Epichirostenotes and how it changes coding

Sullivan et al. (2011) just named two new caenagnathids, Ojoraptorsaurus boerei for a partial pubis and Epichirostenotes curriei for ROM 43250, a specimen from the Horseshoe Canyon Formation described as Chirostenotes by Sues (1997).  Jaime Headden wrote a great post on the situation here and I agree with his assessment.  I'm extremely doubtful Ojoraptorsaurus can be diagnosed, given the large amount of interspecific variation in most theropods and the low number of comparable caenagnathids.  But that's not too important considering it's just a partial pubis.  My main concern here is a more practical one about Epichirostenotes.

Ischia previously referred to Chirostenotes (from Sues, 1997).  A- RTMP 79.20.1, which is still placed in Chirostenotes pergracilis. B- ROM 43250, now the holotype of Epichirostenotes curriei.  The only other shared elements are ilial fragments and a sacrum for which no differences have been noted.

How should we now code Chirostenotes?  The genus has been used in many analyses, including the Theropod Working Group matrix, which I've been correcting for the description of a new paravian.  In that matrix, it is apparently based on a combination of the Chirostenotes, Macrophalangia and Caenagnathus holotypes, as well as partial skeletons RTMP 79.20.1 (Currie and Russell, 1988) and ROM 43250.  It wouldn't be too important, except ROM 43250 is our only described source for coding Chirostenotes' maxilla, braincase, cervicals, dorsals, caudals and pubis.  So if we leave it out, we're losing a lot of information.  And without a more complete caenagnathid to code, and few overlapping elements, there's a large chance it won't group with Chirostenotes, so could harm oviraptorosaur topology (like coding Caenagnathus separately did for Senter, 2007).  But combining it with Chirostenotes could be misleading once Elmisaurus and Hagryphus are added, since nothing argues ROM 43250 isn't closer to these latter genera.  While ROM 43250 isn't comparable to either, a second specimen from the same formation (metatarsal II CMN 9570, unmentioned by Sullivan et al.) is distinctive from Elmisaurus due to its lack of fusion and straight distal end.  These are plesiomorphies though, so do not argue strongly for its referral to Chirostenotes.  And the metatarsal isn't comparable to ROM 43250 anyway, so any referral to Epichirostenotes is based purely on size and provenence.  But nothing argues the Horseshoe Canyon specimens aren't Chirostenotes either, since so far the apomorphies of Chirostenotes are only known from the mandible (assuming Caenagnathus collinsi is properly synonymized) and other parts of the metatarsus.  The minor differences between the ischia of Epichirostenotes and RTMP 79.20.1 are just like those found between individuals of Tyrannosaurus rex, Microraptor zhaoianus and other species.  The distinction boils down to size (which could easily be ontogenetic) and provenence.  Now this doesn't make Epichirostenotes a nomen dubium, because the braincase and maxilla are certainly distinct from comparable named theropods, it's just that no other named caenagnathid can be compared for the most part. 

Tyrannosaurus rex ischia to show interspecific variation.  Left- FMNH PR2081 left and right (from Brochu, 2003); Right top- CM 9380 (from Osborn, 1906); Right bottom- AMNH 5027 (from Osborn, 1916).

Note how the Tyrannosaurus ischial variation mirrors that between Chirostenotes and Epichirostenotes.  The latter's ischial diagnosis is-
1. "Ischium long and expanded posteriorly; broad behind obturator process."  There is no known comparative length difference, since Epichirostenotes doesn't preserve an ilium and Chirostenotes doesn't preserve a pubis.  The posterior expansion and breadth posterior to the obturator process refers to the greater depth in Epichirostenotes.  As seen most distinctly between the upper right and lower left pictures above.
2. "obturator process expanded and triangular." This refers to the greater depth of the obturator process and non-rectangular tip in Epichirostenotes.  As seen between the two left pictures above.
3. "having a prominent anterior proximal hook-like projection." This refers to the pubic peduncle being longer and more ventrally projecting in Epichirostenotes, enclosing the obturator notch more.  Note the two right pictures above also differ in the length and angle of the ventral portion of the pubic peduncle.
Also notice the other differences within Tyrannosaurus.  The lower right pic has a narrower body proximal to the obturator process.  It also has a longer and more rounded proximodorsal process.  The two right pics have curved shafts compared to those on the left.

So it's a very awkward situation.  I'd bet curriei really is a distinct species from pergracilis, if only because that seems to be true for other theropods compared between those formations (though the published evidence for this is usually as tenuous as the current case).  But the known remains don't justify that anatomically, and whether curriei is more closely related to Chirostenotes than Elmisaurus or Hagryphus is basically unknowable.  If it is closer to pergracilis, then I could see only the most extreme splitter keeping them as separate species based on known remains, let alone genera.  Maybe CM 78000 and 78001 will help sort things out, and it would have been prudent to wait until Sues and Lamanna finish describing them before dealing with the taxonomy of ROM 43250.  I think for now I'll just call ROM 43250 Chirostenotes? curriei and keep the Chirostenotes OTU intact that way.  There's no evidence against it at least, even though it's not necessarily true.  And it's not unheard of for other taxa in the matrix.  The Struthiomimus OTU has always included both the Dinosaur Park S. altus and the unnamed Horseshoe Canyon species represented by AMNH 5257 and exceptionally complete RTMP 90.26.1.  If someone were to name the latter "Epistruthiomimus unnecessari" based on Longrich's comment the metacarpus is more slender, would we have to break up our Struthiomimus OTU?  Note that like the caenagnathid situation, the described differences between species are few and of debatable significance, while there has been no study showing they form a monophyletic group based on apomorphies.  So the facts are the same, but the new genus for ROM 43250 just complicates matters.

