Citipati or IGM 100/42?

Another mini-post.  Everyone's familiar with IGM 100/42, that oviraptorid that was the classic example of its family through the 80's and 90's.  It's known from an almost complete skeleton first mentioned by Barsbold in 1981.

Skull of IGM 100/42, courtesy of Auditore.

Everyone's also familiar with Citipati osmolskae, the nearly complete specimen that was named in 2001 and whose skull was described by Clark et al. (2002).  The most famous nesting oviraptorid Big Mama (Clark et al., 1999) and the stil undescribed Big Auntie have been assigned to this species as well, as has the most famous oviraptorid embryo (Norell et al., 2001).

Citipati osmolskae holotype (copyright AMNH)

Now these specimens are similar, and may indeed be congeneric, but this hasn't been demonstrated yet.  While Osmolska et al. (2004) found IGM 100/.42 to be the sister taxon of Citipati osmolskae in their cladistic analysis, Lu (2004) found that it was the sister taxon to Oviraptor or Conchoraptor (depending on taxa included) using Maryanska et al.'s (2002) characters.  The point of this post is that some phylogenetic analyses have been quite sloppy in regard to exactly which oviraptorid they are coding.  The first phylogenetic analysis to include either was the TWG analysis, which started with Norell et al. (2001).  They called it Oviraptorid IGM 100/42.  Note the progression of what this OTU is labeled as the TGW analysis is modified in future works-

Norell et al., 2001 (Ostrom volume) Oviraptorid IGM 100/42
Clark et al., 2002 (Mesozoic Birds) Oviraptorid IGM 100/42
Hwang et al., 2002 (Microraptor) IGM 100/42
Xu et al., 2002 (Incisivosaurus) IGM 100/42
Xu et al., 2002 (Sinovenator) IGM 100/42
Makovicky et al., 2003 (Byronosaurus) Citipati osmolskae
Hwang et al., 2004 (Huaxiagnathus) Citipati osmolskae
Lu, 2004 (thesis) Citipati osmolskae
Makovicky et al.; Makovicky and Norell; Norell and Makovicky, 2004 (Dinosauria 2) Citipati osmolskae
Xu and Norell, 2004 (Mei) Citipati osmolskae
Kirkland et al., 2005 (Falcarius) Citipati
Makovicky et al., 2005 (Buitreraptor) Citipati osmolskae
Mayr et al., 2005 (Archaeopteryx) IGM 100/42
Novas and Pol, 2005 (Neuquenraptor) Citipati osmolskae
Gohlich and Chiappe, 2006 (Juravenator) Citipati
Norell et al., 2006 (Tsaagan) Citipati osmolskae
Hwang, 2007 (enamel thesis) Citipati
Martinelli and Vera, 2007 (Achillesaurus) Citipati osmolskae
Senter, 2007 (coelurosaurs) Citipati osmolskae* (see below)
Turner et al., 2007 (Shanag) Citipati osmolskae
Turner et al., 2007 (Mahakala) Citipati osmolskae
Xu et al., 2007 (Gigantoraptor) Citipati osmolskae
Novas et al., 2008 (Orkoraptor) Citipati osmolskae
Xu et al., 2008 (Anchiornis) Citipati osmolskae
Zhang et al., 2008 (Epidexipteryx) Citipati osmolskae* (see below)
Makovicky et al., 2009 (Beishanlong, Xiongguanlong) Citipati osmolskae
Zanno et al., 2009 (Nothronychus graffami) Citipati osmolskae
Zheng et al., 2009 (Tianyuraptor) Citipati osmolskae* (see below)

You can see it changed inexplicably in 2003.  For unknown reasons, it was dropped from the Graciliraptor and Pedopenna versions, which I assume to mean it's absent in Xu's (2002) thesis.  You might say this kind of relabeling is harmless, but I find it misleading.  If someone didn't follow the sequence of permutations of the TWG matrix, they could think the codings were based on specimens described in the literature.  After all, Citipati's holotype is a complete skeleton, though it remains undescribed except for the furcula.  Lu (2004) referred to it as Citipati osmolskae in his revisions of the TWG matrix, but coded IGM 100/42 and Citipati separately for his versions of Maryanska et al.'s matrix.  So one of his Citipati's was not comparable to his other Citipati.  Even worse, Senter (2007) used the IGM 100/42 codings as Citipati osmolskae, then coded IGM 100/42 as a separate taxon!  So really his matrix has two copies of IGM 100/42.  Oddly, there are coding differences and they are not sister taxa.  Zhang et al. (2008) copied this in their Epidexipteryx analysis, as did Zheng et al. (2009) in their Tianyuraptor analysis.  So this problem can worm its way through the literature unnoticed.

In conclusion, if anyone is going to use the TWG matrix (and I know you are), please label your OTU IGM 100/42.  Or else defend the assertion IGM 100/42 belongs to Citipati osmolskae.  Taxonomy via data matrix should be avoided.

Pterosaur Relationships

Pterosaurs on a theropod blog?!  What has the world come to?  Well, a consequence of having a blog based on material for my website and projects is that when I'm too busy to work on them, the post count lightens.  But I had some thoughts based on a recent DML message that's been repeated numerous times in the past.  It concerns the sister taxon to Pterosauria.  In the literature, we find two hypotheses- David Peters thinks they're related to protorosaurs within Lepidosauromorpha; everyone else thinks they're related to dinosauromorphs within Archosauromorpha.  Now it would be easy enough to just say Peters is a fringe researcher and that we should go with the professional consensus view.  But I don't believe that's justified here.  Certainly Peters has methodological problems.  His Photoshop method has been shown to fail multiple times (Bennett, 2005) and I don't believe half the things he sees are real.  Plus he doesn't understand how to perform a phylogenetic analysis correctly in multiple respects.  So do I trust his analyses?  Absolutely not.  But does that mean he's wrong?  No.  The ironic thing, and the point of this post, is that the other side is almost as bad.  Oh sure they (probably) make less anatomical errors and have a better understanding of correlation and ordering for characters, but their matrices are flawed in other ways.  Bennett (1996) had Lepidosauromorpha and Prolacertiformes (now recognized as polyphyletic) as OTUs, and the former was the outgroup.  Sereno's (1990, 1991) "analyses" never include conflicting data so are demonstrations of hypotheses instead of tests.  Benton (1999) only included archosauriforms.  Hone and Bennett's (2008) supermatrix method oddly included both lower level taxa (e.g. Squamates, Champsosaurus) AND the higher level taxa they belong to (e.g. Lepidosauromorpha, Choristodera), but even stranger these taxa did not group with themselves, showing the matrix is highly flawed.  One obvious way is actually the exact thing I complained about earlier on this blog- many taxa are only coded for a small percentage of characters.  What good are 324 characters if Dinosauria is only coded for 90 of them, or Lepidosauromorpha for 78 of them?  Thus no published study is a useful test of pterosaur origins and they might as well be left as Sauria incertae sedis until someone takes the time to do an analysis properly.

