Saturday, December 31, 2011

Happy New Year! The Database is updated!

Check it out!  All the 2011 taxa are there.  I'm off to party....

Surprise! Jeholornis palmapenis isn't valid.

What's that you say?  ANOTHER supposedly new Jehol basal avialan is just a junior synonym of a known species?!  Shock!  Gasp!  This time it's none other than the armless Jeholornis palmapenis (insert priapic joke here).  On the plus side, at least the description is better than others so far published, so this will help when coding Shenzhouraptor sinensis for matrices.

O'Connor et al. (2012) listed several characters supposedly distinguishing this taxon from Jeholornis prima.

The single preserved maxillary tooth and second empty alveolus contrast with IVPP V13274 (the prima holotype), V13550 and V13553 (both referred to prima), which have been reported to lack maxillary teeth. Yet jeholornithid teeth are often unpreserved due to their small size and low number, as seen by palmapenis' lack of dentary teeth (considered preservational by O'Connor et al.) and LPM 0193's (the Shenzhouraptor holotype) lack of any recognizable teeth. Even palmapenis only preserves one of the at least two maxillary teeth it had on that side. Thus the absence of maxillary teeth in other specimens may easily be preservational.

The presence of two pairs of anterior dorsal pleurocoels was listed as diagnostic (grading into a single pair posteriorly), but pleurocoel number often varies between different vertebrae and even sides of the same vertebra in theropods. Anterior pleurocoel number has not been described in any other jeholornithid specimen, but IVPP V13353 shows single pairs in dorsals nine and eleven, and three pairs in ten. Until palmapenis is shown to be consistantly unique in pleurocoel number, this character is not considered diagnostic.

Comparison of palmapenis ilium (top; after O'Connor et al., 2012) with prima (bottom; after Zhou and Zhang, 2003).  Note the ventral edge of the postacetabular process (blue) is not significantly more concave in palmapenis.  Note also the obvious breakage of the ilium (circled in red), making the dorsal border look highly convex.  The upper right picture shows superimposed and flipped images of the anterior left ilium and posterior right ilium to show the dorsal margin (surrounded by green) is straight.  Note that when the dorsal margins are lined up this way, the preserved posteroventral portion conveniently follows the outline of the other pubic peduncle.

The ilium is supposedly strongly convex dorsally, but it's clear the anterodorsal portion has merely been broken off, with no dorsal margin remaining anterior to the acetabular midpoint. The margin posterior to this is slightly convex as in other jeholornithid specimens. The anterior dorsal margin is preserved on the disarticulated left ilium, which forms a similar overall ilial dorsal convexity to other jeholornithids when rotated into place. Similarly, though the postacetabular process was described as strongly concave ventrally, the concavity is almost identical to that in IVPP V13353 (20% distance from line stretching from top of acetabulum to ventral postacetabular tip is 20% of ilial depth above acetabulum, compared to 19%) and other jeholornithids (the supposedly straight margin of IVPP V13274 looks slightly curved in the photo, and any difference would be insignificant in any case).

The dorsally curved ischium was also said to be diagnostic, but the distal ischium is unpreserved in the prima holotype, with the reconstructed portion being part of the tibia or fibula instead. Indeed, O'Connor et al. state ischial curvature is unclear in other Jeholornis specimens. LPM 0193 shows a dorsally curved ischium, albeit less so than in palmapenis.

In the tail, the transition point was stated to be more gradual (in central elongation) and posterior (at caudal seven instead of six) in palmapenis than IVPP V13550. Yet the transition point is also different in IVPP V13353, where the first elongated caudal is five, and IVPP V13274, where it seems to be at four (an unlabeled caudal is disarticulated adjacent to the last sacral). Differences in transition point abruptness are present as individual variation in other taxa, such as two nearly identical Microraptor specimens (CAGS 20-7-004 and 20-8-001), where the difference between lengths of caudals three and four is 9% in one and 53% in the other). Both caudal differences are thus more probably individual variation.

Finally, the diagnosis lists "elongated caudals possess chevrons with hooked articulations", but these articulations are not mentioned again and photos show normal, straight dorsal, anterior and posterior ends as in other paravians.

Of the diagnostic characters listed for prima by O'Connor et al., the ones not mentioned above are all unknown in palmapenis (except the robust dentary, which is true for all jeholornithids). In the text, the dentaries are said to appear unfused unlike the prima holotype, but they note this may be due to poor preservation. It may also be due to ontogeny, as palmapenis is smaller and has an unfused metatarsus. The text also states the ilium differs in having a bround rounded preacetabular process supposedly unlike IVPP V13274, but this is due to the latter being in medial view and not showing the ventral flange that would be lateral to the cuppedicus fossa, as seen in IVPP V13353 and LPM 0193.

So of the listed differences from prima, only the difference in maxillary dentulousness can even be plausibly considered true and not subject to individual variation. Ironically there are some valid differences not mentioned in the text. The dentary is a third deeper than the prima holotype and IVPP V13350, which is opposite the expected trend for a juvenile. The ischium slightly expands at its tip, unlike the Shenzhouraptor holotype. But since the first difference is not observable in the Shenzhouraptor type (whose anterior dentary angles beneath the skull) and the second difference is not observable in the prima type (whose distal ischium is broken off), these would form a weak differentiation from either species. As both character states are derived in Avialae, Shenzhouraptor and prima could not be united by their counterpart states. Instead, until they are shown to have a consistant variation between multiple specimens, the differences are more readily ascribed to individual variation as is found in any theropod known from large sample sizes (Allosaurus, Tyrannosaurus, Microraptor, Archaeopteryx). Jeholornis palmapenis is here made a junior synonym of Shenzhouraptor sinensis.

