growth series (A. libratus, T. bataar) available with which to make comparisons."  Harsh, as the libratus sample in 1988 didn't get younger than "sternbergi".  But again, not a very useful point of contention.

#10- "That’s a good point! I have to admit that I was late on the scene as well (Carr and Williamson, 2004)."  In your defense, by 1999 the specimen was viewed as either a new species megagracilis, or an entire new genus Dinotyrannus.  Bakker et al. didn't have that excuse in 1988.

#11- "The bottom line is that the relative maturity of specimens and their taxonomic identity must be considered separately..."
Er, that seems contrary to your main philosophy and methodology, and of science basically.  You established an ontogenetic series in libratus, then compared Nanotyrannus and Maleevosaurus to that to go a long way to determining their age.  You also found striations and unfused bones in Nanotyrannus, but the importance of these also depend on their variation in other specimens with known age.
If Nanotyrannus were magically proven to be an adult, for instance, your whole argument for Maleevosaurus being a juvenile Tarbosaurus would collapse.  All of the juvenile libratus characters present in Maleevosaurus would also be present in adult Nanotyrannus, so Maleevosaurus could be an adult as well.  I don't think this situation is true (barring juvenile bone grain existing in paedomorphic adults), but philosophically it seems valid.

"Williamson and I (2004) showed that ‘Stygivenator’ is referable to T. rex, but Larson (2013) did not engage with the evidence that we presented."
This is a good example.  IF Nanotyrannus is valid and sister to Tyrannosaurus, then the Tyrannosaurus-like characters you identified in "Stygivenator" don't mean it is Tyrannosaurus, because Nanotyrannus also has them.  They would only go as far to show "Stygivenator" was in the Nanotyrannus-Tyrannosaurus group.  Since Larson already believes this, he doesn't need to engage with them.

#Y- You say "it is curious that people are a lot less upset about my hypothesis that Maleevosaurus is a juvenile T. bataar".  I think it's just that less people have bothered with it.  You (1996, 1999) used Maleev's figures to argue the supposed cranial apomorphies were juvenile characters, but no one's even addressed Carpenter's (1992) postcranial characters (tall cervical neural spines; reduced acromion on scapula; pronounced spur-like obturator process; downcurved ischium; and metatarsals III and IV don't overlap the metatarsals medial to them much), adult characters (closed neurocentral sutures and fused astragalocalcaneum) or examined the specimen themselves since Maleev's work AFAIK.

References- Gilmore, 1946. A new carnivorous dinosaur from the Lance Formation of Montana. Smithsonian Miscellaneous Collections. 106, 1-19.

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

Carpenter, 1992. Tyrannosaurids (Dinosauria) of Asia and North America. in Mateer and Chen (eds.). Aspects of nonmarine Cretaceous geology. Beijing, China. Ocean Press. 250-268. 

Carr, 1996. Cranial osteology and craniofacial ontogeny of Tyrannosauridae (Dinosauria: Theropoda) from the Dinosaur Park Formation (Judith River Group, Upper Cretaceous: Campanian) of Alberta. Masters Thesis. University of Toronto. 358 pp.

Carr, 1999. Craniofacial ontogeny in Tyrannosauridae (Dinosauria, Coelurosauria). Journal of Vertebrate Paleontology. 19, 497-520.

Currie, 2003. Cranial anatomy of tyrannosaurid dinosaurs from the Late Cretaceous of Alberta, Canada. Acta Palaeontologica Polonica. 48(2), 191-226. 

Tsuihiji, Watabe, Tsogtbaatar, Tsubamoto, Barsbold, Suzuki, Lee, Ridgely, Kawahara and Witmer, 2011. Cranial osteology of a juvenile specimen of Tarbosaurus bataar (Theropoda, Tyrannosauridae) from the Nemegt Formation (Upper Cretaceous) of Bugin Tsav, Mongolia. Journal of Vertebrate Paleontology. 31(3), 497-517.

Larson, 2013. The case for Nanotyrannus. in  Parrish, Molnar, Currie and Koppelhus (eds.). Tyrannosaurid Paleobiology. Indiana University Press. 15-54.

If there's one thing that can interrupt the Lori analysis to get me back to the blog, it's this.  So, "Ingenia" has been renamed.  Finally.  Mike Christopher Taylor noted this back in 2004 (ironically, I was the first person to comment on it), and we know Barsbold had been informed his genus was preoccupied.  So a decade later we get a paper renaming it Ajancingenia by someone named Jesse Easter.  Who?  Is this going to be another Megapnosaurus situation?  Barsbold's involvement or consent isn't noted anywhere.  In any case, on to the paper.  The holotype and paratype material list looks familiar, perhaps because I wrote them.  That's right, Easter just copied my materials list and deleted the measurements as Cau handily illustrates on his blog.  At least the Database is getting used.  That's not SO bad.  But then I start reading the content.

"A number of specimens have been referred to Ajancingenia over the years."  Yes that's true.  I detailed that on the Database and... this is just my entry padded with some morphological comparisons.  The next paragraph is even worse.  I wrote-

"As with Conchoraptor, no evidence has ever been published defending the placement of paratypes or referred material in "Ingenia". Indeed, the sternum of IGM 100/33 differs from the holotype in lacking fusion between sternal plates (Barsbold, 1983), IGM 100/31 is said to lack fibulocalcanear contact (Lu, 2004) unlike the holotype, IGM 100/33 has ventrally keeled sacrals while the holotype has ventrally grooved sacrals, and varying amounts of sacral vertebrae have been described (7 by Barsbold, 1983; 8 in IGM 100/31 by Lu, 2004). Multiple taxa may be represented, or these may simply be ontogenetic/individual variation and/or illustration or descriptive error. The measurement table in Fanti et al. will prove useful to refer specimens based on ratios once it is examined."

Easter wrote-

"The assignment of the paratypes to Ajancingenia has been questioned partially due to reported variation in the number of sacral vertebrae. MPC-D100/30 has seven ventrally grooved sacrals, while MPC-D100/33 has eight ventrally keeled sacrals. MPC-D100/33 also lacks fusion between the sternal plates (Barsbold 1983). MPC-D100/31 has eight sacral vertebrae, and reportedly lacks fibulocalcanear contact (Lü 2004). These variations may indicate that more than one taxon is represented. However, they may also be caused by ontogenesis, intraspecific variation, or descriptive error, and hence I retain these specimens as Ajancingenia yanshini."

Well that's just all my data rewritten.  After I spent time compiling this data back in 2007, why aren't I a coauthor?  So I wrote the editorial staff of Zootaxa, and between that and Easter's recent post on Jaime's blog, we have the following information.

Easter originally did cite me in his publication, but reference to my website was deemed inappropriate by the editors, so this was removed from the final draft.  The editor has assured me he didn't realize the significance of my website to the paper and would have changed it to a pers. comm. if he knew.  This leads to a few issues.  Why was reference to the Paleobiology Database (Fara, 2001) retained in the References while The Theropod Database was not?  Why didn't Easter counter that I was the source of significant portions of his data when the editors did this?  Honestly, a citation isn't even the proper attribution for using someone elses' compiled data.  Easter should have first asked me, then listed me in the Acknowledgements as responsible for that information.