Avialan alvarezsaurs I: Cranial Characters

In this series of posts examining the evidence for placing alvarezsaurs in various parts of the theropod tree, I decided to break up the bird part due to the huge number of characters suggested.  Various analyses have suggested alvarezsaurids are members of Avialae, here used in the sense of closer to birds than Deinonychus.  In addition, some of these have placed alvarezsaurids closer to modern birds than Archaeopteryx, which means they fall into Ornithurae sensu Gauthier.  This alvarezsaurid-ornithothoracine clade was usually called Metornithes, but that name is valid for the smallest group containing Aves and Mononykus, regardless of where the latter falls.  So if alvarezsaurids are arctometatarsalians, Metornithes is a senior synonym of Maniraptoriformes.  If alvarezsaurids are basal maniraptorans, Metornithes is a subset of Maniraptora.  Thus the term Metornithes will not be used in the discussion below.  One problem with these early phylogenies is that many basal avialans were not yet known, except Archaeopteryx, ornithothoracines and in 1995 and later, confuciusornithids (not actually included in analyses until 2000).  Thus exactly where alvarezsaurids would fall in comparison to taxa like scansoriopterygids, Shenzhouraptor or omnivoropterygids is not obvious.  The following is a list of every cranial character found to support placing alvarezsaurids in Avialae (first 18 characters) and its subgroups (characters 19-26), based on every analysis to support this arrangement.  These were (not including later variations)- Perle et al., 1993; Chiappe et al., 1996; Novas, 1996; Chiappe et al., 1998; Forster et al., 1998; Chatterjee, 1999; Holtz, 2000; Chiappe, 2001; Maryanska et al., 2002.  Most found them to be ornithurines, though the last two found them to be outside the Archaeopteryx+Aves clade.

1. Premaxilla long and pointed with long nasal process (Holtz, 2000). A composite of three characters, none of which are in TWG and only one of which is in Choiniere et al. (premaxilla angled <70 degrees). However, it is composited there with the proportion of the premaxilla which is anterior to the external nares so is difficult to evaluate the codings for. In any case, Shuvuuia has a very short premaxilla which is blunt and has a short nasal process (Sereno, 2001), unlike most birds. It was thus miscoded by Holtz. Haplocheirus is similar.

2. Premaxillary teeth conical (Holtz, 2000). In both TWG and Choiniere et al.. Miscoded- Allosaurus, Giganotosaurus, Incisivosaurus, Troodon, Sinornithosaurus, Saurornitholestes, Tsaagan, Velociraptor, Deinonychus, Utahraptor. Not coded- Daspletosaurus, Sinovenator. Premaxillary teeth are unknown in Shuvuuia (Chiappe et al., 2002), so Holtz miscoded it. It turns out that Haplocheirus has the character though, potentially supporting avialan alvarezsaurs. However, the character is not unique to avialans. Basal troodontids and oviraptorosaurs also have it (the condition in therizinosaurs is unknown), so this could be congruent with a basal maniraptoran placement as well.

3. Nasal shorter than frontal (Maryanska et al., 2002). Not in TWG, but in Choiniere et al. as part of a character coding for rostrum length and composited with maxilla length compared to premaxilla length. Again, the compositing means I won't be evaluating its accuracy, but again this was miscoded in Shuvuuia which has longer nasals than frontals (Sereno, 2001). Haplocheirus is similar.

4. Jugal shallow or rod-like under orbit (Maryanska et al., 2002). Not in TWG, but in Choiniere et al. when specified to define the cross section, not necessarily the depth. Miscoded- Garudimimus, Rahonavis. Not coded- Acrocanthosaurus, Carcharodontosaurus, Dromiceiomimus, Byronosaurus, Saurornithoides, Buitreraptor, Velociraptor, Shenzhouraptor, Sapeornis, Confuciusornis, Yixianornis. Haplocheirus lacks this, so does not support avialan alvarezsaurs.

5. Frontals anteriorly triangular (Forster et al., 1998). In both TWG and Choiniere et al.. This is not true in Shuvuuia, where the nasofrontal suture is W-shaped (Sereno, 2001), or Haplocheirus where it is transverse. It was thus miscoded by Forster et al. and its accuracy in Choiniere et al.'s matrix is not examined here. It is present in the derived Ceratonykus though.

6. Squamosal-quadratojugal contact absent (Chiappe et al., 1996). In both TWG and Choiniere et al.. Miscoded- Garudimimus, Deinonychus, Archaeopteryx. Not coded- Daspletosaurus, Harpymimus, Oviraptor, Conchoraptor, "Ingenia", Mei, Saurornitholestes, Dromaeosaurus, Scansoriopteryx, Epidexipteryx, Sapeornis, Confuciusornis. As no avialans were coded, except Archaeopteryx which was miscoded as having the contact, it couldn't test the homology of Shuvuuia's condition. Absent in Haplocheirus, so does not support avialan alvarezsaurs.

7. Quadratojugal joined to quadrate by ligament (Chiappe et al., 1998). Not in TWG or Choiniere et al.. Not reported in Haplocheirus, so potentially supports avialan alvarezsaurs. However, the distribution of this character is largely uncertain since many maniraptoriforms have at least loosely sutured articulations which make determination difficult or ambiguous.

8. Parietals and laterosphenoids unfused (Forster et al., 1998). Not in TWG or Choiniere et al.. Forster et al. miscoded basically every taxon, as their Ornithurae has fusion and their non-avialan taxa lack it (e.g. tyrannosaurids, Compsognathus, ornithomimids, oviraptorids). The condition in Shuvuuia is unreported otherwise, though even if I trusted Forster et al.'s coding it would be compatible with any topology where they are outside Ornithurae sensu Chiappe (Hesperornis and more derived birds). The condition in Haplocheirus is unknown.