Testing Harding's idea- Constraining topologies based on adding taxa in stratigraphic order

On the DML, Grant Harding proposed an idea.  Run cladistic analyses using only the earliest taxa, then sequentially add later taxa, but each time constrain the topology to match the trees found using only earlier taxa.  I tried it using my corrected TWG matrix, which at the moment covers all the taxa and characters up to Hwang et al. (2004).

So for example, the first run included only Jurassic taxa- Sinraptor, Allosaurus, Ornitholestes, Compsognathus and Archaeopteryx.  The tree found was (Sinraptor,Allosaurus(Ornitholestes(Compsognathus,Archaeopteryx))), which is standard.  It disagrees with the total data tree in having Ornitholestes and Compsognathus switched, presumably because of the lack of ornithomimosaurs, therizinosaurs, other compsognathids, etc..  If this were a more complete analysis, you'd have Haplocheirus, scansoriopterygids, Pedopenna, Lori and Anchiornis there as well as all the non-maniraptoriform Jurassic coelurosaurs. 

I then added the taxa which lived slightly later- Shenzhousaurus, Incisivosaurus and Sinovenator.  I constrained the analyses to only find trees agreeing with the relationships found using the Jurassic taxa.  This resulted in- (Sinraptor,Allosaurus(Ornitholestes(Compsognathus(Shenzhousaurus(Incisivosaurus(Sinovenator,Archaeopteryx)))))). This matches the total tree besides the point noted above.  Again, a more complete analysis would have Dilong, Kinnareemimus, Nqwebasaurus, Graciliraptor, Mei, Sinusonasus, "Eoconfuciusornis" and maybe a few other birds.

In any case, I added the following groups next-
- Harpymimus, Pelecanimimus.
- Utahraptor.
- Caudipteryx, Confuciusornis, Sinornithosaurus, Huaxiagnathus, Sinosauropteryx.
- Deinonychus, Microvenator, Sinornithoides, Alxasaurus, Microraptor, IGM 100/44.
- Garudimimus, Segnosaurus, Erlikosaurus, Achillobator.

Then I hit a snag.   The next group was Patagonykus, Unenlagia comahuensis and U? paynemili.  None of these taxa has a definite position in the cladogram when constrained to match the topology of the previous taxa.  The Unenlagia species are both some kind of paravian, while Patagonykus is at least as derived as compsognathids, but is not an ornithomimosaur, therizinosaur, avialan or eudromaeosaur.  And there's no way to constrain a tree to include uncertain relationships like these.  The only taxon left to include before the big end Campanian-Maastrichtian group was Alvarezsaurus, but it didn't help, since it emerges as a compsognathid-grade taxon without affecting Patagonykus' relationships.  So that's a problem with this kind of analysis.  The same is true of the many early fragments that show character combinations unique to certain clades (e.g. Jurassic dromaeosaurid teeth with high DSDIs).  These are normally useless to include in analyses since they don't have different codings than more complete later specimens, but in this variety of analysis, they'd be potentially useful early on but would form polytomies later if not deleted.

Another issue is that many taxa have unconstrained ages, and adding these in order of their earliest possible age, mean age, etc. is going to likely change the results.

To get a finished result of sorts, I simply did not constrain the position of Patagonykus, Unenlagia or U? paynemili in the final run with Campanian-Masstrichtian taxa, since they come out somewhere within their polytomies in the total data analysis anyway, though I did still force Alvarezsaurus to be compsognathid-grade.  The end result was a tree 19 steps longer than the unconstrained tree.  The primary differences are-

- Alvarezsaurus is by compsognathids due to its position before parvicursorines were added.
- Ornitholestes (thanks to the Jurassic analysis), therizinosaurs (thanks to Alxasaurus when analyzed with basal ornithomimosaurs) and Patagonykus+parvicursorines (probably due to following therizinosaurs) are outside Maniraptoriformes.
- Pelecanimimus is an ornithomimosaur due to alvarezsaurids not being included until after it was added.
- Microvenator is a basal maniraptoran due to the absence of more complete caenagnathoids until later runs.
- Caudipteryx is an oviraptorosaur thanks to clading with Incisivosaurus early on.
- Troodontids are paraphyletic to dromaeosaurids instead of to birds (except that Sinovenator is still an avialan), and Microraptor is a basal dromaeosaurid instead of a basal avialan.

So some results are closer to the consensus while others aren't.  I suppose the real test will be to see if any of these relationships are found when I add more taxa and characters to the complete analysis.

Rieppel's reptile matrix and the turtle problem

Which group turtles are most closely related to is one of the greatest problems in vertebrate paleontology.  Traditionally parareptiles, deBraga and Rieppel (1997) and variations on that matrix find them to be close to Sauropterygia in Lepidosauromorpha, while molecular analyses find them to be archosauromorphs.  Recently, Lyson et al. (2010) added Proganochelys and Eunotosaurus to the Rieppel matrix, along with six characters they share,  and found turtles now clade with it inside Parareptilia instead.  What Lyson et al. don't mention is that diapsid turtles are only seven steps longer.  Not much of a difference, but it's something, right?  I'm not so sure.  Looking at the characters, there are huge problems.  I give Peters a lot of (deserved) flack for the poorly designed characters in his amniote analysis, but this honestly isn't any better.  Let's examine some problems...