Referennces- Zhou and Zhang, 2003. Jeholornis compared to Archaeopteryx, with a new understanding of the earliest avian evolution. Naturwissenschaften. 90, 220-225.
O'Connor, Sun, Xu, Wang and Zhou, 2012. A new species of Jeholornis with complete caudal integument. Historical Biology. DOI: 10.1080/08912963.2011.552720

Monday, December 26, 2011

Merry Christmas! It's Xu's Thesis

I received a wonderful Christmas present this year- a copy of Xu's (2002) thesis on Liaoning deinonychosaurs which I've wanted for a decade now.  It's referenced in most of Xu's publications, but not in many others, and since it's not available in pdf, the info is difficult to come by.  This is one of the best publications on theropods I've read, so I'll sum up the contents here.

The first section is an osteology of the holotype of Sinornithosaurus.  The cranial and pedal sections have been published (as Xu and Wu, 2001 and Xu and Wang, 2000), but the axial description was most interesting to me.  It preserves 21 presacral vertebrae and the first nine caudals, yet these are not easily identified in the original tabloid description, unlike the pectoral girdle, manus and pelvis, which show most of their characters in the original figures.

The second section is an osteology of Microraptor's holotype, but also a specimen otherwise unmentioned in the literature- incomplete skeleton IVPP V13475 from the Jiufotang Formation, missing only some caudal vertebrae and the left manus.  This provides us with the Microraptor skull description I've been waiting for, and is what the reconstruction in Xu et al.'s (2011) paper is from, and what many of the codings for Microraptor in Xu and Zhang's (2005) matrix are from.  The rest of the description is less useful now that we have Hwang et al.'s (2002), but does feature interesting details like a large coracoid fenestra as in Sinornithosaurus and a straight pubis unlike other microraptorians.

The third section is an osteology of the then-undescribed Graciliraptor, so "Graciliraptor lujiatunensis" Xu, 2002 is a nomen nudum used prior to 2004. The description is better than the published version, but not by much since it was published in a real journal, and the specimen is fragmentary to begin with.

The fourth section is my favorite- a detailed osteology of the holotype and paratype of Sinovenator.  The species name is given as changae, as opposed to changii, since Li noted it was grammatically incorrect.  Creisler noted this on the DML that year too, but suggested changiae. Since it's named after a woman named Chang, I think changae would be right, but as I note on the Database, the Fourth Edition of the ICZN no longer requires emendations based on this reasoning (Article 31.1.3).  Nomenclature aside, the description is excellent and includes such needed things as an anterolateral view of the coracoid, posterior view of the braincase, and multiple views of presacral vertebrae.  Since we really don't have any detailed published descriptions of basal troodontid anatomy, and Sinovenator is basically complete (missing most of the palate, the quadratojugal, part of the mandible, half the cervicals, the post-26 caudals, ribs, and part of the hand), this section is vital to anyone studying paravian phylogeny.

The next section is about the feathers of Liaoning dromaeosaurids, which I normally would find boring, except that among the specimens described and photographed are Microraptor gui paratypes IVPP V13477 and V13320.  Of course, M. gui was a year away in 2002, so Xu refers to them as Sinornithosaurus sp. and Microraptor sp. respectively.  Interestingly, IVPP V13320 has completely serrationless teeth, while most Microraptor specimens have only distally serrated (posterior) teeth, and NGMC 00-12-A has posterior dentary teeth with serrations on both carinae.

The last section is one I would normally be very excited about- the phylogenetic analysis.  But it's basically the same as Xu and Zhang's (2005) with one less character and without Scansoriopteryx, Shenzhouraptor and Pedopenna (careful readers will note two mentions of Shenzhouraptor as an unnamed new bird without a pygostyle and one mention of Zuolong as an unnamed basal coelurosaur).  Xu runs lots of variations (cranial only, postcranial only, only basal taxa, only derived taxa, excluding various taxa) that would have been very interesting back in 2003, but since so many new taxa are lacking, are now more of historical interest like my Evaluating Phylogenetic Analyses section.  One good thing is that he describes several of the characters in depth and even provides graphs showing ratio distributions, so that they can be evaluated better than most TWG characters.

Xu ends with extensive measurement tables for the specimens described in the osteologies, but unfortunately not for the M. gui paratypes.  I would have liked more illustrations, but Xu's descriptions are top notch, and are badly needed for taxa described in tabloids like Sinornithosaurus and Sinovenator.  I don't know why most of this material was never published, since it's been written up for almost a decade now.  Similarly, I can only hope something of this caliber is written up for Beipiaosaurus and Mei.  Unfortunately, I only have a hard copy, so cannot send pdfs yet.

References- Xu and Wang, 2000. Troodontid-like pes in the dromaeosaurid Sinornithosaurus. Paleont. Soc. Korea Special Publication. 4, 179-188.
Xu and Wu, 2001. Cranial morphology of Sinornithosaurus millenii Xu et al. 1999 (Dinosauria: Theropoda: Dromaeosauridae) from the Yixian Formation of Liaoning, China. Canadian Journal of Earth Sciences. 38, 1739-1752.
Hwang, Norell, Qiang and Keqin, 2002. New specimens of Microraptor zhaoianus (Theropoda: Dromaeosauridae) from northeastern China. American Museum Novitates. 3381, 1-44. 
Xu, 2002. Deinonychosaurian fossils from the Jehol Group of Western Liaoning and the coelurosaurian evolution.  PhD Thesis. Chinese Academy of Sciences. 325 pp.
Xu and Zhang, 2005. A new maniraptoran dinosaur from China with long feathers on the metatarsus. Naturwissenschaften. 92, 173-177.
Xu, You, Du and Han, 2011. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature. 475, 465-470.

Friday, December 2, 2011

Top 10 Most Poorly Described and Illustrated Mesozoic Theropods

Look at that, I managed to skip a month between posts.  The hazards of coding, illness and other such excuses.  Here's a quickie that was fueled by my annoyance at any significant primary literature while coding Adasaurus.  These are the theropods whose publically available information is the most paltry compared to the completeness of their remains, and have been officially described already in the literature.  The relative importance of the taxon isn't a factor, and taxa whose remains are lost aren't considered due to the impossibility of their redescription.