But Easter is completely new to publication, so perhaps he was just naive.  Then again, he posted on The Fossil Forum " Additionally, a number of specimens have been labeled "Ingenia" over the years, several of which have since been transferred to new genera.  Hence, I reassessed the identification of a number of these specimens."  Sure, YOU reassessed their identification....

As for Barsbold's involvement, Easter himself admits on Jaime's blog "Prior to undertaking this project I made every effort to contact Barsbold with full intention of co-authoring this paper with him."  So no, Barsbold was not consulted.  I've emailed Barsbold before, about "Tonouchisaurus" and such, so he's not impossible to contact.  Indeed this does seem to be a Megapnosaurus situation.  As Brad McFeeters said on Facebook, "So this is basically a paper that any one of us could have written, but didn't."  Hey, I did write it.  Sort of.  Who out there wants to rename "Ischyrosaurus"? "Coelosaurus"?  Supplies are limited, act now!  The editors knew this but let it pass.  Which is ethically questionable, I'd say.  And that Fossil Forum post by Easter says "I undertook this project back in the spring after consulting with Rinchen Barsbold".  So either you consulted with Barsbold, or you made every effort to consult with him.  One of those is a lie.

So, Easter copies data, makes no effort to retain the attribution and performs classic taxonomic claim jumping.  What else is there?

His only figure- credited to Jennifer Haruta, but is clearly precisely redrawn from Sabath's illustration in Barsbold et al.'s (1990) Oviraptorosauria chapter in "The Dinosauria".  But flipped!  Amusingly, this makes the caption of it being right elements in anterior/dorsal view nonsensical, since they would be left elements if the figure were accurate.  So you rename someone's genus, then use a figure from their work, but feel the need to redraw and flip it?  Sounds legit.  It's not like this is an obscure picture.  EVERYONE owns a copy of "The Dinosauria", and anyone qualified to review an oviraptorid paper would recognize it.

You know which subfamily Easter refers Ajancingenia to?  Ingeniinae.  But... that has to include the nematode Ingenia.  The oviraptorid subfamily needs to be renamed Ajancingeniinae.  But no reviewer noticed.  Seems basic for anyone reviewing a paper on nomenclature.  I don't expect random reviewers to be familiar with my website and aware of the plagiarism, but these along with the Barsbold thing are obvious, major issues.  But at least they cut references to my website.  That was the important thing.  You'll forgive me if I'm cynical.

So what now?  The editorial staff at Zootaxa have certainly been friendly and punctual, but apparently the only recourse is to issue an erratum explaining this.  Which is better than nothing, but less than ideal.  Sure this generation will be aware of the issue thanks to blog posts and Facebook, but 100 years from now Easter (2013) will be seen as a pretty good paper finally renaming "Ingenia".  How many people then will have the erratum downloaded?  The repercussion for rewriting others' data as your own seems to be a note is published saying you did this.  I'm less than pleased.

So any budding taxonomists should check out my entry on "Coelosaurus"here.  As I say, "the theropod genus Coelosaurus was preoccupied by Coelosaurus (Owen, 1854), an indeterminate centrum with a broken but fused neural arch and subcircular amphicoelous ends" and "while the tibia does differ from other ornithomimids', it cannot be placed in a known genus or species."  Just rewrite what I say and have at it.  You can be responsible for Unpronounciblecoelosaurus antiquus, and Leidy's long dead, so there's not even that worry.  Get someone to redraw Leidy's figure and flip it and you're all set.  Did I mention I'm cynical?

References- Barsbold, Maryanska and Osmolska, 1990. Oviraptorosauria. in Weishampel, Dodson and Osmolska (eds). The Dinosauria. University of California Press, Berkeley. pp. 249-258.

Fara, 2001. Khermeen-Tsav locality (SMPE) (Cretaceous of Mongolia). Available from: http://paleodb.org/?a=basicCollectionSearch&collection_no=11582 (Accessed 5 August 2013).

Easter, 2013. A new name for the oviraptorid dinosaur "Ingenia" yanshini (Barsbold, 1981; preoccupied by Gerlach, 1957).  Zootaxa. 3737(2), 184-190.

I like to make sure all named taxa are in the Database every New Years, no matter how much I neglect the site otherwise, so here you go- Dahalokely, "Arcovenator", Siats, Aorun, Yutyrannus, Juratyrant (officially), Lythronax, Jianchangosaurus, Ningyuansaurus, Ganzhousaurus, Leptorhynchos, Yulong, Nankangia, Wulatelong, Jiangxisaurus, Aurornis, Eosinopteryx, Acheroraptor, Yurgovuchia, Xinghaiornis, Shengjingornis, Gobipipus (finally official!), Xiangornis, Zhouornis, Jiuquanornis, Piscivoravis, Schizooura, Yumenornis, Changmaornis and Yanornis guozhangi have all been added.

One surprising thing has been how many of the new taxa were "acquired" from fossil dealers or other less specified private collectors, with at least five being examples. 

Also, this electronic ICZN thing hasn't made citations any simpler.  As usual we have taxa published physically (e.g. Ganzhousaurus), taxa published validly electronically in electronic journals (e.g. Dahalokely), and taxa published invalidly electronically in physical journals (e.g. "Arcovenator"), but now we also have taxa published validly electronically in physical journals that have been not yet been physically published (e.g. Aorun, Piscivoravis).  The latter make an odd case because their citations are valid 2013 publications, but there will be an identical version published physically in a 2014 issue.  So how are we citing these?  Two parallel citations of identical content?  Ugly and redundant.

As for two nomina nuda you may not have heard of, try "Plesiosaurodon" and "Farragochela".

Now to finish numbering the Lori characters (who knew formatting could be so time-consuming)....

Hi everyone.  With Lori "done", let's try to get more blog posts up this year.  First is something Molnar told me about last year and gave me permission to discuss since he wasn't going to write it up.  So I wrote about it in the Database in September, then forgot to mention it once I uploaded the revised pages on New Years.  Without further ado...

Figure 1. Comparison between Vitakridrinda syntype snout MSM-155-19 (top; from Malkani, 2010) and Pabwehshi holotype snout GSP-UM 2000 (bottom; from Wilson et al., 2001).  Both in sagittal section.

Vitakridrinda's syntype snout (originally described as abelisaurian by Malkani) is a really good match for the baurusuchid crocodyliform Pabwehshi.  Pabwehshi is from the same formation and about 50% larger, though the latter measurement will vary based on how far down the snout each cross section is. The nasal diverticulum seen in Vitakridrinda is listed by Wilson et al. (2001) as an autapomorphy of Pabwehshi, but the internal anatomy of other baurusuchid snouts is poorly known, though Baurusuchus, Stratiotosuchus and Wargosuchus at least lack evidence of it in the external naris. Under Molnar's interpretation, Malkani's dorsal palatal process (dpp above) is the secondary palate, the ventral palatal process (vpp) is the mandible, the cavity between these is the oral cavity, and the cavity in the ventral palatal process is the Meckelian canal. This leaves almost all of Malkani's supposed lateral surface as matrix which needs to be prepared to expose bone. Thus his supposed bite punctures are merely grooves excavated in the matrix, while his 'combat teeth' are tooth cross sections ventral to the dentary. Malkani's scenario of intraspecific combat causing these features is thus exposed as being fanciful. While most features of Vitakridrinda's snout as described by Malkani are based on misinterpretation, it should be noted Pabwehshi has labiolingually compressed tooth crowns with mesial and distal serrations and a more convex mesial edge as in abelisaurids.