Composite Characters
Many characters describe more than one variable in morphology, which is not useful.  These can have states describing different variables (e.g. teeth serrated vs. teeth large) or multiple variables described in a single state (e.g. teeth large and serrated vs. teeth small and unserrated).  A common variant is to have "x feature absent" as a state of a character which otherwise describes different morphologies (e.g. teeth serrated vs. teeth unserrated vs. teeth absent).  The only way an absent state should be in a character that's not simply "absent vs. present" is if the variable is number (e.g. two centrales vs. one centrale vs. no centrale) or size (e.g. quadratojugal large vs. quadratojugal small vs. quadratojugal absent).  Characters with this issue are-

1. Premaxilla exposure: exposure anterolateral to external nares small restricted to low posterolateral process forming less than one-half the height of the premaxilla (0); posterolateral process tall reaching dorsal process (1).
6. External nares exposure: dorsal process of premaxilla broad restricting nares to a lateral exposure (0); dorsal process narrow resulting in dorsal exposure of nares (1).
8. Choana palatal exposure: parallel medial border of maxilla (0); deflected posteromedially (1); hidden in palatal view (2).
17. Lacrimal morphology: present and contributing to exteral nares (0); present at least as long as tall, but excluded from external nares (1); if present snall[sic], restricted to orbital margin, or absent entirely (2).
30. Postorbital/supratemporal relationship: in contact (0); not in contact (1); supratemporal absent (1).
38. Quadrate excavation: absent along posterior edge (0); posterior edge deeply excavated forming a concave region (1); quadrate greatly reduced (2).
42. Quadratojugal morphology: present and horizontal dimension exceeds vertical dimension by a factor of at least three (0); present but vertical dimension exceeds horizontal by a factor of at least two (1); present, but greatly reduced and restricted to condylar region (2); absent (3).
49. Pineal foramen position: located in the middle of the body from the parietal (0); displaced posteriorly (1); displaced anteriorly (2); absent (3).
51. Lower temporal fenestra: absent (0); present quadratojugal included (1); present quadratojugal excluded (2); open ventrally (3).
52. Postparietal: present and paired (0); present but fused (1); absent (2).
60. Orientation of paroccipital process: extends laterally forming 90° with parasaggital plane (0); paroccipital process deflected posterolaterally at an angle of about 20° from the transverse width of the skull (1); paroccipital process deflected dorsolaterally at an angle of nearly 45° (2).
65. Ventral braincase tubera: absent (0); present and restricted to basioccipital (1); present, very large, and restricted to basisphenoid (2).
73. Interpterygoid vacuity: anterior end tapers sharply (0); anterior border cresentric (1); absent (2).
74. Suborbital fenestra: absent (0); present but with contribution from either maxilla or jugal along lateral border (1); present, but with both maxilla and jugal excluded from lateral border (2).
75. Cultriform process: long, exceeding length of parasphenoid body and reaching forward to the level of the posterior limit of the internal nares (0); short, not reaching the level of the internal nares (1).
81. Ectopterygoid: present and edentulous (0); present and dentigerous (1); absent replaced by medial process of jugal (2); absent replaced by lateral process of pterygoid (3).
83. Coronoid process: absent (0); present formed by coronoid (1); present formed by dentary (2).
94. Tooth implantation: set in deep sockets ( ); loosely attached to medial surface of jaw (1); ankylosed to jaw (2).
100. Vertebral central articulations: amphicoelous (0); platycoelous (1); other (2).
106. Trunk neural arches: swollen with heavy zygapophyseal butress (0); narrow, strongly excavated neural arch with no heavy butress (1); swollen, but with narrow tall zygapophyseal butress (2).
118. Acromion process: absent (0); present, blade-like, parallelogram in lateral aspect, and arising from the lateral edge of the scapula (1); present, triangular in lateral aspect, and arising from ventromedial border of scapula (2).
126. Supinator process: large angled away from humeral shaft (0); large confluent with shaft (1); small or absent (2).
136. Pubic tubercle: if present small and directed anteroventrally (0); large and strongly turned ventrally (1).
139. Femoral shaft: short and stout (0); sigmoidally curved and slender (1).
141. Femoral trochanter major: absent (0); present and deflected distally from the proximal head of the femur (0); pyramidal in shape and nearly in line with the head of the femur (2); similar in shape to state (1) but positioned at mid-shaft length (3).
149. Astragalus/calcaneum relationship in adult: never fused (0); fused (1); hinge present (2).
159. Fifth pedal digit: longer than first digit (0); shorter and more lightly built than first (1).

Lyson et al.'s new character 176 is also a composite-

176. Dermal skull tuberosities: absent (0); tuberosities present (1); tuberosities and pits present (2); honeycomb texture present (3).