10. Anserimimus
Anserimimus' holotype is a skeleton missing only some cervicals and the skull, but only the scapulocoracoid, manus and metatarsus were described and illustrated by Barsbold (1988).  Kobayashi and Barsbold (2006) helped a bit, as does Bronowicz's (2011) fragmentary but well described specimens.  But what keeps this from scoring higher is the availability of good photos of the mount (e.g. this) and Kobayashi's (2004) coding it for several matrices.

9. Tie between Cristatusaurus, Deltadromeus and Afrovenator
These taxa all have a common theme- Sereno described them (well, he described Suchomimus, which I sink into Cristatusaurus).  Published by the king of the Science tabloid, featuring a Paulian skeletal and several zoomed in line drawings, these taxa have yet to be redescribed in detail.  While there are photos of mounted skeletons available, these are all casts.  The best source of information on these are the matrices of Rauhut (2003) and Benson (2010).

8. Aucasaurus
Basically complete, but only the proximal tail, arm and lower hindlimbs have been illustrated and briefly described.  Recently, the braincase was also described, though I lack that paper so far.  Ceratosaur matrices like Carrano and Sampson (2007) have some info.

7. Inosaurus
Known from quite fragmentary remains, but very poorly described and only illustrated by two partial vertebrae (apparently my tracing survives unattributed online).  Is it even dinosaurian?

6. "Chilantaisaurus" zheziangensis
Dong (1979) gave this proximal tibia and partial pes a fairly useless description and illustrated two pedal digits in ventrolateral view and curving towards the viewer. :|  Therizinosaurian affinities have been suggested, but it's not been examined since.

5. Kaijiangosaurus
Only a few vertebrae, pectoral girdle and proximal/distal metatarsal outlines have been illustrated, and the description has yet to be translated from Chinese.  An online photo shows a lot more is known, but also that size differences mean more than one individual/taxon are present.

4. Conchoraptor
Ah, Conchoraptor.  You might be asking how can this be obscure when there are so many skeletons casted.  I've even seen two in person.  The problem with Conchoraptor is that it's unsure just which specimens belong to it, besides the holotype (of which we have illustrations of the skull, and a manus and metatarsus that presumably belong to it or a paratype).  None of the articulated skeletons photographed online have the right manual proportions or slender metatarsal II, and crestless skulls like ZPAL MgD-I/95 (the one described by Osmolska, 1976 and which Kundrat has recently been describing braincase details of) and the one on Witmer's lab page identified as "Ingenia" could belong to other oviraptorids.  No one has ever provided a modern diagnosis, described the holotype in any detail or justified the referral of other specimens.  This makes depending on matrices more risky than for other taxa listed here, since their OTU could be chimaerical for all I know.

3. Rinchenia 
This has been illustrated in the literature even more seldomly than Conchoraptor, since at least ZPAL MgD-I/95 has papers dedicated to it.  We only have the skull, mandible, overly schematic ilium and a single caudal vertebra illustrated.  Lucky for us, Auditore was able to obtain photos of the holotype and illustrate it as detailed by Cau on his blog.  As for Conchoraptor, Norell et al. (2001), Lu (2004) and Maryanska et al. (2002) all provide codings, which can be trusted more for Rinchenia since there's only the holotype (though I note a recent incorrect trend of referring IGM 100/42 to it).

2. Adasaurus
The muse for this post only gets second place.  For Adasaurus we must depend on a few schematic drawings (pelvis, metatarsus, pedal digit II), since Barsbold (1988) neither described it besides noting a couple features, nor does he allow photos to be circulated.  There was a photo of the holotype online which has since disappeared, but shows Barsbold's pelvis illustration is inaccurate, and to make it worse Kubota (pers. comm. to Senter, 2010) indicates the supposed small sickle claw doesn't belong.  I'm just hoping Kubota plans to redescribe the taxon like Kobayashi did for Barsbold's basal ornithomimosaurs.  Until then, we depend on codings from Norell et al. (2001), Senter (2007) and Longrich and Currie (2009), and a few scattered notes.  Hopefully Turner et al.'s upcoming dromaeosaurid monograph has some juicy photos.

1. Chilantaisaurus? sibiricus
There are a lot of fragmentary taxa known from a tooth or a vertebra that are poorly described (usually in a useless archaic way) and illustrated in a photo from a single view.  What makes sibiricus stand out is that Riabinin (1914) didn't even identify which element the holotype was, let alone try to describe its features.  He just said it was hollow and belonged to the limb of a fairly large theropod, probably a megalosaurid (named as Allosaurus? sibiricus).  Even worse, he didn't illustrate it, only [Edit: Chure 2000 and Benson and Xu 2008 were incorrect about the lack of illustration and brevity of description; I've since examined the taxon here] providing six measurements (proximal width 48 mm, proximal depth 39 mm, distal width 68 mm, distal depth 62 mm, cavity width 22 mm, cavity depth 17 mm).  Huene (1932) identified it as a distal metatarsal IV without rationale, but said only that it did not permit exact characterization and probably belonged to an allosaurid (renamed Antrodemus? sibiricus).  Molnar et al. (1990) then said it was "almost identical with that of C. tashuikouensis in form and proportions of the distal condyle", so questionably referred it to that genus.  You now possess the entirity of published information on sibiricus.  Makes the available information on Adasaurus seem like an overflowing feast.

Tuesday, October 25, 2011

Cladistics good, Aurorazhdarcho bad

Today I'm reporting on two papers, one good, one bad.  Both involve cladistics, but besides that are basically unrelated.