I think this is a really good observation, and have since learned that Molnar heard it from Wilson, one of Pabwehshi's coauthors.  In November, Malkani himself independently contacted me for advice with manuscripts, one of which also uses Wilson's suggestion.  He came to different taxonomic conclusions than I did, but agrees on the basic point of the snout being from a croc, which further strengthens the idea.

This of course leads to the question of what the rest of the Vitakridrinda type material belongs to.  The limb bone (femur?) segments (MSM-59-19, 60-19) are possibly theropod due to their supposed inturned head, distinct neck, and hollowness, though Malkani (2009) states a section "has fibrous bone network in the hollow", so perhaps they are not actually hollow. The stated lack of an anterior trochanter may support a crocodiliform identity, or may be due to preservation. The supposed braincase (MSM-61-19) matches Baurusuchus as poorly and ambiguously as it does abelisaurids, so remains an unidentified object. The supposed tooth cross section (MSM-62-19) works as well for Pabwehshi as it does for abelisaurids.  So the basic answer is that the published data is too crummy to tell.  This is unfortunate because exactly what specimen the name Vitakridrinda should be connected to is uncertain.  Malkani refers to all of the type material as the holotype, as he thought they all belonged to one individual.  Since the ?braincase and ?femora were found 100 meters away from each other, this seems unlikely, and one (or the snout) should really be selected as a lectotype.  Malkani's manuscript will clarify some of this if it is published, but I fear without further preparation and better photography, Vitakridrinda's possible synonymy with Pabwehshi and syntypic identification will remain uncertain.

What is Pabwehshi?

Finally, because it's me, some phylogenetic tests!  I thought it would be simple to just add Vitakridrinda/Pabwehshi to the baurusuchid part of my croc tree, but then saw a more recent paper (Montefeltro et al., 2011) examining baurusuchid phylogeny excluded it from the family.  Those authors referenced another paper (Larsson and Sues, 2007; top tree in figure 2) that found it sister to a clade of sebecidsand peirosaurids instead.  They named this clade Sebecia, and noted similarity between Pabwehshi and the peirosaurid Hamadasuchus in particular, which had not been included in prior analyses that found Pabwehshi to be a baurusuchid.  And so I had to enter the confusing and conflicting world of croc phylogeny.

What I found was interesting.  First, Larsson and Sues excluded Pabwehshi a priori because "it has a sagittal torus on its maxillary palatal shelves, absent in the putative baurusuchids".  So they didn't test it themselves, and indeed if added to their matrix, Pabwehshi comes out sister to other baurusuchids.  Second, adding Hamadasuchus to those earlier analyses that placed Pabwehshi in Baurusuchidae does make Sebecia more likely than before (by 1-4 steps), though it is still unparsimonious.  Sebecia takes 8 extra steps to enforce in these early analyses.  But in none of those cases does Pabwehshi move to Sebecia, needing 1-4 additional steps to go there once Sebecia is enforced.  As analyses get larger and more recent, it takes increasing numbers of extra steps to move it, and it's always closer to sebecids than to Hamadasuchus.

Figure 2. Comparison of Larsson and Sues' (2007) topology at top to Pol et al.'s (2012) below.  Note the top one has orange sebecids sister to green peirosaurids to make Sebecia, while the bottom one based on a much larger analysis has sebecids sister to red baurusuchids instead.  They also differ in that the top one has blue neosuchians sister to Sebecia, whereas sebecians are interspersed throughout the other taxa in the bottom one to form a huge Notosuchia to leave neosuchians basal instead.  Red Pahwehshi is a sebecian on top, but a baurusuchid on bottom.

The most recent analysis (Pol et al., 2012; bottom tree in figure 2) is much larger (347 characters, 88 taxa) than Larsson and Sues' (158 characters, 33 taxa) and includes a ton more postcranial characters, and postcranial codings for taxa like Baurusuchus, Sebecus, Notosuchus and Araripesuchus that were not coded postcranially by Larsson and Sues due to a lack of material/description.  It takes 4 extra steps to move Pabwehshi to Sebecia if the latter is forced to exist, and again is close to sebecids in that case.  Forcing Sebecia to exist in the first place though only takes 5 extra steps, which isn't too bad.  However, it ends up in that uruguaysuchid+pierosaurid clade which is sister to other notosuchians.  To get it to be sister to the blue neosuchians like in Larsson and Sues' tree takes 16 more steps, so seems unlikely.  As Pol et al. describe in their paper, this is due to all of the new characters and codings for Sebecus et al.'s postcrania, so while Sebecia itself isn't dead, Larsson and Sues' placement for it may be.

Importantly, even when Sebecia is enforced, Pabwehshi still clades with baurusuchids and most analyses (including the largest ones) take 4 extra steps to move it into Sebecia. This suggests there is no sebecian signal in Pabwehshi, as does the lack of a particular position within Sebecia when it is forced to be there (sister to either Bretesuchus, Iberosuchus, or a wildcard basal sebecid). Notably it is always attracted to sebecids though, which are sister to baurusuchids in non-sebecian phylogenies, as opposed to being isolated or close to Hamadasuchus as in Larsson and Sues' paper. While Hamadasuchus is important for making Sebecia itself more likely (by 1-6 extra steps), it only made Pabwehshi more likely to be a sebecian in one analysis, and then only by one step.

And there ends our foray into croc phylogeny.  See more detail on the material and analyses at the Database entry.  I'd love to add more taxa to Pol et al.'s analysis, like the large number of notosuchians that were left out, and the newly redescribed Shartegosuchidae that seems to be basal to Neosuchia+Notosuchia, so are probably important for settling the basal relationships of those clades.  But there's only so much time, and based on the rampant miscodings and poorly defined characters in theropod analyses, I'm not confident croc analyses are any better.  Which means checking matrices, which means acquiring literature past my current 372 croc pdfs, which means lots of work, so next time it's back to theropods.

References- Wilson, Malkani and Gingerich, 2001. New crocodyliform (Reptilia, Mesoeucrocodylia) from the Upper Cretaceous Pab Formation of Vitakri, Balochistan (Pakistan). Contributions from the Museum of Paleontology. The University of Michigan. 30(12), 321-336.

Larsson and Sues, 2007. Cranial osteology and phylogenetic relationships of Hamadasuchus rebouli (Crocodyliformes: Mesoeucrocodylia) from the Cretaceous of Morocco. Zoological Journal of the Linnean Society. 149, 533-567.

Malkani, 2009. New Balochisaurus (Balochisauridae, Titanosauria, Sauropoda) and Vitakridrinda (Theropoda) remains from Pakistan. Sindh University Research Journal (Science Series). 41(2), 65-92. 

Montefeltro, Larsson and Langer, 2011. A new baurusuchid (Crocodyliformes, Mesoeucrocodylia) from the Late Cretaceous of Brazil and the phylogeny of Baurusuchidae. PLoS ONE. 6, e21916.