Unordered Characters
All characters were ran unordered, but some kinds of characters need to be ordered, when one state is intermediate.  Sometimes the intermediate state isn't placed between the others, which means the states have to be switched and recoded in the matrix for the ordering to work.  Other times, some of the states should be ordered, but others don't belong in the same character since they describe different variables (as noted above).  These can only be fixed by dividing the character.  Characters with this issue are-

19. Skull proportions: preorbital skull length equal to postorbital length (0); preorbital length exceeds postorbital skull length (1); postorbital length exceeds preorbital skull length (2).
35. Squamosal lateral exposure: ventral process long, descends to level limit of orbital margin (0); ventral process short, terminates prior to reaching ventral orbital margin (1); ventral process absent or restricted to region above dorsal limit of orbit (2).
42. Quadratojugal morphology: present and horizontal dimension exceeds vertical dimension by a factor of at least three (0); present but vertical dimension exceeds horizontal by a factor of at least two (1); present, but greatly reduced and restricted to condylar region (2); absent (3).
47. Parietal skull table: broad with the mid-line, transverse, width not less than half of the length measured along the element’s midline (0); constricted with the length exceeding the width by at least three times (1); forming saggital crest (2).
49. Pineal foramen position: located in the middle of the body from the parietal (0); displaced posteriorly (1); displaced anteriorly (2); absent (3).
53. Supratemporal: present and large with its transverse dimension nearly equal to its parasaggital dimension (0); present but reduced so that its transverse dimension is less than half of its parasaggital dimension (1); absent (2).
55. Tabular: present but restricted to dorsal region of occiput (0); present but ventrally elongate descending to lvel[sic] of occipital condyle (1); absent (2).
59. Posttemporal fenestra: absent (0); present but diameter less than half of the diameter of the foramen magnum (1); large posttemporal fenestra with a diameter at least eqqual[sic] to that of the foramen magnum (2).
76. Palatal process of pterygoid: extends anterior to the anterior limit of the palatine (0); forms oblique suture with palatine but process ends before reaching anterior limit of palatine (1); forms transverse suture with palatine (2).
78. Dentition on transverse flange: present as a shagreen of teeth (0); present but with one large distinct row of teeth along the posterior edge of the transverse flange (1); edentulous (2).
82. Mandibular joint: even with occiput (0); behind occiput (1); anterior to occiput (2).
88. Splenial: enters mandibular symphysis (0); present but excluded from mandibular symphysis (1); entirely absent (2).
89. Angular lateral exposure: exposed along 1/3 the lateral face of the mandible (0); exposed only as a small sliver along the lateral face (1); absent from lateral aspect (2).
100. Vertebral central articulations: amphicoelous (0); platycoelous (1); other (2).
115. Interclavicle: anterior end rhomboidal (0); T-shaped but with broad transverse bar with its anteroposterior dimension at least 1/4 the transverse width of the bar (1); T-shaped but transverse bar slender with its anteroposterior dimension much less than 1/4 the transverse width (2).
117. Scapula: short and broad with its height not exceeding its width (measured at the level of the glenoid) by more than three times (0); tall and blade-like with its height exceeding the width by at least a factor of four (1); tall and slender nearly cylindrical in cross-section (2).
126. Supinator process: large angled away from humeral shaft (0); large confluent with shaft (1); small or absent (2).
129. Radius/ulna ratio: radius shorter than ulna (0); radius longer than ulna (1); radius and ulna subequal (2).
142. Intertrochanteric fossa: well defined (0); reduced (1); absent (2).
150. Astragalus/distal tarsal IV articularion: articulation poorly defined (0); articulation well defined (1); articulation absent (2).
158. Number of pedal centralia: both lateral and medial centralia present (0); medial pedal centralia lost (1); both centralia lost (2).
161. Pedal phalangeal formula: 2, 3, 4, 5(4), 4 (0); 2, 3, 4, 4, 3 (1); 2, 3, 3, 4, 3 or less (2).
165. Body osteoderms: absent (0); present but few restricted to mid-line (1); present but spread all over back (2).
166. Osteodermal ridges: absent (0); fine regular spaced ridges (2); heavy irregularly spaced ridges (3).

Lyson et al.'s new character 176 also has states that should be ordered once it is divided into 2 separate characters-

176. Dermal skull tuberosities: absent (0); tuberosities present (1); tuberosities and pits present (2); honeycomb texture present (3).

Characters Which Do Not Cover All Possibilities
The character states must combine to cover the possible range of morphologies, but sometimes gaps are left between them, which makes coding taxa within that gap problematic.  Examples of this are-