Tom Holtz notified the DML of a new paper by Brazeau (2011).  I highly recommend anyone making or examining a cladistic analysis read this work.  He basically outlines many of the problems I describe in the Evaluating Phylogenetic Analyses page of my website.
- Don't make "pseudo-ordered" characters of the form "bone x absent (0); bone x lacks feature A (1); bone x has feature A (2)", because if it's unordered PAUP has no reason to know to group all taxa with bone x together.  If it's ordered, it solves that problem, but has the probably undesired effect of assuming feature A is related to the loss of the bone.
- Don't have multiple characters implicitly coding for the same thing, with absence of that thing a state in addition to states coding for the presence/absence of a feature on the thing.  So "bone x absent (0); bone x present (1)" and "bone x absent (0); bone x present and without feature A (1); bone x present and with feature A (2)" should not both exist.  Have one character for the bones's absence/presence, and another character for each feature of the bone.  Just code taxa without the bone as inapplicable for characters about that bone's feature.  But be sure to set PAUP to collapse 0 length branches if you use inapplicable characters (TNT and NONA collapse them automatically).
- Don't make compound characters.  Each character should code for only one variable.
- Remember that "0" does not mean "primitive".  0 has to be a distinct state just like 1, 2 or any other number.  So don't make a character like "deltopectoral crest shape not described by any of the other states (0); crest round (1); crest triangular (2)", because there are lots of other shapes besides round and triangular, but PAUP could easily make state 0 synapomorphic for some clade.  That could end up grouping taxa with rectangular, pentagonal, etc. crests together as having the same condition, which is clearly not justified.
- As a consequence of this, making ordered multistate characters is better than making a series of less inclusive bistate characters.

The second paper was announced today- the description of a new taxon of pterosaur.   Frey et al. (2011) described Aurorazhdarcho, which is a damned cool name.  Unfortunately, the paper goes downhill from there.

First, they assign Aurorazhdarcho to the new family Protazhdarchidae.  Are there really people who still think you can make up a family-group name that's not eponymous with an existing genus?  Without a Protazhdarcho (which doesn't exist), there can be no Protazhdarchidae.  And Frey et al. can't use the excuse that Protazhdarchidae is "just a clade" since they explicitly say "nov. fam." and "we propose to erect a new family, the Protazhdarchidae..."  Tim Williams brought up the possibility on the DML that maybe the genus was originally named Protazdarcho and later changed, but the family name wasn't caught in time (though barring a VERY last minute change or editorial messiness I would hope the peer reviewers would still catch it), and if that's the case I apologize to the authors for this insulting paragraph.  Regardless, my insults in the next two paragraphs still apply. ;)

Second, Protazhdarchidae is monotypic, so is useless anyway.  Maybe I was too hasty in dismissing Jaime's suggestion for purely monotypic theropod families in the year 2100, since apparently it's not just Ji and other Chinese workers who are stuck in the archaic typological mindset.  The taxonomic world has moved beyond subjective difference being a reason to name a new clade/grade, please join the rest of us in the 21st century.

Third, Frey et al. include the highly flawed section "Problems with cladistic analysis".  Note they don't actually include Aurorazhdarcho in an analysis.  Why not?  "The main reason is that the low wing attachment is reason enough to align the specimen with the azhdachoid construction, which separates the group from all other Pterosauria."  I suppose Halloween IS a good time for Huene's ghost to rear its head, insisting on the importance of key characters.  We then get this lovely gem-

"If the low position of the glenoid fossa is regarded as original tetrapod, the azhdarchoid pterosaur construction has retained the low articulation of the front limbs and thus must have separated in the early history of the Pterosauria, possibly during the Triassic. Then, the high wing articulation could have evolved several times independently within the Pterosauria. If the low wing articulation is regarded as derived, the re-development of the primitive position of the glenoid fossa has to be explained. To resolve this question, a reinvestigation of the shoulder girdle of early Pterosauria would be necessary. For now, this problem remains unresolved pending an engineering approach concerning the consequences of low wing attachment, too. Hence, the character should be dismissed because of its evident functional impetus and unclear origin (Frey et al. 2003a)."

Did anyone else hear a distinguished gentleman in a sepia photograph read the above statements?  A single primitive character does not mean an entire clade is basal- we must examine the entire set of characters to determine which are more likely to be reversals or convergences.  We don't have to explain why any character evolved, nor should our ability to hypothesize why one state could evolve from another affect our choice in character polarity.  I'm very interested in what exactly all the characters we use were actually good for, but the analysis comes first THEN the evolutionary scenario.  Frey et al. are guilty of the same thing BADists are- wanting to know the scenario first and basing the phylogeny off that.  As for their last sentence, since every(?) character that's not the result of genetic drift has some functional importance (and how would we ever test that in extinct taxa?), that's not a reason to exclude them from analyses.  And since origins are only made clear once you run an analysis, excluding a character due to its 'unclear origin' is just nonsensical.

The rest of their "problems" are basically of the form "character x influences character y since both are parts of some functional whole, and until we know how these influences work, we shouldn't include either character in cladistic analyses."  So glenoid position influences deltopectoral crest shape and so on.  Frey et al. are fundamentally wrong in their demand to know function before phylogeny, and that anatomy alone isn't enough to know when characters are strictly correlated.  All you need to do is check the matrix to see if every taxon with character x also has character y, and if every taxon without x also lacks y.  Now if you do find exact correlation and it's logically impossible to have a condition with x and without y and vice versa, THEN you can delete the character.  Otherwise you might have a character complex like the paravian sickle claw where claw hyperextendability, size and curvature are certainly all functionally related, but should still be coded as separate characters since they're independent (e.g. Archaeopteryx lacks large size, Borogovia lacks strong curvature).  Now I suppose some characters might be correlated due to combinations of osteology that are only logically impossible once soft tissues are taken into account, and not just simple muscular biomechanics as Frey et al. suggest, but even such details as involving expression of the same gene at the same time.  Yet we'll never know most soft tissue anatomy for most fossil taxa (and even living taxa are poorly studied in this regard), so to rule out such correlation in our matrices is basically impossible.  We can either try to determine phylogeny now while excluding the logically correlated characters, or wait forever until we have fully examined a complete living growing example of each taxon to eliminate the possibility of correlation for each character.  I vote for the former.

Incidentally, given Frey et al.'s lack of a modern phylogenetic perspective, I don't trust their placement of Aurorazhdarcho in Azhdarchoidea.  Maybe it is, I'm not qualified to say, but I await the results of someone using a modern approach.