Pol, Leardi, Lecuone and Krause, 2012. Postcranial anatomy of Sebecus icaeorhinus (Crocodyliformes, Sebecidae) from the Eocene of Patagonia. Journal of Vertebrate Paleontology. 32, 328-354. 

Hi everyone.  Today we're looking at O'Connor and Sullivan's (2014) paper reinterpreting Zhongornis.  As the abstract says "The recently described maniraptoran theropod Zhongornis haoae, known from a single juvenile specimen, was originally identified as a bird. However, morphological re-evaluation reveals striking resemblances to both Oviraptorosauria and Scansoriopterygidae."  Well, does it?

No.

This is one of those papers that got worse and worse as I read more of it.  It seems to be written to reach a certain conclusion, but finds a different conclusion that is basically unacknowledged.  There are only a few actual reinterpretations of anatomy, namely the sacrum as having less vertebrae (5-6 instead of 6-7), the tail as having more vertebrae (~20 instead of 13-14), a less elongate coracoid and an ischium without a proximodorsal process (reinterpreted as the ilial peduncle).  Are these better than Gao et al.'s (2008) original interpretations?  It's impossible to tell, since the figures are terribly compressed jpegs that show artifacts even in the line drawings.  I've requested better versions from O'Connor but have yet to receive a reply.  Regardless, let's look at the evidence Zhongornis is closely related to scansoriopterygids and/or oviraptorosaurs.

The stated similarities to scansoriopterygids are as follows-

1. Short and deep skull.  Expected in any juvenile.
2. Short humerus (humerofemoral ratio 104% compared to scansoriopterygids' 98-112%).  Also expected in younger specimens, and a similar distance from adult Confuciusornis (114-127%) as the juvenile Liaoxiornis (108%) is from the adult Cathayornis (117%).
3. Weakly curved manual unguals with low flexor tubercles.  The curvature is actually similar to confuciusornithids and other basal birds.  O'Connor and Sullivan have a simplistic idea of basal birds and deinonychosaurs having more strongly curved manual unguals than oviraptorosaurs or scansoriopterygids, but there is a lot of variation in each. Also Scansoriopteryx and Epidexipteryx actually have large flexor tubercles.
4. Reduced number of caudal vertebrae (~20).  This is only true in Epidexipteryx (16) and admitted to be absent in Scansoriopteryx (~30-35).  This is also true in pygostylians of course (e.g. juvenile Dalingheornis with unfused caudals has ~20).
5. No distinct transition point or elongated distal caudals.  This is untrue in scansoriopterygids, where the distal vertebrae are elongate with reduced neural spines and transverse processes.  It can't really be evaluated in pygostylians with a pygostyle, though juveniles lacking a pygostyle like Dalingheornis are similar to Zhongornis and Epidexipteryx.
6. 'Incipient' pygostyle.  This phrase is used incessantly throughout this paper, but is never defined sufficiently.  The distal caudals in Zhongornis and Epidexipteryx are unfused (Scansoriopteryx's are unpreserved), so are not strictly pygostyles.  O'Connor and Sullivan cite Persons et al. (in  press) as attributing an incipient pygostyle to Caudipteryx, because "the last five vertebrae appear to be tightly integrated into an inflexible unit." But this is true of any coelurosaur, as the last caudals generally have flat articular surfaces and often elongate zygapophyses. Any pygostyle development is at least as true in pygostylians as it is in Epidexipteryx.
7. No obturator process.  Also true in Pygostylia, Jeholornithidae and Omnivoropterygidae.
8. Penultimate pedal phalanges longest.  This is not true in Scansoriopteryx, which has III-3 equal to III-1 and IV-4 equal to IV-1.  It is unpreserved in Epidexipteryx.  II-2 is longer than II-1 in most basal avialans as well, including confuciusornithids.
9. Manual phalanx I-1 longer than metacarpal II.  This is untrue in Zhongornis (94%) and scansoriopterygids (91% in Scansoriopteryx), and is similar to basal avialans (91% in Balaur; ~92% in Confuciusornis) and basal oviraptorosaurs (~93% in Similicaudipteryx; 89-93% in Caudipteryx).
10. Lack of proximodorsal ischial process.  This would be similar to scansoriopterygids, but the poor preservation proximally and great simiarity in shape to taxa with such processes (e.g. juvenile enantiornithine GMV-2158) make this equivocal at least.

Left ischia in lateral view of Zhongornis (top; after O'Connor and Sullivan, 2014), juvenile enantiornithine GMV-2158 (middle; after Chiappe et al., 2007), Scansoriopteryx holotype (bottom ; after Czerkas and Yuan, 2002).  Note the similarity between Zhongornis and GMV-2158, suggesting the process on the upper right is the proximodorsal process and not the iliac peduncle.

So we have no good scansoriopterygid characters in Zhongornis. 

How about oviraptorosaurian ones?

1. Low number of sacrals.  This could easily be ontogenetic, as juveniles often have less sacral vertebrae than adults.  The enantiornithine GMV-2158 has six sacrals for instance, when adult enantiornithines have seven or eight.  So if O'Connor and Sullivan are right that Zhongornis has 5-6, that would work if the adult had seven sacrals like confuciusornithids.
2. 'Incipient' pygostyle.  The argument used above works here- incipiency is a vague descriptor and any pygostyles are present in pygostylians as well.
3. Concave anterior narial margin formed by premaxilla.  This is true in the vast majority of theropods, pygostylians included.
4. Long frontals.  This is a confusing character to list here, since oviraptorosaurs usually have shorter frontals than most coelurosaurs due to their longer parietals.  Thus frontal length doesn't provide evidence Zhongornis is an oviraptorosaur.
5. Frontals narrow anteriorly and greatly expanded posteriorly.  Another confusing character, since oviraptorosaurs generally have less triangular frontals than most coelurosaurs.
6. Short and robust tail.  The tail is about equally short in juvenile pygostylians (e.g. length 1.59 times femoral length in Dalingheornis), Zhongornis (1.54) and basal oviraptorosaurs (~1.5 in Caudipteryx, 1.36 in Similicaudipteryx).  Oviraptorosaurs' tails are robust due to long chevrons (unpreserved in Zhongornis) and transverse processes (short in Zhongornis).  Thus there is no evidence Zhongornis has a tail that is robust for its length.
7. Robust furcula.  Basal oviraptorosaurs like Protarchaeopteryx, Similicaudipteryx and Caudipteryx actually have gracile furculae, and basal avialans like confuciusornithids have robust furculae.
8. Pointed epicleidia on furcula.  This is similar to some oviraptorids (Oviraptor, Citipati), though lacking in others (Khaan, Conchoraptor, "Ingenia", Jiangxisaurus, Heyuannia).  Unfortunately, other oviraptorosaurs do not preserve epicleidia in anterior/posterior view.
9. Metacarpal I 33% of metacarpal II length.  While shorter in many basal avialans, this is even stated by the authors to be present in Confuciusornis, and is even longer in Changchengornis and Balaur.  
10. Metacarpal I wider than metacarpal II.  Again, this is present in confuciusornithids and Balaur.
11. Manual phalanx I-1 subequal in length to metacarpal II.  As discussed in scansoriopterygid-like character 9 above, this is similar in Zhongornis, Confuciusornis and Balaur.
12. Weakly curved manual unguals.  As noted above, there is a lot of variation in oviraptorosaurs, with e.g. Protarchaeopteryx having more strongly curved unguals than Caudipteryx.  The curvature in Zhongornis isn't more similar to oviraptorosaurs' than pygostylians'.
13. Long nasals.  Another confusing character, since oviraptorosaurs have shorter nasals than most coelurosaurs.
13. ~20 caudal vertebrae.  This is not different from basal pygostylians as e.g. the juvenile Dalingheornis holotype has about 20 caudal vertebrae while lacking a pygostyle.
14. Reduced manual digit III of three phalanges. This may not be true (a short III-1 may be hidden), but the similarity to Caudipteryx's two phalanges noted by O'Connor and Sullivan is problematic for two reasons. First, as they state, Sapeornis has less than four phalanges on digit III (also true in Balaur). More importantly, the authors are not proposing a caudipterid identification for Zhongornis, and more basal oviraptorosaurs like Protarchaeopteryx and Similicaudipteryx have an unreduced digit III.