20. Prefrontal/palatine antorbital contact: narrow forming less than 1/3 the transverse distance between the orbits (0); contact broad forming at least 1/2 the distance between the orbits (1).
26. Frontal proportions: length exceeds width by at least four times (0); length no greater than twice the width (1).
27. Frontal morphology: parallelogram shaped (0); hour-glass shaped (1).
42. Quadratojugal morphology: present and horizontal dimension exceeds vertical dimension by a factor of at least three (0); present but vertical dimension exceeds horizontal by a factor of at least two (1); present, but greatly reduced and restricted to condylar region (2); absent (3).
45. Stapes morphology: robust with its greatest depth exceeding one-third of its total length (0); slender with the length at least four times the depth (1).
47. Parietal skull table: broad with the mid-line, transverse, width not less than half of the length measured along the element’s midline (0); constricted with the length exceeding the width by at least three times (1); forming saggital crest (2).
59. Posttemporal fenestra: absent (0); present but diameter less than half of the diameter of the foramen magnum (1); large posttemporal fenestra with a diameter at least eqqual[sic] to that of the foramen magnum (2).
61. Paroccipital process morphology: slender with anteroposterior dimension not exceeding dorsoventral dimension (0); heavy with anteroposterior dimension at least 1/3 greater than dorsoventral dimension (1).
64. Basi/parasphenoid ratio: narrowest transverse width no more than 60% of the maximum length measured from basipterygoid process to posteriomost limit (0); narrowest part (waist) exceeds 80% of the length (1).
114. Clavicle: interclavicular process of clavicle broad and blade-like with the maximum anteroposterior length at least 1/3 of its transverse dimension (0); slender with its anteroposterior length less than 1/5 of the transverse dimension (1).
124. Humeral shaft/distal end ratio: shaft length less than 1/3 the maximum width of the distal end of the humerus (0); shaft long at least four times the width of the distal end (1).
154. Metatarsal V: long and slender with length exceeding the width of the base by at least three times (0); short and broad with base width equivalent to at least twice the length of the element measured along its midline (1).

Poorly Defined Characters
These are too numerous to mention, but many characters lack a quantification.  Some are especially bad, like "Limbs: short and stout (0); long and slender (1)." 

The latter two kinds of characters don't really affect the matrix, they just make coding new taxa problematic since you could have a different concept of "stout" or "large" or how curved or angled something has to be to count.  Who knows if Li et al.'s coding of Odontochelys or Lyson et al.'s coding of Proganochelys and Eunotosaurus used the same concepts as deBraga and Rieppel's original codings?  Even considering only the first two kinds of character errors though, 47 of the 168 characters are affected.  That's 28%. 

Ordering the (non-composite) characters is easy enough.  After deleting Testudines (since Proganochelys was used as a major source, and is now its own OTU), it takes 7 more steps to place turtles in Diapsida in Lyson et al.'s original matrix.  After proper ordering, the topology is the same except kuehneosaurs are now sister to a clade of lepidosaurs and sauropterygians instead of in a trictomy with both groups.  It now takes 8 more steps for diapsid turtles.  After proper ordering and deleting the composite characters, the consensus tree differs in that Macroleter is closer to derived parareptiles than lanthanosuchids and Acleistorhinus, and Sauria breaks down except for Trilophosaurus+Rhynchosauria and sauropterygians, with prolacertiforms oddly basal.  It now only takes three steps to place turtles in Diapsida though.  In all of these analyses, they are sister to sauropterygians when in Diapsida.

Factor in the small number of characters and taxa, and my conclusion is that amniote matrices aren't good enough to tell us much about turtle relationships yet.

Qiliania a confuciusornithid?

Another quiet month due to working on publishable projects, but here's something I noticed when getting an update for my site ready.

Ji et al. (2011) described the new bird taxon Qiliania, based on a pelvis and hindlimbs.  They included it in O'Connor et al.'s Shanweinao matrix, along with three unnamed Xiagou enantiornithines, Soroavisaurus and Archaeorhynchus.  It emerged as an enantiornithine, which is what the authors describe it as.  But then there's this statement- "DNHM D2522 (the holotype of Rapaxavis pani; Morschhauser et al., 2009) and PKUP-V1069 (the holotype of the basal ornithuromorph Longicrusavis houi; O’Connor, Gao & Chiappe, 2010) were removed (see Supporting Information)."

Well that's weird.  Why would you remove those two taxa?  Unfortunately, the supplementary information just lists tree descriptions and gives the codings for the added taxa.  They're the only undescribed taxa from O'Connor et al.'s Shanweinao matrix, but O'Connor is an author of Qiliania too.  O'Connor was first author of the Longicrusavis description, which was submitted almost a year before the Qiliania paper was submitted.  The Rapaxavis description came out two months before the Qiliania paper was submitted.  So I can't see any reason the Qiliania authors wouldn't trust the codings and have the resources to check them.

In any case, the interesting point is that when Rapaxavis and Longicrusavis are left in, the cladogram is different.  Confuciusornithids, 'Jeholornis' (= Shenzhouraptor) and Sapeornis now form successively more distant outgroups to Ornithothoraces.  Zhongornis is a confuciusornithid as I proposed.  Relationships in Enantiornithes are almost completely different, with all the CAGS specimens avisaurids, a clade of Las Hoyas taxa with Eoenantiornis sister to it and a Gobipteryx+Vescornis clade.  In Ornithuromorpha, hongshanornithids and songlingornithids are sister taxa.  But most important for a paper on Qiliania, that genus is now a confuciusornithid.

This is based on the short ischium, posteriorly excavated tarsometatarsus (also in avisaurids) and J-shaped metatarsal I (also in some enantiornithines).  Forcing it to be an enantiornithine is only one step longer (which rearranges enant topology again), so I'm not arguing Ji et al. were wrong to place it in that clade, but I do wonder why they excluded taxa which were already coded.  At the least, this shows the importance of including taxa in analyses and suggests Qiliania may be better placed as Pygostylia incertae sedis.