References- Brazeau, 2011. Problematic character coding methods in morphology and their effects. Biological Journal of the Linnean Society. 104, 489-498.

Frey, Meyer and Tischlinger, 2011. The oldest azhdarchoid pterosaur from the Late Jurassic Solnhofen Limestone (Early Tithonian) of Southern Germany. Swiss Journal of Geosciences. DOI: 10.1007/s00015-011-0073-1

Friday, October 21, 2011

Xiaotingia commentary, is Archaeopteryx a deinonychosaur?

I just wrote this for the DML and figured it could be useful to post here.

The majority view, as in the conclusion found by almost every cladistic analysis which has tackled the problem, is that Archaeopteryx is a basal avialan.  The recent controversy has been over the analysis in Xu et al.'s (2011) description of Xiaotingia.  This is a version of the Theropod Working Group analysis which goes back to Norell et al. (2001).  Specifically Xu et al. (2011) added a few taxa and several characters to...
- Zhang et al.'s (2008) analysis which added Epidexipteryx and a few characters to...
- Senter's (2007) analysis which completely recoded and added many characters and taxa to...
- Kirkland et al.'s (2005) analysis which added several characters and a few therizinosaurs to...
- Hwang et al.'s (2004), which is based on Xu et al.'s (2002), which is based on more analyses still all the way back to Norell et al. (2001).

So it's a re-re-re-re-re-analysis of a huge dataset.  Running this dataset with Xiaotingia results in Archaeopteryx being a basal deinonychosaur instead of a basal avialan.  Note this isn't a big move, since Deinonychosauria and Avialae are sister groups.  It just moves from the base of one group to the base of the other.  Note also that despite what the hype would indicate, this result isn't very well supported.  Forcing Archaeopteryx back to its normal position as a basal avialan only takes TWO more evolutionary steps.  That's not significant at all, and furthermore the analysis itself is flawed as detailed below. 

When you run an analysis like this, certain characters need to be "ordered".  So that for instance, taxa with six sacral vertebrae are seen as intermediate between taxa with five and taxa with seven sacrals.  If you don't order the character, "six sacrals" is counted as a character that has no definite relationship to other numbers of sacral vertebrae, so you'd get weird results like grouping Rahonavis and Shenzhouraptor together to the exclusion of more derived birds because of their shared primitive sacral number.  Also, ordering changes the amount of steps a character takes to evolve, since if it's unordered, you can go from five to nine sacrals as easily as you can go from five to six sacrals.  When we try to find out if Xu et al. ordered their characters, we have to follow the lineage of analyses all the way back to Kirkland et al.'s (2005) version, which only says one character was ordered but doesn't say which.  Xu et al. seem to ignore that anyway, since I get their results by running their analysis unordered.  Running Xu et al.'s analysis with all characters ordered adds over 100 steps, which of course completely overpowers our two step difference we noted above.  While not every character should be ordered, many should be.  Importantly, when characters are ordered, Archaeopteryx comes out as a bird.

So how much of Xu et al.'s result is due to not having the right characters ordered?  We don't know unless someone goes through the tedious steps of looking through all the characters and choosing which should be ordered.  You can see how this could be important for Archaeopteryx, since any intermediate state it has between birds and deinonychosaurs will be counted as equally different from both instead of being a bit closer to birds (assuming the deinonychosaurian condition is primitive).

Another problem is that Xu et al.'s analysis doesn't include all of the relevent taxa and characters that other versions of the analysis do.  Senter's newest (2010) analysis (which is a modification of his 2007 one) includes most of the same taxa but has many new codings and takes seven more steps to place Archaeopteryx in Deinonychosauria.  Zanno et al.'s (2009) analysis (which has a rather different lineage going back to Hwang et al. 2004 and so doesn't include any of Senter's numerous modifications) contains a different mix of characters, adds Mahakala and Shanag, but lacks scansoriopterygids, Sapeornis, Protopteryx, NGMC 91 and Bambiraptor.  Forcing deinonychosaurian Archaeopteryx is six steps longer in it.  Makovicky et al.'s (2010) analysis (which is more similar to Zanno et al.'s) includes yet a different mix of characters and taxa needs eight more steps.  Most recently, Turner et al. (2011) have a TWG-based analysis centered on deinonychosaurs and birds, including taxa not found in the Xiaotingia analysis like Hesperonychus, Graciliraptor, Tianyuraptor, Austroraptor, Mahakala, Jinfengopteryx, two undescribed basal troodontids, Jixiangornis and a lot of birds.  Based on their taxon sample I bet they also included the numerous bird-related characters of Clarke's analyses.  And this analysis found Archaeopteryx to be a bird, though I can't say how well supported that is since they haven't released their data matrix yet (grrr).

So we can see that most analyses find Archaeopteryx to be 6-8 steps more likely to be a bird, while Xu et al. found it to be 2 steps more likely to be a deinonychosaur.  Each analysis includes some data others don't, and all have miscodings.  Until someone combines the information (which I'm finishing up), we won't know if say adding Xiaotingia to Turner et al.'s analysis would make Archaeopteryx a deinonychosaur, or if adding Jinfengopteryx to Xu et al.'s analysis would make Archaeopteryx a bird.

Until that time, I'd say it could be either, but that both the number of analyses and the strength of support in those analyses slightly favor it being a bird. 

Saturday, October 15, 2011

Theropoda in the Amazing Year 2100

One of my pet peeves is the cavalier attitude many dinosaur paleontologists have recently in regard to the priority and validity of old taxa.  Whether it's lazy dismissal of genera as nomina dubia without an analysis showing this is true, dumping family-level names based on supposed nomina dubia despite the ICZN having no rules about this, making up new definitions for established clades, or just plain old replacement of clade names because the eponymous genus isn't as complete or deeply nested as another.  If this trend continues, we may face the following horrifying vision of the future...