Only the narrowly pointed epicleidia are more similar to some oviraptorosaurs than to basal pygostylians.  O'Connor and Sullivan go on to compare scansoriopterygids with oviraptorosaurs, listing supposedly shared characters, and stating "We suggest that accumulating morphological information regarding both scansoriopterygids and basal oviraptorosaurs may eventually demonstrate that the former clade is either on the oviraptorosaurian stem or nested within basal Oviraptorosauria (Fig. 3), and convergently evolved ‘avian characteristics’ as a result of adaptation to an arboreal lifestyle."

Analysis and unjustified conclusions

Of course just listing characters isn't that useful, and O'Connor and Sullivan proceed to add Zhongornis to the Xiaotingia version of Senter's TWG matrix.  They recover it as the most basal avialan, followed by Scansoriopterygidae, Jeholornis and Avebrevicauda.  Deinonychosaurs (including archaeopterygids) are sister to Avialae, with oviraptorosaurs and therizinosaurs more basal.  So hypotheses unsupported, right?  You'd think so, but the authors go on as if the opposite had occured.

Strict consensus tree of O'Connor and Sullivan (2014).  Note Aves should either be within Ornithuromorpha or at the Paraves node, depending on the definition used.  Is it suspicious the Paraves clades are flipped so that Zhongornis and scansoriopterygids are next to oviraptorosaurs?

 "Scansoriopterygidae is recovered as the sister taxon to Aves, with the two together forming the clade Avialae."

Since when is Jeholornis+Avebrevicauda Aves?  Aves is either crown birds, or Archaeopteryx plus crown birds, which would be Eumaniraptora here.

"Zhongornis is resolved as sister taxon to Avialae (Scansoriopterygidae + Aves) supporting our hypothesis that Zhongornis is closely related to scansoriopterygids."

First, the scansoriopterygid+jeholornithid+avebrevicaudan clade doesn't correspond to any proposed definition of Avialae.  Either Zhongornis is an avialan because it's closer to Aves than dromaeosaurids and/or troodontids (Gauthier, 1986), because it has wings for powered flight homologous to Aves (Gauthier and de Queiroz, 2001) (moreso than scansoriopterygids seem to at least) or because it's in the Archaeopteryx+Aves clade (Gauthier and Wagner, 2001).
Second, it's only closely related in the Petersian sense of being sister to a clade including scansoriopterygids and another branch.  You could just as validly say Zhongornis is closely related to Jeholornis+avebrevicaudans.

"A relationship between Zhongornis and Scansoriopterygidae is supported by six characters (101, 103, 166, 273, 317, and 325); however, scorings for most of these characters are ambiguous in Zhongornis because of missing data. The only one whose presence can be confirmed in Zhongornis, namely the fact that the minor digit is shorter than the major digit, is absent in Epidendrosaurus."

Er.... a relationship can't be supported by characters that are unknown in one of the two taxa.   Having a supporting character lacking in one taxon is even less sensical.  Obviously character 325 (manual digit III longer than II) can't support this clade if it is absent in Zhongornis.  I'm honestly not sure what this list is supposed to be.  I'd say it's a list of Avialae characters in ACCTRAN (where traits are optimized as evolving as early as possible, so that the basalmost avialan Zhongornis is modeled as having characters unknown for it but present in more derived birds), except 325 should just be a scansoriopterygid character and the actual list of avialan characters should include e.g. obturator process absent.  Alas, O'Connor and Zhou don't include their matrix, so we can't know for now.

We get numerous proclamations such as-
"This study reveals new morphological information that strongly suggests the holotype of Zhongornis is a juvenile scansoriopterygid or close scansoriopterygid relative."
"Based on new morphological data and comparisons with other avian and non-avian taxa, we suggest that the Early Cretaceous ‘bird’ Zhongornis haoae may in fact be either a member or a close relative of the Scansoriopterygidae"
"Revised anatomical interpretation of the tail and more detailed comparisons with non-avian dinosaurs strongly suggest that Zhongornis haoae is not a bird but a member or close relative of the enigmatic maniraptoran clade Scansoriopterygidae."

The analysis didn't even suggest Zhongornis is a scansoriopterygid, let alone strongly suggest it.  Again the authors ignore the equally strong suggestion from their analysis that Zhongornis is a close relative of more derived avialans.

"The apparent scansoriopterygid affinities of Zhongornis would suggest the clade persisted from the Mid-Late Jurassic Daohugou times into Early Cretaceous Jehol times."

Whoah whoah... now the placement of Zhongornis in Scansoriopterygidae is apparent?  

"Zhongornis also bears some similarity to basal oviraptorosaurs, supporting the hypothesis that the Jurassic scansoriopterygids may be stem-group relatives of the Cretaceous Oviraptorosauria."

Apparently it didn't, since scansoriopterygids are avialans in their tree, while oviraptorosaurs are further removed than deinonychosaurs.  And I'm sure Mike Keesey is wondering what the crown-group oviraptorosaurs are. ;)
And tying both MIA hypotheses together...

"The relatively short forelimbs and short hallux in Zhongornis may suggest this taxon is a basal scansoriopterygid, close to the divergence of this clade from basal oviraptorosaurs, although this is inconsistent with its occurrence in the Yixian."

Well, IF Zhongornis were a scansoriopterygid and IF scansoriopterygids were oviraptorosaurs, that might be true.  Though Zhongornis actually has longer forelimbs (84% of hindlimb length, excluding phalanges) than scansoriopterygids (70-81%), and an equally long hallux (I-1 23% of metatarsal II).  So even this doubly hypothetical scenario then doesn't match with the evidence.