Incidentally, O'Connor et al.'s matrix is also the one Kurochkin et al. (2011) used for their Mystiornis paper.  They added Anchiornis, Mei, Avisaurus, Vorona and Mystiornis and found the latter four formed a clade one node closer to Aves than Archaeopteryx.  With Anchiornis being in a polytomy with this clade and more derived birds, this suggests a systematic coding error by the authors for their added taxa, which can unfortunately not be confirmed since the matrix was not published.  I added Mystiornis, Avisaurus and Vorona myself and found the latter two fall out in their normal positions (derived enantiornithine and basal ornithuromorph), while Mystiornis is an ornithothoracine outside of Longipterygidae and Hongshanornis+Aves.  When these taxa and Ji et al.'s taxa are all ran together, Mystiornis is sister to Avisauridae (similar to Cau's Megamatrix) and Qiliania stays as a confuciusornithid. 

Theropod Working Group matrix recoded

As part of my large in progress paper, and the description of a new paravian I'm coauthoring, I've been going through the TWG matrces.  The first was by Norell et al. in 2001, and included many less taxa and characters than the current ones do.  Their original topology (based on running the matrix through PAUP, it is a bit different than the one they published) using their higher taxonomy was-

|--Sinraptor 
|--Allosaurus 
`--+--Tyrannosauridae
   |  |--Albertosaurus 
   |  `--Tyrannosaurus 
   `--Coelurosauria
      |--Ornithomimosauria
      |  |--Pelecanimimus 
      |  |--Harpymimus 
      |  |--Garudimimus 
      |  `--+--Gallimimus 
      |     `--Struthiomimus 
      `--Maniraptora
         |--Ornitholestes 
         `--+--Alvarezsauridae
            |  |--Alvarezsaurus 
            |  `--+--Patagonykus 
            |     `--Mononykinae
            |        |--Shuvuuia 
            |        `--Mononykus 
            `--+--+--Dromaeosauridae
               |  |  |--Sinornithosaurus 
               |  |  |--Unenlagia 
               |  |  `--+--Achillobator 
               |  |     |--Utahraptor 
               |  |     |--Dromaeosaurus 
               |  |     |--Deinonychus 
               |  |     |--Velociraptor 
               |  |     |--Tsaagan
               |  |     |--Adasaurus 
               |  |     `--Saurornitholestes 
               |  `--Avialae
               |     |--Rahonavis ostromi
               |     `--+--Archaeopteryx 
               |        `--Confuciusornis 
               `--+--Troodontidae
                  |  |--Sinornithoides 
                  |  `--+--Byronosaurus 
                  |     `--+--Troodon  
                  |        `--+--Saurornithoides 
                  |           `--Zanabazar
                  `--+--Therizinosauroidea
                     |  |--Alxasaurus
                     |  |--Erlikosaurus 
                     |  `--Segnosaurus
                     `--Oviraptorosauria
                        |--+--Chirostenotes 
                        |  `--Avimimus 
                        `--+--Microvenator 
                           `--+--Caudipteryx 
                              `--Oviraptoridae
                                 |--Oviraptor 
                                 |--Rinchenia
                                 |--IGM 100/42
                                 |--Conchoraptor 
                                 `--"Ingenia" 

The result of recoding all the taxa is-

|--Sinraptor
|--Allosaurus
`--Coelurosauria
   |--Tyrannosauridae
   |  |--Gorgosaurus
   |  `--Tyrannosaurus
   `--+--Ornitholestes
      `--Maniraptoriformes
         |--Ornithomimosauria
         |  |--Garudimimus
         |  `--+--Harpymimus
         |     `--Ornithomimidae
         |        |--Gallimimus
         |        `--Struthiomimus
         `--Maniraptora
            |--+--Alvarezsauridae
            |  |  |--Pelecanimimus
            |  |  |--Alvarezsaurus
            |  |  `--+--Patagonykus
            |  |     `--Parvicursorinae
            |  |        |--Shuvuuia
            |  |        `--Mononykus
            |  `--Therizinosauroidea
            |     |--Segnosaurus
            |     `--+--Alxasaurus
            |        `--Erlikosaurus
            `--+--Caudipteryx
               `--+--Oviraptorosauria
                  |  |--Avimimus
                  |  |--Chirostenotes
                  |  |--Microvenator
                  |  `--Oviraptoridae
                  |     |--Oviraptor
                  |     `--+--IGM 100/42
                  |        `--"Ingeniinae"
                  |           |--Conchoraptor
                  |           `--+--Rinchenia
                  |              `--"Ingenia"
                  `--Paraves/Eumaniraptora
                     |--Dromaeosauridae
                     |  |--Sinornithosaurus
                     |  |--Utahraptor
                     |  |--Dromaeosaurus
                     |  |--Tsaagan
                     |  |--Deinonychus
                     |  |--Achillobator
                     |  |--Adasaurus
                     |  |--Velociraptor
                     |  `--Saurornitholestes
                     `--Avialae
                        |--Sinornithoides
                        |--Troodontidae
                        |  |--Byronosaurus
                        |  `--+--Saurornithoides
                        |     `--+--Zanabazar
                        |        `--Troodon
                        `--+--Archaeopteryx
                           `--Ornithurae
                              |--Confuciusornis
                              `--Unenlagiinae
                                 |--Rahonavis
                                 `--Unenlagia

Notice there are a couple odd things probably caused by a lack of characters- Alxasaurus sister to Erlikosaurus (one more step needed to change), Caudipteryx outside Oviraptorosauria (also one more step). Yet there are also some interesting plausible groupings such as the derived Harpymimus, alvarezsauroid Pelecanimimus, alvarezsaur-therizinosaur clade, basal Oviraptor, Zanabazar+Troodon and  ornithurine Unenlagiinae.  Note also that it resembles the standard topology more than TWG's original in a non-maniraptoriform Ornitholestes, paravian Troodontidae and more basal Caudipteryx.