- Coelophysoidea (based on a complete neotype for Coelophysis bauri, the only known material for the first 66 years having been ignored as archosaur scrap; IT'S ALREADY TRUE!)
- Sinodilophosauridae (people still refuse to use Dilophosauridae, but the describers of what was originally Dilophosaurus sinensis came up with their own name for this clade)
- Averostra (because enough people misused Bakker's Neotheropoda so that they forgot he created it for this node and started using a term published 16 years later instead)
-- Ceratosauria
--- Majungasauroidea (Abelisaurus was deemed too fragmentary, and Carnotaurus is still only known from one specimen. Majungasaurus itself is now based on a complete neotype found in 2068)
---- Masiakasauridae
---- Majungasauridae
-- Tetanuriformes (someone finally got enough followers after redefining Tetanurae to be less inclusive, thus Tetanurae has different meanings depending on what year a paper was published)
--- Suchomimia
---- Tayntonsauridae (after a incomplete articulated megalosaur was found in Megalosaurus' type beds, it was named to 'solve' the confusion surrounding Megalosaurus' association.  All Megalosaurus remains were then referred to Tayntonsaurus)
---- Suchomimidae (Yes, ignoring Spinosauridae, Baryonychidae, Irritatoridae and Cristatusaurus)
--- Tetanurae
----Sinraptoroidea (after Allosaurus fragilis was shown to be a nomen dubium, people incorrectly said a family level name couldn't be based on it)
----- Sinraptoridae (no comment needed)
----- Neoallosauridae (people declared Allosaurus, Labrosaurus, Creosaurus and Epanterias to be undiagnostic in a footnote of the paper describing Big Al as Neoallosaurus in 2035)
----- Carcharodontosauria
------ Neovenatoridae
------ Acrocanthosauridae
------ Shaochilongidae
------ Tyrannotitanidae
------ Carcharodontosauridae (ignoring the stable stem-based definition of Carcharodontosauridae, people kept redefining it to be less and less inclusive)
---- Tyrannosauroidea (despite including the following two families, both named prior to Tyrannosauridae...)
----- Coeluridae
----- Compsognathidae
----- Tyrannosauridae
---- Avesternes (someone named it in 2019 and people started to ignore Maniraptoriformes)
----- Ornithomimosauria (based on a neotype for Ornithomimus edmontonicus, even though O. velox was the type species and brevitertius has priority over edmontonicus)
----- Eunothronychia (Therizinosauria was defeated the same way it gained usage, once graffami was given its own genus)
----- Citipatia (Oviraptor was too fragmentary, so the clade was renamed once Citipati's holotype was fully described in 2023. IGM 100/42 remains undescribed and called the Zamyn Kondt oviraptorid as of 2100)
----- Bimedicamentodontidae (Troodon is a long forgotten name, and no the family hasn't been subdivided yet despite there being 73 described diagnostic genera)
----- Dromaeosauridae (miraculously unaffected, but Barsbold's estate owns Adasaurus, which no one is allowed to circulate holograms of)
----- Shuvuuiformes (because of... well, you get the drift by now)
----- Birdia (we finally got sick of the semantic arguments)

Only you can prevent this terrifying prediction from becoming reality.  Support priority, follow the ICZN until another code is viable (the Phylocode remains unofficial as of 2100, but rumors are Phylonyms is almost complete and that it will start as of 1-1-21xx), and remember a named taxon is valid until shown otherwise by a detailed redescription and comparison.

Saturday, September 17, 2011

Planet Dinosaur Review

Since I reviewed Dinosaur Revolution, I might as well tackle the other big dino documentary that came out this month.  As with Dinosaur Revolution, this review only covers the first episode, which in this case was about Cenomanian North Africa.

Planet Dinosaur's special effects range from decent to sad.  While I could go on about the little details like Ouranosaurus chewing like a mammal, having depressions where its laterotemporal fenestrae are, Microraptor lacking primaries attached to its second finger and having wings which are too short, etc., the simple truth is that the dinosaurs are less accurate and less believable as real objects.  The maniraptorans (Troodon, Microraptor, Epidexipteryx) are especially poor.  That's not to say it's all bad.  The Rugops (possibly an Aucasaurus from the Auca Mahuevo episode) and Sarcosuchus look pretty good, the Spinosaurus is decent except for its short tail, and the Ouranosaurus dying had nice motions and rapid breathing.  Seeing this show really made me realize how good the models and animation were in Dinosaur Revolution though.  It's such a shame the talent/money spent on the latter couldn't have been used for a program like Planet Dinosaur.

As far as behavior goes, it was refreshing to see dinosaurs acting like dinosaurs.  There are a few stupid things, like Spinosaurus eating part of a fish, then leaving to catch more ("with prey plentiful, Spinosaurus can afford to be wasteful").  Or Rugops' subsequent portrayal as an obligate scavenger.  Or Spinosaurus slashing the fish with its hands, only to eat tiny bits at a time. But at least nothing they do is human-like.  The behavior is largely defended by reference to actual studies (see below), and the show does a good job of making a story based on these.  The larger narrative of Spinosaurus being the largest and last spinosaurid and dying from climate change was flawed because Late Cretaceous African dinosaurs are poorly known, and Hone et al. (2010) and Candeiro et al. (2004) described Santonian spinosaurids.  But Candeiro et al.'s conclusion was doubted in their 2006 paper and Hone et al.'s study is quite new.  Bearing in mind I don't know how accurate the paleoclimatology was, the larger story felt more plausible than Dinosaur Revolution's apparently tacked-on story of how dinosaur parenting helped their success.

My favorite part of Planet Dinosaur is that it manages to explicitly incorporate numerous journal articles.  These are shown in informational panels with the year of publication, age, country, and figures from the original articles or photos of specimens referenced by them.  They even managed to rotate one of Stromer's Spinosaurus vertebra drawings in 3D, haha.  We have Stromer (1915), Dal Sasso et al. (2005), Amiot et al. (2010), Dal Sasso et al. (2009), Sereno et al. (1996), Tanke and Currie (2000), Sereno et al. (2008), Kellner (2004), Charig and Milner (1986), and a biomechanical strength analysis of Carcharodontosaurus' jaws.  I don't know how much I agree with some of the conclusions (like amphibious spinosaurids), but at least they're actually from the scientific literature and not just random made-up possibilities. 
There are ocassional errors, like overlaying a tyrannosaurid dentary on Sinraptor's skull, or using Stromer's reconstruction as the basis of the Spinosaurus skeletal, resulting in one of the worst reconstructions I've seen.  It's good they knew to tilt it horizontal and give it the right skull, but the anatomy!  Sacral neural spines lateral to the ilium, the femur articulating with the postacetabular process, two sets of pubes... I could insult it all day. 