9. Posterior tympanic recess opens in otic recess (Chiappe et al., 1996). In both TWG and Choiniere et al.. Miscoded- Tyrannosaurus, Sinovenator, Byronosaurus, Saurornithoides, Troodon. Not coded- Acrocanthosaurus, Gorgosaurus, Pelecanimimus, Chirostenotes, "Ingenia". The condition in Haplocheirus is unknown, so potentially supports avialan alvarezsaurs. However, it is also present in Pelecanimimus, Falcarius and troodontids, meaning it could be congruent with other hypotheses as well.

10. Occiput directed ventrally (Holtz, 2000). Not in TWG or Choiniere et al.. This seems true in Haplocheirus, so potentially supports avialan alvarezsaurs.

11. Foramen magnum taller than wide (Holtz, 2000). In both TWG and Choiniere et al.. However, Holtz miscoded Alvarezsauridae since Shuvuuia does not have this character (Chiappe et al., 1998). Haplocheirus also lacks it and its accuracy in Choiniere et al.'s matrix is not examined here.

12. Neck of occipital condyle not constricted (Holtz, 2000). In both TWG and Choiniere et al.. Miscoded- Sinraptor, Dilong, Tyrannosaurus, Avimimus, Troodon, Dromaeosaurus. Not coded- Acrocanthosaurus, Carcharodontosaurus, Giganotosaurus, Daspletosaurus, Struthiomimus, "Ingenia", Microraptor. This is true in Haplocheirus, so potentially supports avialan alvarezsaurs. However, it is also present in most maniraptoriforms except some oviraptorosaurs, so was miscoded by Holtz.

13. Triradiate palatine (Chiappe et al., 1998). In both TWG and Choiniere et al.. Miscoded- Shenzhousaurus, Archaeopteryx. Not coded- Neovenator, Gorgosaurus, Daspletosaurus, Juravenator, Chirostenotes, Sinornithosaurus, Dromaeosaurus, Sapeornis. Absent in Haplocheirus, so does not support avialan alvarezsaurs.

14. Splenial not widely exposed laterally (Holtz, 2000). In both TWG and Choiniere et al.. Miscoded- Compsognathus. Not coded- Daspletosaurus, Juravenator, Pelecanimimus, Caudipteryx, Buitreraptor, Saurornitholestes, Shenzhouraptor. This is true in Haplocheirus, so potentially supports avialan alvarezsaurs. Yet this is also found in almost every theropod except most deinonychosaurs so was only an avialan character in Holz's analysis due to his lack of deinonychosaur monophyly.

15. Coronoid absent (Chiappe et al., 1998). In both TWG and Choiniere et al.. Miscoded- Shuvuuia, Citipati, Scansoriopteryx. Not coded- Acrocanthosaurus, Daspletosaurus, Compsognathus, Segnosaurus, Caudipteryx, Conchoraptor, "Ingenia", Shenzhouraptor, Sapeornis. Since Shuvuuia was miscoded, this character could not function to support avialan alvarezsaurs. The condition in Haplocheirus is unknown, so potentially supports this relationship. However, ornithomimosaurs and therizinosaurs show this as well.

16. Elongate and tapering retroarticular process (Holtz, 2000). In TWG, but not Choiniere et al.. Both Shuvuuia and Haplocheirus have this, but Holtz miscoded Archaeopteryx as having it as well. In actuality, almost all avialans lack it, so it does not support this relationship.

17. Unserrated teeth (Chiappe et al., 1996). In both TWG and Choiniere et al.. Miscoded- Compsognathus, Avimimus, Sinovenator, Microvenator, Adasaurus. Not coded- Daspletosaurus, Alxasaurus, IGM 100/44, Scansoriopteryx, Shenzhouraptor. Oddly, only some toothless taxa are coded as inapplicable. Absent in Haplocheirus, so does not support avialan alvarezsaurs.

18. Teeth uncompressed and unrecurved (Forster et al., 1998). Not in TGW, but in Choiniere as the same composite of characters, with an additional state added compositing crown elongation as well. Miscoded- Shenzhousaurus, Harpymimus, Anserimimus, Buitreraptor, Sinornithosaurus, Microraptor, Archaeopteryx. Not coded- Acrocanthosaurus, Carcharodontosaurus, Giganotosaurus, Mapusaurus, Beipiaosaurus, IGM 100/44, Sinornithoides, Adasaurus, Utahraptor, Scansoriopteryx, Yixianornis. Absent in Haplocheirus, so does not support avialan alvarezsaurs.

Skull of Haplocheirus (modified from Choiniere et al., 2010) showing features which agree (green) and disagree (red) with placing alvarezsaurs as birds in various analyses.  Numbers match character numbers in this post.

19. Maxillary fenestra absent (Perle et al., 1993). In both TWG and Choiniere et al.. This was based on the partial maxilla of Mononykus, found before complete skulls of Shuvuuia showed a fenestra in a different position. Thus Mononykus may have had one as well, and Choiniere et al.'s codings are not evaluated for accuracy, though a glance shows taxa left uncoded like Allosaurus and Archaeopteryx, which obviously have the fenestra. Haplocheirus has one as well.

20. Slot in ventral process of lacrimal for jugal absent (Holtz, 2000). Not in TWG or Choiniere et al.. This has never been explicitly described in Shuvuuia, though Sereno (1999) agreed with Holtz's coding and Holtz et al. (2004) later switched Alvarezsauridae's coding. Thus the coding for Alvarezsauridae is controversial. In any case, examination shows basically all maniraptoriforms lack it, contra Holtz's original coding, but agreeing with the 2004 coding. Haplocheirus' condition is unknown, but the character is ignored as it has no affect on alvarezsaurs' position given current data.

21. Postorbital-jugal contact absent (Chiappe et al., 1996). Not in TWG or Choiniere et al.. Absent in Haplocheirus, so does not support ornithurine alvarezsaurs.

22. Dorsal jugal process absent (Forster et al., 1998). Not in TWG or Choiniere et al.. Absent in Haplocheirus, so does not support ornithurine alvarezsaurs.