For those interested, the following number of additional steps are needed for-

Carnosaurian tyrannosaurids as in Molnar et al. (1990)- 4. 

Maniraptoran tyrannosaurids as in Sereno (1999)- 8.

Ornitholestes as an allosaurid (Paul, 1988)- 11. 

Ornitholestes less derived than tyrannosaurids- 3.

Ornitholestes as a maniraptoran- 2.

Ornitholestes as a dromaeosaurid as in Makovicky (1995)- 11.

An ornithomimosaur-alvarezsaurid clade- 2.

Alvarezsaurids as basal maniraptorans outside therizinosaurs+oviraptorosaurs+paravians- 3. 

Alvarezsaurids as basal paravians- 2.

Alvarezsaurids as avialans- 11.

Alvarezsaurids as ornithurines- 10 (13 with Alvarezsaurus too, which otherwise goes to Oviraptorosauria).

Alvarezsaurids and therizinosaurs joining with ornithomimosaurs as in Sereno (1999)- 5.

Enigmosauria- 2.

Oviraptorosauria being closer to birds than dromaeosaurids or troodontids- 10.

Arctometatarsalia as in Holtz (1994)- 45.

"Pneumatocrania" as in Holtz (1992/1994)- 28.

Bullatosauria- 22.

Deinonychosauria- 15(!).

Archaeopteryx being a troodontid - 4.

Dromaeosaurids being ornithurines (closer to birds than Archaeopteryx as in Paul)- 3 (troodontids also join them)

Unenlagiines being dromaeosaurids- 1.

Senter's (2007) eudromaeosaur topology- 8.

Longrich and Currie's (2009) eudromaeosaur topology- 9.Russell and Dong's (1994) crazy topology- 23.

Of course, without important taxa like basal tyrannosauroids, the mess of basal coelurosaurs, Deinocheirus, Shenzhousaurus, Haplocheirus, Falcarius, Beipiaosaurus, Protarchaeopteryx, Incisivosaurus, Pedopenna, Buitreraptor, Mahakala, Shanag, Microraptor, Austroraptor, Mei, Sinovenator, Jinfengopteryx, scansoriopterygids, Anchiornis, Shenzhouraptor, Dalianraptor, Jixiangornis and omnivoropterygids, those numbers aren't too important.  But adding these taxa and the new characters of more recent TWG analyses is the next step...

The myth of coding from specimens firsthand and the untapped resource of photos

You've probably heard it many times.  Advice from professional paleontologists about the proper way to code specimens.  For instance, here's Brochu from the DML in 2000-

"One thing I've noticed as associate editor of JVP is that reviewers are growing less patient with phylogenetic analyses that do not address the specimens themselves, and which instead code taxa from publications. This is being viewed increasingly as unacceptable, and I wholeheartedly embrace that view. It's the specimens that are our primary data."

I completely agree that the specimens are our primary data and that coding from specimens is preferrable to any other resource.  When I was younger back in 2000 and such, I would picture a paleontologist poring over a specimen in his hands, turning it this way and that under the light, only to triumphantly type a 0 or 1 into Nexus Data Editor and move on to the next character.  If only the world were so kind.  The dirty truth is that this is generally not the way things work, and indeed can't be, given financial and business considerations.

Any decent cladistic analysis needs a large number of taxa, and for most analyses this means specimens will be spread over the world.  For the original TWG analysis of Norell et al., seeing all the relevent specimens would mean going to the AMNH, BMNH, BPM, BSP, BYU, CEU, CMN, DINO, FMNH, GMV, HMN, IGM, IVPP, JM, LH, MNU, MOR, MUCP, NGMC, PIN, PVPH, ROM, RTMP, UA, UCMZ, USNM, WDC, YPM and ZPAL collections.  China, Mongolia, Russia, Argentina, Poland, England, Spain, Germany, Canada and over ten states of the US.  If you're lucky, you'll see the specimens on a traveling exhibit (with the caveat it usually makes them harder to examine up close) or on loan to another museum.  Many museums have casts, but these are of varying quality.  Realistically, very few paleontologists are going to have the resources to see all the specimens.  Travel cost is simply too high.

But people do manage to travel, and many papers indicate specimens were consulted for coding.  I myself visited the AMNH twice, and they happened to have many IGM specimens at the time as well.  When I write my papers, I'll put down my reference for Saurornithoides as "AMNH 6516".  But the truth is my codings don't come from looking at the specimen in person.  I saw it, I held it, sure.  But when you visit a museum collection, you get 6 hours or so per day, since they're only open for so long.  And there are usually several revelent specimens in a museum, sometimes an extremely large number (AMNH, IGM, IVPP, MOR, RTMP, etc.).  Moreover, there are usually rules about removing only one specimen from cabinets at a time, filling out cards to replace them in the meantime, etc..  And you want to be careful, since nobody wants to be "the one who dropped Ornitholestes' skull".  If I were to try to code Ornitholestes for the TWG matrix while looking at it in the AMNH collections, it would near certainly take my entire time for that day and more.  Any good matrix has at least a couple hundred characters, often several hundred.  It takes time to code.  And while people have the resources to visit museum collections, I highly doubt most have the resources to return every day for a week or two.  And realistically, matrices aren't made by having a list of characters, and running through them for every taxon, a taxon at a time.  Often comparing taxa will lead to new interpretations (as in my therizinosaur accessory trochanter example) or a taxon's morphology will lead you to redefining your states or adding a new character.  Who's going to go back to New York to see if Ornitholestes has more than ten maxillary teeth after they've rewritten their character to be "11 or more teeth" instead of "9 or more"?  And once you have a new/revised matrix several years down the line, and new taxa have been discovered, are you supposed to go on your whorlwind worldwide tour again?  Curators can do these things for specimens in their care, as can other researchers who live by a museum or have specimens on loan to them, but nobody can do them for the majority of specimens.