Please put this travesty out of its misery
And yet other details of their informational panels are accurate, such as Irritator and Siamosaurus being inconspicuously listed as additional spinosaurids on the map.  Overall, it's quite good.  I actually learned what Onchopristis was, and that there's a partial Spinosaurus maxilla with an Onchopristis tooth embedded in it (not just MSNM V4047 with its embedded vertebra).  There's also apparently a Spinosaurus neural spine found in 2008 in Morocco that had been broken in life, which I had never heard of.  Any time a dinosaur show manages to teach ME something, I'm impressed. 

So I quite liked Planet Dinosaur.  It's almost the exact opposite of Dinosaur Revolution- generally inaccurate restorations behaving fairly realistically, packed full of references to specific discoveries in the literature, telling us what we know and why.  I'll be watching the following episodes, and contra my earlier statement I'll probably tune in to the other Dinosaur Revolutions too.  I'll just have to treat the latter like the Transformers 2 of dinosaur programs- pretty to watch, but turn off your brain.  On the other hand, I'll be interested to see if Planet Dinosaur presents any more discoveries I hadn't heard of. 

Tuesday, September 13, 2011

Dinosaur Revolution review

Well, that was painful.  I decided to join the trend and review the show that's been so hyped- Dinosaur Revolution.  Little did I know my yearly allowance of eyerolls would be used up.  I only watched the frirst episode "Evolution's Winners" and frankly have no desire to sample more.

First the good.  The models were usually excellent, with non-pronated hands and all that good stuff.  I especially enjoyed the dilophosaurian snouts on the Cryolophosaurus, and the Mongolian mammals which weren't just shrews or mice.  I also liked the homage to Dryptosaurus and Ceratosaurus artwork in the Cryolophosaurus section (though I don't think they could really stand on their tails, given how most theropod chevrons look).  The Gigantoraptor's feathering was more problematic, as it seemed more like a naked theropod covered in feathers than an actual feathered creature like a bird, where body outlines are hidden and feathers interact and fold.  Its wings were always held out in front, which for a display is fine, but even the female who wanders up is posed this way.  The animation itself was a mixed bag.  Most moved smoothly, but the Saurosuchus looked unnatural for instance.  Similarly, the rendering was good for most, but the therapsids in the opening seen looked plasticy.  What's that you say?  My "good" paragraph's actually mostly full of criticisms?  Guess that prepares the way for the rest of the review...

What made Dinosaur Revolution most difficult to watch is the rampant anthropomorphism.  Basically none of the subjects actually behaves like a reptile, or a bird, or even a non-ape mammal for that matter.  They're chock full of human mannerisms.  You can always tell what they're supposed to be feeling, as if brains that size could even house such emotion.  But it's not just behavior.  My jaw dropped at the blatant 'sexy eyelash' marks on the female Eoraptors.  Why not just go the whole hog and give them real eyelashes they can flutter alluringly?  Then the male's heart (shaped like a heart of course) could project from its chest like a piston.  Would have been almost as realistic as the expectant smile he shows as she approaches in the actual program.  Even ignoring the behavior, the plotlines have so many "entertaining" improbable portions, like the Eoraptor unwittingly throwing a therapsid into Saurosuchus' mouth, that any illusion you're watching reality is destroyed.  And what was up with that swarm of hostile flies chasing the Antarctic fauna and killing the lizard... for blood!  Is this a 1950s horror movie or something?

Which would have all been excusable if the show at least taught us something.  Then it'd be a Dinosaur Train for adults, which wouldn't be my idea of a good program to watch, but would at least educate the part of the public that finds documentaries boring.  But no, I don't think there was any actual paleontological data contained in that hour, besides most of the portrayed anatomy and a few basic facts like "birds are dinosaurs" and "Cryolophosaurus is from Antarctica".  I say "most" because while the models were largely accurate, they sometimes contained some fictional aspect.  The rhamphorhynchoid tail fin on the female Eoraptors, for instance.  Or the highly elaborate wattles and soft horns on the male Gigantoraptor.  And when it comes to behavior, we have bower-building Eoraptors, color flushing Cryolophosaurus which killed the young of rival males, a stomping and twirling Gigantoraptor mating dance, Glacialisaurus which lived in harems (which we so know from the partial hindlimb...), etc.  It's not that these soft parts or behaviors are impossible, but Joe Public's only going to remember Gigantoraptor as "that goofy rainbow-colored thing that dances" or Eoraptor as "those raptors that cutely chirp and build mounds to select mates, and then care for their baby who adorably falls down, awwww".  So you're emphasizing the fictional aspects of these animals, while not going into any of the actual known interesting facts about them.