23. Quadrate articulates with braincase (Novas, 1996). Not in TWG or Choiniere et al. except as a corollary of a character coding for a divided quadrate head. Unknown in Haplocheirus so potentially supports ornithurine alvarezsaurs. This character is more widespread than usually given credit though as even most tyrannosaurids have a surface extending distally from the quadrate head that articulates with the braincase. Even ignoring this primitive condition, at least oviraptorosaurs, troodontids and Mahakala also have the condition among maniraptoriforms, though eudromaeosaurs lack it.

24. Separate otic head of quadrate (Forster et al., 1998). In both TWG and Choiniere et al.. Miscoded- Deinonychus, Yixianornis. Not coded- Acrocanthosaurus, Giganotosaurus, Mapusaurus, Gorgosaurus, Daspletosaurus, Compsognathus, Harpymimus, Garudimimus, IGM 100/44, Scansoriopteryx, Sapeornis, Apsaravis. Unknown in Haplocheirus so potentially supports ornithurine alvarezsaurs. However, among birds only Confuciusornis, Enaliornis and some neoavians have well separated heads like Shuvuuia, so convergence is most likely by far.

25. Parietal sagittal crest absent (Forster et al., 1998). In both TWG and Choiniere et al.. However, Choiniere et al. have two sagittal crest characters, one coding for height and one for axial length. This unfairly weights the presence of a crest (since both characters have a state for 'crest absent'). To mitigate this, all taxa coded as lacking a crest in one of the characters are changed to unknown in my recoding. Miscoded- Dilong, Ornitholestes, Citipati, Troodon, Tsaagan. Not coded- Allosaurus, Acrocanthosaurus, Carcharodontosaurus, Giganotosaurus, Gorgosaurus, Daspletosaurus, Juravenator, Pelecanimimus, Shenzhousaurus, Harpymimus, Garudimimus (oddly coded as inapplicable), Dromiceiomimus, Struthiomimus (also coded inappicable), Erlikosaurus, Incisivosaurus, Caudipteryx, Avimimus, Oviraptor, Conchoraptor, "Ingenia", Sinovenator, Saurornitholestes, Velociraptor, Deinonychus, Scansoriopteryx, Archaeopteryx, Sapeornis, Confuciusornis. Unknown in Haplocheirus so potentially supports ornithurine alvarezsaurs. Yet this is also found in ornithomimosaurs, Erlikosaurus and basal troodontids among maniraptoriforms.

26. Dentary teeth set in groove (Chiappe et al., 1996). In both TWG and Choiniere et al.. I already covered this character in the ornithomimosaur post. Unknown in Haplocheirus so potentially supports ornithurine alvarezsaurs. However, it is also present in Pelecanimimus and troodontids, and more importantly is only found in a few derived ornithuromorphs among birds.

As before, a summary of the codings for relevent taxa.  They are divided into supposed avialan (1-18) and supposed ornithurine (19-26) characters.

                          111111111 12222222

                 123456789012345678 90123456


Haplocheirus     010000???10101?100 0?00????
Tugrik           ????????????1????? ????????
Shuvuuia         0?01011?1101111111 0?111111
Ceratonykus      ???111???1???1?1?? ??1111??
Mononykus        ????????1???????11 ????1???

Ornithomimosaur  00001001p001011010 0100?01p

Scansoriopteryx  ????01???????11011 ??00?01?
Epidexipteryx    010??1?????????11p ??10??0?
Archaeopteryx    11011111111101101p 00001010
Shenzhouraptor   ???1?????????1101? 0?00???0
Dalianraptor     0????????????1???? ????????
Jixiangornis     0???????????????1? ???0???-
Yandangornis     1-??????????????-- ???????-
Zhongjianornis   1-01????????????-- ???1???-
Sapeornis        010001??????11101? 0?0010?-
Confuciusornith  1-11011????1?1?0-- 0?00111-
Ornithothoraces  110p011011p1p1p010 0-p010p0

Of the 26 suggested cranial characters, only nine hold up as even potentially supporting alvarezsaurids as birds.  Of these, several (2, 12, 14, 23) are present basally in Maniraptora.  Of the others, several are also found in ornithomimosaurs (9, 15, 25), therizinosaurs (9, 15, 25) or troodontids (9, 25).  Of the remaining, character 7 is hard to unambiguously score for most maniraptoriforms as noted above, leading only character 10 (occiput directed ventrally) as strong evidence for the relationship.  Of the nine potentially valid characters, Choiniere et al.'s analysis includes six.  Yet they did not code alvarezsaurids for one of these, making the total functionally five.  The effect of recoding in Choiniere et al.'s matrix will be examined at the end of this series.

The First Asian Alvarezsaur

... ever found, that is.  The avialan alvarezsaur post is taking a while since there have been 95 proposed characters supporting it, and Choiniere et al. include more of them.  In the mean time, now that I have a blog, I get to do filler posts pictures of the day.  So here's AMNH 6524, the first alvarezsaurid discovered, back in 1923.  Back then it was only identified as a bird-like dinosaur. It was not until 1993 that it was identified as an alvarezsaurid (Norell et al., 1993). Originally identified as Mononykus, it is more likely Shuvuuia or Parvicursor as it is from the Djadokhta Formation.  It's mostly too damaged to see useful details in, but in the upper right you can see the parallel pubis and ischium with broad contact, a parvicursorine synapomorphy.

Norell, Chiappe and Clark, 1993. New limb on the avian family tree. Natural History. 9/93, 38-43.