So how do people "code from specimens"?  They take photos.  Lots of photos.  And they code from those.  They're often better than the literature because they're in color and from as many angles as you want, but with the internet publication quality is improving.  There would be almost no reason to see Australovenator for myself, for instance, since Hocknull et al. did such a good job of photographing it.  There are certainly things photographs don't show well- sutures and restoration on some specimens, depth of depressions, some texture.  But these are hardly numerous enough to justify hundreds of dollars to see yourself.  "The literature" has gotten a bad name, but its photos can be just as good as your own, and its descriptions are usually written by people with as much or more knowledge and experience as you.  This is good news for all of us though, since it means anyone can have access to the same resources the professionals use for most specimens, without travel costs.  The internet's gone a long way to providing a Shiny Digital Future for publication access, but I think we could do more. 

What if there was an online database of specimen photos, in high resolution color, that anyone could access?  The museums' permission would be needed of course, and undescribed specimens could be excluded if under study, but it sure beats everyone spending their resources to photograph the same things.  It's also better than the current situation where people have photos of poorly described specimens, but aren't allowed to distribute them, even if they've been in the literature for over a decade and have no plans for redescription.  The odd thing is, a person is generally allowed to travel to the collection and take their own photos, but not recieve or distribute those which have already been taken.  I don't want people to think I'm just bitter about lacking access myself, as there are plenty of specimens I have photos of (both taken myself and kindly provided by others) and aren't allowed to distribute.  So I'm on both sides.  But surely such a system is broken when we're witholding information from each other that we could get for hundreds of dollars in travel fees and won't be redescribed soon anyway. 

I'd be willing to throw my (distributable) photos into such a project if someone were to set it up.  The primary obstacle besides getting museum permission would be the huge storage space, but it could probably even be done on Flickr or Picasa.  What does everyone think?

Accessory trochanters in therizinosaurs

While doing my work on the TWG matrix, I noticed something interesting.  A brief intro to the structures described here is helpful.  Theropods have an anterior trochanter (also called lesser trochanter) on the front of their proximal femur.  In birds and various maniraptoriforms it partially or completely fuses to the greater trochanter to form a trochanteric crest.  First recognized in Microvenator, a lot of taxa also have another trochanter right below the anterior trochanter, called the accessory trochanter.  Supposedly, therizinosauroids have a low, separate anterior trochanter but no accessory trochanter.  I think people have just been confusing their accessory trochanter for an anterior trochanter, while the real anterior trochanter is fused in a trochanteric crest.  Note the figure below...

The top row is from Hutchinson's (2001) femoral paper.  The anterior trochanter is 'lt' while the accessory trochanter is 'at'.  I've outlined the accessory trochanter in purple in all figures.  On the left bottom we have basal therizinosaur Falcarius (from Zanno, 2010a), which Zanno correctly realized has both an accessory trochanter and an anterior trochanter which is closely appressed to the greater.  The outline drawing is of Alxasaurus (from Russell and Dong, 1994), which was supposed to have a low cylindrical anterior trochanter.  But note that it is low in position like an accessory trochanter instead and that the greater trochanter is as wide as those taxa which incorporate the anterior trochanter into a trochanteric crest.  Next on the bottom row is an anterior view of Segnosaurus (from Zanno, 2010b).  Here too the anterior trochanter is supposed to be low (labeled flt), but again I think it matches an accessory trochanter more.  Finally, in the lower right is Chirostenotes (from Currie and Russell, 1988) in anterior view.  It was described as having a very low anterior trochanter, which would be quite unlike any avetheropod, but makes sense as an accessory trochanter.  As ornithomimosaurs and basal oviraptorosaurs have the most distinct accessory trochanters, it makes sense that therizinosaurs and Chirostenotes would too.

References- 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.
Hutchinson, 2001. The evolution of femoral osteology and soft tissues on the line to extant birds (Neornithes). Zoological Journal of the Linnean Society. 131, 169-197.
Russell and Dong, 1994. The affinities of a new theropod from the Alxa Desert, Inner Mongolia, People’s Republic of China. Canadian Journal of Earth Sciences. 30, 2107-2127.
Zanno, 2010a. Osteology of Falcarius utahensis: Characterizing the anatomy of basal therizinosaurs. Zoological Journal of the Linnaean Society. 158, 196-230.
Zanno, 2010b. A taxonomic and phylogenetic re-evaluation of Therizinosauria (Dinosauria: Maniraptora). Journal of Systematic Palaeontology. 8(4), 503-543.