Sadly, this paper reminds me most of something from Feduccia or Martin.  O'Connor and Sullivan start with a relationship in mind and list characters to support it, but these are generally incorrect or equally correct for the opposing hypothesis.  They also often compare characters to different taxa in a group, so Zhongornis is like oviraptorids but not Caudipteryx in A and B, and like Caudipteryx but not oviraptorids in X and Y, so therefore is like oviraptorosaurs.  Phylogenetic terms are misapplied, and the result of any analysis is only important in the ways that it agrees with their ideas, not in the ways it disagrees.  One gets the impression the original draft never even included an analysis, as the discussion doesn't take it into account and the authors seem not to know how to evaluate their ideas with that dataset.  What they should have done is constrain scansoriopterygid and oviraptorosaurian Zhongornis to see how unparsimonious those hypotheses are, then constrain oviraptorosaurian scansoriopterygids including or excluding Zhongornis.  I've done that in the Lori analysis, and will say the results are much closer to their cladogram than their written ideas.

References- Czerkas and Yuan, 2002. An arboreal maniraptoran from Northeast China. Feathered Dinosaurs and the Origin of Flight. The Dinosaur Museum Journal. 1, 63-95.

Chiappe, Ji ans Ji, 2007. Juvenile birds from the Early Cretaceous of China: Implications for enantiornithine ontogeny. American Museum Novitates. 3594, 46 pp.

Gao, Chiappe, Meng, O'Conner, Wang, Cheng and Liu, 2008. A new basal lineage of Early Cretaceous birds from China and its implications on the evolution of the avian tail. Palaeontology. 51(4), 775-791.

O'Connor and Sullivan, 2014. Reinterpretation of the Early Cretaceous maniraptoran (Dinosauria: Theropoda) Zhongornis haoae as a scansoriopterygid-like non-avian, and morphological resemblances between scansoriopterygids and basal oviraptorosaurs. Vertebrata PalAsiatica. 52(1), 3-30. 

Persons, Currie and Norell, in press. Oviraptorosaur tail forms and functions. Acta Palaeontologica Polonica. doi: http://dx.doi.org/10.4202/app.2012.0093

You all know the big Eoraptor monograph was finally published as Sereno et al. (2013) containing the first detailed description of the material.  It may have taken 22(!) years from discovery to publication, but it's an excellent paper.  I previously examined the evidence Martinez et al. (2011) provided for Eoraptor being a sauropodomorph when they announced the idea in their Eodromaeus paper.  I found numerous coding issues and errors, such as composite codings and miscodings, which when partially corrected recovered a theropod Eoraptor instead, and also noted few of the proposed theropod characters had been included in their matrix.

Since then, we have the new basal theropod Daemonosaurus, redescriptions of basal sauropodomorphs Chromogisaurus and Pantydraco, redescriptions of all heterodontosaurids, redescriptions of the near/basal-dinosaurs Saltopus and Nyasasaurus, a version of Yates' analysis finding Eoraptor to be a sauropodomorph and more characters from Nesbitt's and Ezcurra's analyses finding it to be a theropod closer to Avepoda than herrerasaurids.  So let's explore the suggested evidence for each position for Eoraptor.  I'll list all novel suggested characters from each analysis, bolding the ones that seem valid.

Outside Eusaurischia (Sauropodomorpha+Theropoda)

 Padian et al. (1999)
1. centra of posterior cervical vertebrae (6-8) subequal in length to those of anterior dorsal vertebrae (refined by Langer, 2004).  This is untrue in Eoraptor, as cervicals 6-8 are 18-23 mm and the anterior dorsals are 16-17 mm.
2. third finger of the manus longer than second finger.  As this is true in Eodromaeus and Tawa, the opposite condition in known sauropodomorphs and avepods is probably convergent.  Herrerasaurus  also has III longer than II, while Guaibasaurus is like sauropodomorphs and avepods.  Though Tianyulong has an avepod-like condition, Heterodontosaurus and derived ornithischians have III longest, so this was more likely the basal condition in Ornithischia.
3. metatarsal I contacts tarsus.  Since this is also true in Sauropodomorpha, the authors had no reason to list it.  It only excludes Eoraptor from Avepoda.

Langer (2004)
4. subnarial premaxillary process extends posteriorly to the external naris.  This is also true in Daemonosaurus, making the basal condition for Theropoda ambiguous.  As Herrerasaurus has this state as well, it's even worse if herrerasaurids are theropods.
5. radius >80% of humerus length.  This is untrue in Eoraptor, which has a ratio of 74%.
6. manual ungual I shorter than metacarpal I.  This is untrue in Eoraptor, which has a ratio of 100%.  Note even if the ratio is actually barely in agreement, Eodromaeus and Tawa have short unguals I too, so it would be another character convergent in avepods and sauropodomorphs.
7. metacarpal III longer than metacarpal II.  Another character also present in Eodromaeus and Tawa, again making sauropodomorphs and avepods convergent. As with the digit length comparison, Guaibasaurus has longer II while Herrerasaurus has longer III.  Also while heterodontosaurids have longer II, other ornithischians and Saltopus have longer III, suggesting the former is convergence.
8. distal end of ischium unexpanded. This is untrue in Eoraptor.
9. medial margin of distal tibia not broader than lateral margin. This is untrue in Eoraptor.

Smith et al. (2007)
10. maxillary tooth count 12-18. Eoraptor has 17, while basal theropods have (9/10)-11 and basal sauropodomorphs don't preserve the area or have unreported counts.  As Saturnalia and Panphagia have 17 and 23 dentary teeth respectively, their maxillary counts were probably within the 12-18 range or higher, not lower as in basal theropods. Thus there is no shared derived state to differ from.
11. lateral surface of anterior end of nasal along the posterior margin of the external naris flat.  Pantydraco and Daemonosaurus also lack this narial fossa, though Panphagia has it.  This means Theropoda is basally ambiguous while Sauropodomorpha is barely basally derived in having the fossa, so the character is not an unambiguous eusaurischian synapomorphy.  For what it's worth, Herrerasaurus also lacks the fossa.
12. posteroventral dentary process far posterior to posterodorsal process.  This is true in basal sauropodomorphs  (Panphagia, Pantydraco) and basal theropods (Eodromaeus, Tawa).  It's not true in ornithischians (Tianyulong, Heterodontosaurus, Eocursor) though, making the condition in Saurischia's outgroup ambiguous (given Silesaurus having the opposite condition).  Again for what it's worth, Herrerasaurus has the same condition as ornithischians.
13. foramen in the ventral part of the splenial absent.  This is difficult to code as the anterior splenial is thin and often broken.  In Sauropodomorpha, Panphagia has a foramen, Lamplughsaura is illustrated without one (though by Chatterjee, whose drawings are often idealized), Plateosaurus is polymorphic, and Lufengosaurus and Adeopapposaurus have it.  In Theropoda, Liliensternus lacks one, Dilophosaurus is illustrated as lacking one but seems to be anteriorly incomplete, and Ceratosaurus has one.  Thus the basal condition in either saurischian clade is unclear though more probably present in sauropodomorphs.  Ornithischians lack the foramen, as does Staurikosaurus though the latter has a poorly preserved mandible.
14. iliac supraacetabular crest shelf-like and short, extending primarily laterally.  This is also true in basal sauropodmorphs (Panphagia, Pampadromaeus) and basal theropods (Eodromaeus,Tawa).
15. ridge on lateral side of tibia for connection with fibula absent. This is untrue in Eoraptor. 