A plea to theropod workers- Code the Taxa in Your Analyses

In the middle of writing the next installment of my alvarezsaur relationships series, I keep coming across a particular problem that's important enough to deserve its own post.  I've often complained about workers leaving out conflicting characters (e.g. Sereno, 1999) or relevent taxa (e.g. Maryanska et al., 2002), but recently I've noticed a more insidious problem.  Somebody will include a character and plenty of taxa, but then only code the character for a few of those taxa.  Oh sure, I don't expect everyone to track down every obscure coding available, so I'd forgive you if you didn't code Avimimus as having a fused sternum or Adasaurus as having an unfused one.  And there are certainly instances where a coding is controversial enough that I could agree being conservative and coding an uncertainty is a valid choice.  But not coding for the presence of a pubic symphysis in Archaeopteryx, or for fibular-tarsal contact in Allosaurus?  That's just lazy.  Now sure you might say that coding Allosaurus for fibular-tarsal contact won't add anything to the analysis, since carnosaurs and taxa closely related to carnosaurs all have the contact, and hey you coded Sinraptor for that character anyway.  But that's assuming you have the phylogeny correct before you even run the analysis, which begs the question of why you're even going through the motions of testing relationships in the first place.  In this particular case, I agree it's relatively harmless, but what about that same analysis (Choiniere et al.'s new Haplocheirus paper) where no birds with closed popliteal fossae were coded for that character?  Instead, all pygostylians were incorrectly left unknown.  This makes it so that derived alvarezsaurids are no longer even attracted to pygostylians in the matrix based on that character, which means that despite including the relevent taxa and character, you're not really testing that hypothesis.  It just breeds complacency and a false impression of consensus, leaving us unlikely to ever find unexpected relationships from our data.  Recent papers which are guilty of this problem are the Smith et al. (2007) Cryolophosaurus analysis, the Xu et al. (2009) Limusaurus analysis and the Choiniere et al. (2010) Haplocheirus analysis.  I know coding for so many taxa can be tedious, but these papers all gave the impression they performed impressively large analyses when they each actually took shortcuts and presented cladograms which aren't representative of the data they purport to include.  As scientists we have a duty to present accurate data to the public.  Virtually no one will bother looking through your matrix to make sure you did things correctly, and that includes peer reviewers and editors unfortunately.  How else to explain how Choiniere et al. could code Rahonavis for the presence of a mandibular character, when anyone who studies theropods knows it doesn't preserve a skull.  They just copied Makovicky et al.'s (2005) codings without thought, assuming they were correct.  But the public sees your cladogram and (justifiably in my opinion) assumes you did the work to create it.

I'll repeat a point that needs to be made depressingly often- the function of cladistic analysis (and science in general) is to question, not to confirm.  It does no good to only feed PAUP the data which supports your idea.  You might as well not even waste the time, and just list the characters instead.  The entire point of cladistic analysis is that it can somewhat objectively weigh competing ideas and tell us which is most parsimonious.  So if you're going to run an analysis, take some time to track down the characters which disagree with your hypothesis and code them for every available taxon.  Hell, send your data to me and I'll code the taxa for you in exchange for being slapped on as a coauthor.  I have a database of theropod codings at my disposal anyway.  That way you save time and your analysis will actually be a useful contribution to science.  Otherwise the general populace may be impressed by your cladogram, but your peers will realize they can ignore it because it didn't include the relevent data.

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.

Xu, Clark, Mo, Choiniere, Forster, Erickson, Hone, Sullivan, Eberth, Nesbitt, Zhao, Hernandez, Jia, Han and Guo, 2009. A Jurassic ceratosaur from China helps clarify avian digital homologies. Nature. 459, 940-944.


Choiniere, Xu, Clark, Forster, Guo and Han, 2010. A basal alvarezsauroid theropod from the Early Late Jurassic of Xinjiang,China. Science. 327, 571-574.

Haplocheirus and support for arctometatarsalian alvarezsaurids

Sereno (1999, 2001) presented 25 characters to support his versions of Ornithomimosauria (therizinosaurs, alvarezsaurs and ornithomimosaurs- characters 1-6, 16 and 17 below) and Ornithomimoidea (alvarezsaurs and ornithomimosaurs- characters 7-15 and 18-25).  They are analysed below with special attention paid to their condition in Haplocheirus and Nqwebasaurus, the latter suggested to be part of this clade by Sereno.  In addition, when a character is used by Choiniere et al. (2010), I've noted which avetheropods they miscoded and which they didn't code but could have.  I term Sereno's hypothesis "arctometatarsalian alvarezsaurs" since by definition, all taxa closer to Ornithomimus than to birds are Arctometatarsalia.

1. Subnarial foramen absent. This is not in the TWG matrices, but is in Choiniere et al.'s. Miscoded- Sinraptor, Juravenator, Garudimimus, Gallimimus, Dromiceiomimus ("Ornithomimus"), Citipati. Not coded- Neovenator, Acrocanthosaurus, Dilong, Ornitholestes, Harpymimus, Struthiomimus, Sinovenator, Sinornithosaurus, Velociraptor. Haplocheirus has a subnarial foramen, so this would only be an ambiguous synapomorphy supporting arctometatarsalian alvarezsaurs.

2. Maxillary preantorbital ramus >50% length of antorbital fossa. Not in TWG or Choiniere et al.. This is untrue for Haplocheirus, but also for Shuvuuia and most ornithomimosaurs including the basal Pelecanimimus and Harpymimus. It does not support arctometatarsalian alvarezsaurs.

3. Antorbital fossa with invaginated ventral margin. This in the TWG matrices, but not Choiniere et al.'s. It seems to be untrue in Haplocheirus and Mononykus, so does not support arctometatarsalian alvarezsaurs.

4. Nasal anteroventral process absent. Not in TWG or Choiniere et al.. This is untrue for Haplocheirus, so this would only be an ambiguous synapomorphy supporting arctometatarsalian alvarezsaurs.

5. Internal mandibular fenestra reduced to a narrow slit or absent. This is in both the TWG and Choiniere et al. matrices. Unfortunately, it is basically repeated another time in Choiniere et al.'s matrix with their character "posterior end of splenial: straight (0); forked (1)", since the slit-like fenestra is primarily caused by the lack of posterior splenial concavity. Miscoded- Ornitholestes, Caudipteryx. Not coded- Acrocanthosaurus, Gorgosaurus ("Albertosaurus"), Garudimimus, Gallimimus, Struthiomimus, Segnosaurus, Chirostenotes, Conchoraptor, "Ingenia", Tsaagan, Shenzhouraptor ("Jeholornis"), Confuciusornis. Haplocheirus has this, potentially supporting arctometatarsalian alvarezsaurs.

6. Posterolateral surangular ridge for muscle attachment absent. Not in TWG or Choiniere et al.. This is true for Haplocheirus, potentially supporting arctometatarsalian alvarezsaurs.

7. Premaxillary internarial process dorsoventrally flattened. This is in both the TWG and Choiniere et al. matrices. Miscoded- Guanlong. Not coded- Acrocanthosaurus, Carcharodontosaurus, Dilong, Gorgosaurus, Juravenator, Ornitholestes, Pelecanimimus, Harpymimus, Garudimimus, Caudipteryx, Avimimus, "Ingenia", Sapeornis, Confuciusornis. Haplocheirus has this, potentially supporting arctometatarsalian alvarezsaurs.

Haplocheirus skull (modified from Choiniere et al., 2010) showing some character states which agree (green) and disagree (red) with placing alvarezsaurids in Arctometatarsalia.

8. Prefrontal dorsal exposure larger than lacrimal. Not in TWG or Choiniere et al.. It seems to be untrue in Haplocheirus and Harpymimus, so does not support arctometatarsalian alvarezsaurs.

9. Enlarged prefrontal orbital flange. Not in TWG or Choiniere et al.. It is moderately developed in Haplocheirus, potentially supporting arctometatarsalian alvarezsaurs.

10. Dentary at least 80% of mandibular length. Not in TWG or Choiniere et al.. It is absent in Haplocheirus, Shuvuuia and ornithomimosaurs, so does not support arctometatarsalian alvarezsaurs.

11. Maxillary and dentary teeth implanted in groove. In Choiniere et al. and in the TWG matrix since Makovicky et al. (2005). Choiniere et al. actually split the character into maxillary and dentary characters, as in their matrix troodontids have the latter but not the former. As the condition in Shuvuuia is only known for the dentary (Suzuki et al., 2002), only that character is discussed here. Miscoded- Caudipteryx, Unenlagia, Rahonavis, Utahraptor, Achillobator. Not coded- Neovenator, Carcharodontosaurus, Giganotosaurus, Falcarius, Beipiaosaurus, Shenzhouraptor. The coding of several taxa which lack teeth or preserved dentaries is disturbing. Also odd is that while derived oviraptorosaurs are rightly coded as inapplicable due to a lack of dentary teeth, toothless ornithomimosaurs and birds are not. The condition is unknown in Haplocheirus but lacking in Harpymimus and Shenzhousaurus, so only ambiguously supports arctometatarsalian alvarezsaurs.

12. Posterior maxillary teeth absent. Not in TWG or Choiniere et al.. This is untrue in Haplocheirus, so only ambiguously supports arctometatarsalian alvarezsaurs.

13. Tooth size in maxillary and dentary rows uniform. Not in TWG or Choiniere et al. to the extent Sereno meant it, though a more homodont state is part of other characters which distinguished therizinosaurs. In any case, Haplocheirus, Pelecanimimus and Shenzhousaurus lack it, so it does not support arctometatarsalian alvarezsaurs.

14. Dentary teeth smaller than maxillary teeth. Not in TWG or Choiniere et al.. This is true in Haplocheirus, but also in nearly all theropods, so is not diagnostic as stated.

15. Chevrons four to five times longer than respective neural spines. Not in TWG or Choiniere et al.. This is untrue in Haplocheirus, Shuvuuia and ornithomimosaurs, so does not support arctometatarsalian alvarezsaurs.

16. Metacarpal I at least 60% of metacarpal II length. This is in Choiniere et al.'s matrix in the form of metacarpal I being "half or less" or "subequal" to metacarpal II in length, which is quite a poorly formed set of states (e.g. 75% fits neither of them). Technically, they speak of the difference between metacarpals II and III because they follow Xu et al.'s (2009) homology of tetanurine digits, which is especially confusing. They themselves forget to do it in character 283 and their supplementary discussion. The TWG started with a decent set of states for this character- "Metacarpal I half the length of metacarpal II (0) or less than half the length of metacarpal II (1), or subequal in length to metacarpal II (2)." but then redefined it to force alvarezsaurids to be non-homologous with ornithomimosaurs- "Metacarpal I half or less than half the length of metacarpal II, and longer proximodistally than wide transversely (0) or subequal in length to metacarpal II (1) or very short and wider transversely than long proximodistally (2)." Miscoded- Allosaurus, Gorgosaurus, Tyrannosaurus, "Ingenia". Not coded- Dilong, Daspletosaurus, Chirostenotes, Avimimus, Oviraptor, Conchoraptor, Mei, Epidexipteryx, Scansoriopteryx ("Epidendrosaurus"). In any case, Haplocheirus lacks it (40%), so only ambiguously supports arctometatarsalian alvarezsaurs (Harpymimus' condition is considered a reversal based on Deinocheirus and Pelecanimimus). Nqwebasaurus also has this.

17. Metacarpo-phalangeal joint of digit I with about fifteen degrees of maximum extension. Not in TWG or Choiniere et al., though the latter do code for extensor pit depth on metacarpals, which is somewhat correlated with it. The condition in Haplocheirus is undescribed, and it remains a potential support for arctometatarsalian alvarezsaurs (again while absent in Harpymimus it is present in Deinocheirus and Pelecanimimus). Nqwebasaurus lacks this.

18. Metacarpals I-III with 60-70% of shafts in mutual contact. Not in TWG or Choiniere et al.. This seems true in Haplocheirus based on the skeletal reconstruction, though a more detailed figure would be helpful for confirmation. The basal condition in ornithomimosaurs is ambiguous, as Deinocheirus, Harpymimus and "Grusimimus" lack it, though Pelecanimimus has it. It thus provides only weakly ambiguous support for arctometatarsalian alvarezsaurs. Nqwebasaurus lacks it.

19. Metacarpal III over 75% of metacarpal II's transverse width. This is absent in the TWG matrix. It is basically present in Choiniere et al.'s matrix, though the dividing ratio is 70%. Miscoded- Huaxiagnathus, Mononykus, Microraptor. Not coded- Gorgosaurus, Daspletosaurus, Pelecanimimus, Harpymimus, Shenzhousaurus, Dromiceiomimus, Gallimimus, Struthiomimus, Chirostenotes, Oviraptor, "Ingenia", IGM 100/44, Sinornithoides, Sinornithosaurus, Velociraptor, Scansoriopteryx, Epidexipteryx, Archaeopteryx, Shenzhouraptor, Sapeornis, Confuciusornis, Yixianornis, Apsaravis. It is absent in Haplocheirus according to their coding, and also in Mononykus and Deinocheirus so does not support arctometatarsalian alvarezsaurs. Nqwebasaurus also lacks it.

Haplocheirus manus (modified from Choiniere et al. 2010) showing the short metacarpal I (labeled as mcII) and distally placed flexor tubercles, which disagree and agree respectively with placing alvarezsaurids in Arctometatarsalia.