Yates (2007)
16. relationship between posterolateral process of the premaxilla and the anteroventral process of the nasal a broad sutured contact.  This is untrue in Eoraptor.
17. size and position of subnarial foramen small (no larger than adjacent maxillary neurovascular foramina) and positioned outside of narial fossa.  Basal theropods (Tawa, coelophysids, Dilophosaurus) lack a subnarial foramen, as do outgroups (ornithischians, Silesaurus).  Thus there is no obvious ancestral condition for the subnarial foramen, nor evidence theropods ancestrally had one.  Herrerasaurus does have this condition.
18. pointed posterolateral process of the nasal overlapping the lacrimal absent. This is untrue in Eoraptor.
19. length of middle to posterior cervical centra (6-8) no more than the length of the axial centrum. This is unknown in Eoraptor, as the axis is fragmentary.
20. laminae bounding triangular infradiapophyseal fossae on dorsal neural arches absent. This is untrue in Eoraptor.
21. transverse width of the first distal carpal less than 120% of the transverse width of the second distal carpal. This is unknown or untrue in Eoraptor, as distal carpal I is either unpreserved or diagenetically fused to the radiale in the left carpus and ~192% the width of distal carpal II. Notably, the basal theropods Eodromaeus and Tawa and basal sauropodomorph Efraasia have a small distal carpal I though, so this is not a eusaurischian character, though Heterodontosaurus does have a large distal carpal I so that ornithischians have an ambiguous basal state. Herrerasaurus has a small distal carpal I.

Martinez and Alcober (2009)
22. no caudosacral.  This is also true in basal theropods (Eodromaeus and Tawa) and ambiguous in sauropodomorphs (true in Pampadromaeus but not Efraasia and more derived taxa).  Guaibasaurus, Sanjuansaurus and Herrerasaurus also lack a caudosacral, though Staurikosaurus may have one.  Ornithischians have a caudosacral.
23. width of metacarpal I shaft less than 35% of length. This is untrue in Eoraptor
.
Bittencourt Rodrigues (2010) also placed Eoraptor basal to Eusaurischia, but this paper has yet to be translated.

What's that?  No characters were bolded?  These turned out particularly bad, with almost half (10-11) not even being present in Eoraptor.  The others are basically all also found in taxa agreed to be basal theropods (11) and/or sauropodomorphs (7).  The best character is the absent anterior splenial foramen, which depends on illustration inaccuracy of a poorly preserved and seldomly exposed element.

Next up- is it a sauropodomorph?

References- Padian, Hutchinson and Holtz, 1999. Phylogenetic definitions and nomenclature of the major taxonomic categories of the carnivorous dinosaurs Dinosauria (Theropoda). Journal of Vertebrate Paleontology. 19(1), 69-80.

Langer, 2004. Basal Saurischia. In Weishampel, Dodson and Osmolska. The Dinosauria Second Edition. University of California Press. 861 pp.

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.

Yates, 2007. Solving a dinosaurian puzzle: The identity of Aliwalia rex Galton. Historical Biology. 19(1), 93-123.

Martinez and Alcober, 2009. A basal sauropodomorph (Dinosauria: Saurischia) from the Ischigualasto Formation (Triassic, Carnian) and the early evolution of Sauropodomorpha. PLoS ONE. 4(2), e4397.

Bittencourt Rodrigues, 2010. Revisao filogenetica dos dinossauriformes basais: Implicacoes para a origem dod dinossauros. Unpublished Doctoral Thesis. Universidade de Sao Paulo. 288 pp.

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

Sereno, Martinez and Alcober, 2013. Osteology of Eoraptor lunensis (Dinosauria, Sauropodomorpha). Journal of Vertebrate Paleontology. 32(Supplement to 6), 83-179.

Way back in the days of yore, I had DML post style called "Details on..." where I would report information about obscure dinosaur taxa.  This was before the modern methods of organized file exchange, so to learn more about a newly reported taxon, you'd generally have to request a paper copy from Tracy Ford.  We were all pretty clueless, so I hoped to spread some knowledge around.  One of my posts from 2000 was "Details on Teyuwasu"*, an enigmatic dinosaur described briefly in an abstract and based on  bones first described in an old German paper that was even harder to acquire.  It seems online information on Teyuwasu is still hard to find, so here's an update 14 years later.

* Btw, while I interpreted Kischlat's statement "the distal process is so developed as to encompass the ascending process of astragalus" as being similar to coelophysoids'anterior overlap, it's actually the posterolateral process extending laterally a bit behind the ascending process as in most dinosauriforms.  Hooray for imprecise translations.

Teyuwasu Kischlat, 1999 vide Kischlat, 2000
= "Teyuwasu" Kischlat, 1999
T. barberenai Kischlat, 1999 vide Kischlat, 2000
= "Teyuwasu barberenai" Kischlat, 1999
Late Carnian-Early Norian, Late Triassic
Alemoa Member of Santa Maria Formation, Brazil
Holotype- (BSPG AS XXV 53) femur (276 mm)
....(BSPG AS XXV 54) tibia (264 mm)
?...(BSPG AS XXV 56-59) dorsal centrum (40 mm), partial ilium, (?) distal ischium, femur
Diagnosis- (proposed) extremely robust femur and tibia (minimum transverse femoral width 19% of length); mound-like fourth trochanter.

A-F: Holotype femur BSPG AS XXV 53 of Teyuwasu barberenai in anterior, medial, posterior, lateral, proximal and distal views respectively. G-L: Holotype tibia BSPG AS XXV 54 in proximal, distal, anterior, medial, posterior and lateral views respectively.  Scale = 100 mm. (after Ezcurra, 2012)

Comments- The material was originally described by Huene (1938) as possibly belonging to his new taxon Hoplitosaurus raui, from slightly higher in the formation. Huene later (1942) renamed it Hoplitosuchus, as Hoplitosaurus was preoccupied by an ankylosaur. The taxon was based on two supposed osteoderms described as aetosaurian, but more recently these have been found to be unidentifiable bones by Kischlat (2000) and Desojo and Rauhut (2008). Kischlat (1999) reinterpreted the femur and tibia as being dinosaurian, though only listed features identifying it to the level of Dinosauriformes. He provided a very brief description and named the taxon Teyuwasu barberenai, but as the publication is a symposium abstract, it is invalid under the ICZN (Article 9.10). Kischlat's (2000) later article has similar information, credits the name to the 1999 paper, but is a valid publication. Ezcurra (2012) described the material in depth, finding it certainly belongs to the silesaurid+dinosaur clade, but that the only dinosaurian character is the inturned femoral head. As the bones have been heavily altered taphonomically, Ezcurra was uncertain if the femoral head orientation was artificial. He notes Kischlat's "two paralell ridges running proximodistally" are fractures formed when the medial femoral head was sheared distally. While Ezcurra declared Teyuwasu to be indeterminate, the robusticty itself is vastly different from other basal dinosauriforms, so should be enough to validate the taxon. If added to the Nesbitt archosaur matrix along with all later published additions (including Nyasasaurus and Saltopus), Teyuwasu emerges as a saurischian based on femur longer or about the same length as the tibia, and medial articular facet of the proximal femur rounded.  It's outside Eusaurischia based on the femoral head being unexpanded, symmetrical fourth trochanter (considered tentative by Ezcurra), cnemial crest not laterally curved, and posterior face of distal tibia without longitudinal ridge.  Some of these characters vary within basal saurischians, which are incompletely sampled by Nesbitt, so I wouldn't bet on a non-eusaurischian identity being most parsinomious once all data are in.  Additionally, the coding indicates the moundlike fourth trochanter is unique among sampled ornithodirans, making this another diagnostic character.