20. Marked flexor depression on distal end of phalanx I-1. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures and it remains a potential support for arctometatarsalian alvarezsaurs. It is also present in Nqwebasaurus.

21. Paired flexor processes on manual phalanx I-1. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures and it remains a potential support for arctometatarsalian alvarezsaurs. It is also present in Nqwebasaurus.

22. Dorsolateral (not dorsomedial as stated by Sereno- Suzuki et al., 2002) tubercle on manual phalanx I-1. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures and is probably not a synapomorphy for alvarezsaurs and ornithomimosaurs since Deinocheirus and Patagonykus lack it.

23. Manual flexor tubercles placed distally. This is present in the TWG matrix, though the character is a composite that also includes manual ungual curvature and flexor tubercle size. A better version is present in Choiniere et al.'s analysis, though that also includes the state "reduced to pyramidal nubbins, as in Limusaurus", which should not be there. Instead, taxa like Limusaurus should be coded for the placement of their tubercles, regardless of size (which could be another character). Miscoded- Gorgosaurus, Shenzhousaurus, Haplocheirus, Epidexipteryx, Archaeopteryx. Not coded- Mapusaurus, Guanlong, Daspletosaurus, Ornitholestes, Troodon. From my measurement, Haplocheirus has the tubercle of manual ungual I placed 25% (at its highest point) down the length of the ventral curve, which is more distal than other taxa they coded as derived (e.g. Ornithomimus). This only ambiguously supports arctometatarsalian alvarezsaurs though, since Deinocheirus lacks it. Nqwebasaurus has it.

24. Ventral surface of manual unguals flat. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures, but is absent in Patagonykus and Albertonykus, so does not support arctometatarsalian alvarezsaurs.

25. Ilia nearly contact dorsally. This is not in the TWG matrix, but is in Choiniere et al.'s. Miscoded- Archaeornithomimus, Rahonavis. Not coded- Sinraptor, Stokesosaurus langhami, Gorgosaurus, Daspletosaurus, Shenzhousaurus, Gallimimus, Struthiomimus, Achillesaurus, Shuvuuia, Alxasaurus, Segnosaurus, Avimimus, Conchoraptor, "Ingenia", Microraptor, Scansoriopteryx, Epidexipteryx, Archaeopteryx, Sapeornis, Confuciusornis. It's particularly problematic that no alvarezsaurids were coded for this character, even ignoring the other omissions. This is not known in Haplocheirus and remains a potential synapomorphy of alvarezsaurs and ornithomimosaurs, though Alvarezsaurus' condition is controversial.

A summary of the twenty-five characters' distribution among relevent taxa is shown below.
Deinoch ????? ????? ???-? 11001 1001?
Pelecan ?01?? ?1?1? 110-? 1111? ??1??
Harpymi 10111 11010 011-? 0000? ?1111
Shenzho ?1?1? ?1??0 010-? ???1? ??0?1
Beishan ????? ????? ???-? ????? ??0??
Grusimi ????? ????? ???-? ??011 1111?
Garudim 10111 11110 -1--? ????? ????1
Sinorni 1111? 11110 -1--0 1?11? ?1111
Anserim ????? ????? ???-0 1?1?? 01111
Dromice 1011? 11110 -1--0 1?11? ?1111
Struthi 10111 11110 -1--0 11111 11111
Gallimi 11111 11110 -1--0 1100? ?1111
Archaeo ????? ????? ???-? 1?001 11111

Falcari ??1?? 0???? 000-? 0?001 100??
Aniksos ????? ????? ???-? ????? ?????
Nqwebas ????? ????? ???-? 10001 1?1??

Haploch 00001 11010 ?00-0 0?10? ??1??
Alvarez ????? ????? ???-? ????? ??1??
Achille ????? ????? ???-? ????? ????1
Patagon ????? ????? ???-? ????1 1010?
Alberto ????? ????? ???-? ????? ??10?
Parvicu ????? ????? ???-? ????? ?????
Tugrik  ????? ????? ?1?-? 1???1 ?11?1
Shuvuui 10111 11110 111-0 111?1 11111
Ceraton ????? ??11? ???-? ????1 11???
Mononyk ??0?? ????? ?1?-? 11101 1111?

So of Sereno's 25 characters, only eight remain as potential synapomorphies. Another seven could support it under ACCTRAN, and the other ten are invalid. Choiniere et al.'s analysis only included three of the eight unambiguous characters, and four of the ambiguous ones. It was thus not a valid test of Sereno's hypothesis.  It's good to note that just because 8-15 of these characters could support arctometatarsalian alvarezsaurs doesn't mean they necessarily would even if included in an analysis.  For instance, Falcarius also has paired flexor processes on phalanx I-1, so maybe this character is primitive for Maniraptoriformes instead.
In addition to the flexor tubercle character above, several characters of Haplocheirus are miscoded based on the figures. Based on figure S5 with its only slightly concave posterior splenial edge, the internal mandibular fenestra is small and slit-like. The anterior dorsal diapophyses are long and extend far laterally past the zygapophyses, unlike derived alvarezsaurids and many maniraptorans. The coracoid has a deep notch below the glenoid, which is an ornithomimosaur character. The obturator process is placed proximally (~21% down the ischium) like ornithomimosaurs and more basal taxa (e.g. Gorgosaurus 28%, Tyrannosaurus 29%, Compsognathus 28%, Ornitholestes 27%, Archaeornithomimus 31%), not at midlength like that of maniraptorans. There is no distal notch between the obturator process and ischial shaft. The skeletal reconstruction shows a deep cleft between the anterior and greater trochanters, which is expected as Alvarezsaurus and Achillesaurus also show this condition (though they are also miscoded).
 
When these characters and those noted above are corrected in the matrix, the resulting cladogram is broadly similar to what the original matrix found (see below).  Exceptions are that Stokesosaurus is sister to Dilong with Guanlong the most basal tyrannosauroid, alvarezsaurs and therizinosaurs are successively closer outgroups to Oviraptorosauria + Paraves, there is no resolution within Therizinosauroidea, Conchoraptor and "Ingenia" are sister taxa, Deinonychosauria and Dromaeosauridae exist with normal content, Rahonavis and Archaeopteryx are basal avialans, and Shenzhouraptor is sister to Confuciusornis, with that pair sister to scansoriopterygids. It only takes three more steps to make alvarezsaurs and ornithomimosaurs are sister taxa, and Ornitholestes and Compsognathidae form successively further outgroups to Maniraptoriformes.  You might be thinking the changes made arctometatarsalian alvarezsaurs less likely, since Choiniere et al. reported only one more step was necessary.  However, from what I can tell, Choiniere et al. never found the most parsimonious trees in their dataset.  Running it in PAUP with the same characters ordered results in trees 1887 steps long, not 1998 steps as reported by the authors.  I think the problem is that they used TNT, which has resulted in few and suboptimal trees for me in the past.  With Choiniere et al.'s original codings for the characters noted above, it takes five more steps to force arctometatarsalian alvarezsaurids.  So really, changing the codings improved their liklihood by two steps.  The actual most parsimonious consensus tree from their data is (compare to their figure S1)-
 
|--Eoraptor
`--+--Herrerasaurus
   `--+--+--Dilophosaurus
      |  `--+--Coelophysis
      |     `--Megapnosaurus
      `--+--+--Ceratosaurus
         |  `--+--Masiakasaurus
         |     |--Abelisaurus
         |     |--Majungasaurus
         |     `--Carnotaurus
         `--+--Cryolophosaurus
            |--Piatnitzkysaurus
            `--+--Monolophosaurus
               |--Afrovenator
               |--Torvosaurus
               |--+--Baryonyx
               |  |--Suchomimus
               |  `--Irritator
               |--Allosaurus
               |--Neovenator
               |--+--Acrocanthosaurus
               |  |--Carcharodontosaurus
               |  `--+--Giganotosaurus
               |     `--Mapusaurus
               `--+--Sinraptor
                  `--+--Coelurus
                     `--+--+--Juravenator
                        |  |--Compsognathus
                        |  `--+--Huaxiagnathus
                        |     `--Sinosauropteryx
                        `--+--+--Guanlong
                           |  |--Dilong
                           |  |--+--Stokesosaurus clevelandi
                           |  |  `--Stokesosaurus langhami
                           |  `--+--Gorgosaurus
                           |     |--Daspletosaurus
                           |     `--Tyrannosaurus
                           `--+--+--Pelecanimimus
                              |  |--Harpymimus
                              |  |--Shenzhousaurus
                              |  |--Archaeornithomimus
                              |  `--+--Garudimimus
                              |     `--+--Anserimimus
                              |        |--Dromiceiomimus
                              |        |--Struthiomimus
                              |        `--Gallimimus
                              `--+--Ornitholestes
                                 `--+--+--Haplocheirus
                                    |  `--+--Alvarezsaurus
                                    |     |--Achillesaurus
                                    |     |--Patagonykus
                                    |     `--+--Albertonykus
                                    |        |--Parvicursor
                                    |        |--Shuvuuia
                                    |        `--Mononykus
                                    |--+--Falcarius
                                    |  `--+--+--Beipiaosaurus
                                    |     |  `--Alxasaurus
                                    |     |--Nothronychus
                                    |     |--Erlikosaurus
                                    |     `--Segnosaurus
                                    `--+--+--Incisivosaurus
                                       |  `--+--Caudipteryx
                                       |     `--+--+--Chirostenotes
                                       |        |  |--Avimimus
                                       |        |  `--Microvenator
                                       |        `--+--Oviraptor
                                       |           |--Citipati
                                       |           |--Conchoraptor
                                       |           `--"Ingenia"
                                       `--+--Mahakala
                                          |--Archaeopteryx
                                          |--Rahonavis
                                          |--Buitreraptor
                                          |--Unenlagia (inc. Neuquenraptor)
                                          |--+--Microraptor
                                          |  `--Sinornithosaurus
                                          |--Adasaurus
                                          |--+--Tsaagan
                                          |  |--Saurornitholestes
                                          |  `--Velociraptor
                                          |--Deinonychus
                                          |--Dromaeosaurus
                                          |--Achillobator
                                          |--Utahraptor
                                          |--+--Sinovenator
                                          |  `--+--+--Mei
                                          |     |  `--IGM 100/44
                                          |     `--+--Byronosaurus
                                          |        `--+--Sinornithoides
                                          |           `--+--Saurornithoides
                                          |              `--Troodon
                                          `--+--+--Epidexipteryx
                                             |  `--Scansoriopteryx
                                             |--Shenzhouraptor
                                             |--Confuciusornis
                                             `--+--Sapeornis
                                                `--+--Yixianornis
                                                   `--Apsaravis
 
But what about the evidence alvarezsaurs are avialans?  That will be examined in the next post.

Haplocheirus the Jurassic alvarezsaur is coming

While I prepare an official blog post on Haplocheirus (skeletal above from Choiniere et al., 2010), the new basal alvarezsaur, there are a couple comments I want to make.  The abstract states it "confirms that this group is a basal member of Maniraptora, the clade containing birds and their closest theropod relatives,"  but their matrix finds alvarezsaurs sister to ornithomimosaurs with the addition of ONE extra step.  One measley step finds Sereno's hypothesis to be supported.  That's not confirmation of anything.  That's basically ambiguous.  In fact, excluding Haplocheirus from the analysis actually results in trees where alvarezsaurs are not placed as basally as they are in some of the trees from the full analysis, so it makes the clade more basally placed if anything.  But wait, in the supplementary info they REDEFINE Maniraptora.  Now all of a sudden, Maniraptora is "Ornitholestes, Archaeopteryx, their most common recent ancestor and all of its descendants."  I know Phylocode isn't official yet, but why change a definition after over a decade of stability and consistancy?  Everyone agrees alvarezsaurs are maniraptorans under that definition (just check out Sereno's trees and my website's phylogeny).  Hell, ornithomimosaurs are (otherwise impossibly) maniraptorans under that definition in my tree.  In any case, I'm adding Haplocheirus to my coelurosaur supermatrix along with all of the supposed arctometatarsalian and bird characters of alvarezsaurids and we'll see what that says today or Friday.  Maybe they'll be unambiguously maniraptoran, but it won't be because I change the definition of the latter clade.

Choiniere, Xu, Clark, Forster, Guo and Han, 2010. A basal alvarezsauroid theropod from the Early Late Jurassic of Xinjiang,China. Science. 327, 571-574. DOI: 10.1126/science.1182143