Besides the femur and tibia, Huene referred additional material to this individual. A centrum identified by Kischlat (2000) as dorsal was stated by Huene to be possibly but not certainly referrable to this specimen. It is 40 mm long, 45 mm tall and wide, rounded in section and barely amphicoelous to amphiplatyan. A ventral ilium was considered very likely to belong to this individual. It has a supracetabular crest and 'strongly recessed' acetabulum, and narrows to 70 mm between the peduncles and blade. An element tentatively identified by Huene as a distal ischium is much too large to belong to this individual, with the distal end 90 mm deep and 60 mm wide. At the proximal break, these dimensions are 53 and 30 mm respectively. The distal end is triangular in section, which is a saurischian character. Finally, Kischlat (2000) mentioned an additional femur which was not noted by Huene. These were all noted by Kischlat as supplementary material for Teyuwasu, though Desojo and Rauhut stated referred Hoplitosuchus material belongs to Rauisuchia and Dinosauria. The centrum, ilium and/or ischium may comprise the 'rauisuchian' material, or this may refer to the two non-avemetatarsalian calcanea also referred to Hoplitosuchus by Huene.

References- Huene, 1938. Ein grosser Stagonolepid aus der jungeren Trias Ostafrikas. Neues Jahrbuch fur Mineralogie, Geologie und Palaontologie. 80(2), 264-278.

Huene, 1942. Die fossilen Reptilien des sudamerikanischen Gondwanalandes. Ergebnisse der Sauriergrabungen in Sudbrasilien 1928/29. Munich: Becksche Verlegbuchhandlung. 332 pp.

Kischlat, 1999. A new dinosaurian "rescued" from the Brazilian Triassic: Teyuwasu barbarenai, new taxon. Paleontologia em Destaque, Boletim Informativo da Sociedade Brasileira de Paleontologia. 14(26), 58.

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

Desojo and Rauhut, 2008. New insights on "rauisuchian" taxa (Archosauria: Crurotarsi) from Brazil. SVPCA 2008 Programme and Abstracts. 18-19.

Ezcurra, 2012. Comments on the taxonomic diversity and paleobiogeography of the earliest known dinosaur assemblages (Late Carnian-Earliest Norian). Historia Natural. 2(1), 49-71.

There's a new amniote analysis out from Ezcurra et al. (2014) emphasizing the lepidosauromorph-archosauromorph split.  Thev changed a ton of codings from the earlier version by Reisz et al. (2010), almost doubled the size of the matrix, properly ordered most characters, made sure inapplicable codings stopped redundancy in most cases, AND got rid of suprageneric OTUs.  Among the negative points are no parareptiles or aquatic diapsids (yet many synapsids) and a lack of many of the traditional series-based characters (e.g. number of phalanges on digit X, number of vertebrae in this segment).  Regardless, this seems to be better than most amniote analyses, and the lepidosauromorph-archosauromorph split is the perfect place to test pterosaur origins.

Among relevant taxa, the matrix has Peters' closest consensus lepidosaur to pterosaurs, Huehuecuetzpalli, plus two more squamates.  It has Macrocnemus, placed even closer to pterosaurs by him, plus three more protorosaurs.  Also Euparkeria and Erythrosuchus for the Bennett hypothesis.  I added two pterosaurs from the basalmost clade (Preondactylus and Eudimorphodon), Megalancosaurus, Longisquama and Eoraptor.  Note this is far from perfect, as incomplete basal dinosauromorphs (lagerpetonids, Marasuchus), more basal simiosaurs (Vallesaurus, Hypuronector), and more derived pterosaurs with well preserved braincases, palates and axial details would all be useful to add.  Not to mention Scleromochlus, Sharovipteryx, Cosesaurus and Atanassov's taxa.  But what does this preliminary test find?

The pterosaurs were closest to Megalancosaurus, but this clade was sister to Eoraptor within Archosauriformes.  No pseudosuchians were included, so it's uncertain if pterosaurs are strictly archosaurs.  What about Longisquama?  Either a tanystropheid protorosaur or a member of the megalancosaur-pterosaur clade, though note I did (conservatively) use Peters' (2000) illustration for the anatomy.  This may bias it toward those interpretations, though his interpretations were far less fanciful back then.

Forcing pterosaurs to be protorosaurs is 9 more steps, so rather unlikely.  Forcing them to be lepidosauromorphs is 17 more steps though, so probably wrong.

Forcing Megalancosaurus to be an archosauriform outside Ornithodira is only two steps longer, so about equally likely.   The same number of steps move it to Tanystropheidae, with Longisquama following, but not pterosaurs.

Forcing Longisquama to be a lepidosauromorph only takes two steps, and it becomes the most basal one.  Forcing it to be sister to Coelurosauravus results in both being basal lepidosauromorphs, which only takes 3 more steps.  Having this pairing outside Sauria as in Senter (2004) is 5 more steps, so less likely.  Adding Megalancosaurus to complete Senter's Avicephala is 9 more steps though, so rather unlikely.

Finally, enforcing Peters' versions of Lepidosauromorpha (with captorhinids, caseids, weigeltisaurids, trilophosaurs, rhynchosaurs, simiosaurs, Longisquama, tanystropheids and pterosaurs) and Archosauromorpha (with derived synapsids, Paleothyris, araeoscelids and younginiforms) takes a whopping 75 extra steps.  This is worse than any alternative phylogeny I've ever tested for anything.

Instead of asking what pterosaurs are, maybe we should be asking if simiosaurs belong in Archosauria.  Recall even in Nesbitt's (2011) huge analysis focusing on archosaur interrelationships, they could be placed in Avemetatarsalia with only five extra steps.  At the time I thought a broader analysis would be more useful for that question, but here they flit between Archosauriformes and Protorosauria with even less difficulty.  Longisquama is pretty clearly too poorly described to strongly favor any alternative, but it's interesting that Senter's placement for it comes out as badly as it does.  As for what pterosaurs are, while archosauriform beats out protorosaur and both beat out lepidosauromorph, I've seen taxa recover from a 9 step disadvantage often, and a 17 step disadvantage rarely, so both of the latter alternatives are still possible.  75 steps?  Not so much.

References- Senter, 2004. Phylogeny of Drepanosauridae (Reptilia: Diapsida). Journal of Systematic Palaeontology. 2, 257-268.

Reisz, Laurin and Marjanovic, 2010. Apsisaurus witteri from the Lower Permian of Texas: Yet another small varanopid synapsid, not a diapsid. Journal of Vertebrate Paleontology. 30, 1628-1631.

Ezcurra, Scheyer and Butler, 2014. The origin and early evolution of Sauria: Reassessing the Permian saurian fossil record and the timing of the crocodile-lizard divergence. PLoS ONE. 9(2), e89165.