But maybe the show could have retained some use if all of this human-like/fictional appearance and behavior was there to illustrate some greater true scientific fact, that even network execs think viewers could remember.  Alas, no.  The implication of the Eoraptor portion was that dinosaur success was due to more complex parental care, but my impression has been that evidence for such care is limited to maniraptorans, supposed evidence for care in hadrosaurs (and thus Ornithischia) has been refuted, and that baby sauropods were too small to associate with adults and aren't apparent in herd trackways.  And even the mosasaur cares for its babies enough to get revenge on sharks for eating them (vengeance is such a widespread trait in squamates...).  As does the Cretaceous mammal, more realistically.  If you want to make the point dinosaurs were probably often brightly colored with display structures as the Gigantoraptor portion tries to, a far superior method would be to show say ten different possibilities for a few species in quick succession.  Changing colors and adding wattles wouldn't be that resource intensitive and would get the idea across to laymen without making it seem like we know they had definite soft features and patterns (I'm guessing the Yixian pigments were unknown when this was made).  The Cryolophosaurus portion taught us about the factual behavior... of lions.  The mosasaur segment taught us... er... "a mother's protective instinct is a force of nature than can change the world."  And the Glacialisaurus one taught us "a little bad luck goes a long way."  That's certainly scientific.  Maybe the next episode will teach us "the disadvantaged underdog can succeed with perseverance and faith in himself."  Sigh

To sum up, watch if you like largely accurate-looking dinosaurs acting like humans in zany situations and learning valuable life lessons.  If you want a show that clearly indicates which parts are based on paleontology, shows dinosaurs as they may have been, and teaches you something about them, keep dreaming.

Friday, September 9, 2011

Tehuelchesaurus and how to describe the affinities of a taxon

I've often complained about the tendency for authors to view their most parsimonious cladogram as "the right" tree, such as here and here.  I note that it's usually more helpful to describe how parsimonious different hypotheses are, since while new analyses usually change the topology somewhat, they rarely support relationships that were strongly rejected before.  Carballido et al. (2011) recently redescribed the sauropod Tehuelchesaurus, and in addition to a detailed osteology and several other important discussions, their paper contains a phylogenetic analysis that did things just the way they should.  The analysis (249 characters, 45 taxa) is based on Wilson's (2002) analysis with added data, including numerous newly added macronarians.  Some characters were ordered, taxa which cause polytomies were deleted a posteriori, and Tehuelchesaurus emerged as a basal camarasauromorph sister to Galveosaurus, not a relative of Omeisaurus as originally thought by Rich et al. (1999).  But instead of simply letting the matter rest there, Carballido et al. included the section "Testing Alternative Positions for Tehuelchesaurus."  Music to my ears.  They tested not only the Omeisaurus alternative (9 steps longer), but also positions slightly more (1 step longer) and less (2 steps longer) than Galveosaurus, and noted the character support for all of these.  In addition, the authors wrote the following which basically covers any plausible position-

"Other positions within basal camarasauromorphs (in any position within the Janenschia/Tastavinsaurus clade, as sister taxon to Europasaurus, more basal than Europasaurus, and as sister taxon to Camarasaurus) and as a macronarian outside Camarasauromorpha, but more derived than Haplocanthosaurus, require three additional steps. Placing Tehuelchesaurus as sister taxon of Haplocanthosaurus results in a suboptimal tree four steps longer than the MPTs, and as the most basal macronarian needs even five additional steps. Even more steps are required to place this taxon in the Titanosauriformes (seven additional steps as a basal somphospondyl and eight additional steps as a basal brachiosaurid).

Any position outside Macronaria also results in considerably suboptimal tree lengths. Five additional steps are needed to make Tehuelchesaurus the most basal diplodocoid, but any position within higher diplodocoids results in trees that are at least ten steps longer than the MPTs. Likewise, placing Tehuelchesaurus outside Neosauropoda requires six additional steps, and any placement among basal, nonneosauropodan taxa results in trees at least nine steps longer than the MPTs. Thus, the possibility of a Jurassic Patagonian clade of sauropods, including Patagosaurus and Tehuelchesaurus, can also be rejected, as it requires 12 additional steps."

The paper succeeds in giving you a much clearer idea of Tehuelchesaurus' relationships than any one cladogram could.  Anybody describing a new taxon should follow their example.

Carballido, Rauhut, Pol and Salgado, 2011. Osteology and phylogenetic relationships of Tehuelchesaurus benitezii (Dinosauria, Sauropoda) from the Upper Jurassic of Patagonia. Zoological Journal of the Linnean Society. DOI: 10.1111/j.1096-3642.2011.00723.x

Wednesday, August 17, 2011

Do we have dromaeosaurid evolution backwards?

The basic evolution of Maniraptora has seemed pretty well established in the past decade, thanks to TWG papers describing Sinovenator, Mei, Mahakala, Xiaotingia and such.  The basal paravian was a little bird-like taxon, like Microraptor on the dromaeosaurid end or Jinfengopteryx on the troodontid end, with genera like Rahonavis and Anchiornis breaking the boundaries even more.  Going further towards the base of Maniraptora, the cranial similarities between scansoriopterygids and basal oviraptorosaurs have suggested a short-snouted herbivorous ancestor, while Shuvuuia and Pelecanimimus have similar skulls that suggest the first maniraptoriform was not a macropredator.  Large, more obviously carnivorous taxa like eudromaeosaurs are seen as reversals to a more traditional theropod lifestyle.  It's a nice story and may be right, but what if it's wrong?

Dromaeosaurid morphology forms a continuum from the extreme of Achillobator with its deep snout, mesially serrated teeth, low DSDI, rather short coracoid, posteriorly facing glenoid, relatively short arms, deep brevis fossa, large anterior pubic boot and proximally placed obturator process, though Deinonychus, Velociraptor, Bambiraptor, Sinornithosaurus, Microraptor, Buitreraptor/Unenlagia and ending at Rahonavis.  Even if the unenlagiines are avialans though, dromaeosaurids need a lot of reversals no matter which direction evolution went.  Note that stratigraphy doesn't strongly support either option.  We have Utahraptor from the Barremian which is very similar to Achillobator, and dromaeosaurid-like teeth with mesial serrations resembling both dromaeosaurines and velociraptorines in the Late Jurassic.  Then again, there's the microraptorian-like Graciliraptor and Shanag which also lived early, and the possible microraptorian "Paleopteryx" from the Morrison.

There's also a possible transitional form between basal coelurosaurs and dromaeosaurids- Ornitholestes.  Like dromaeosaurids, Ornitholestes has a third premaxillary tooth much smaller than the first two, short cervical vertebrae with tall neural spines, prominent anterior cervical epipophyses, a crest-like ventral tuberosity on the humerus, an enlarged second pedal ungual and a transversely expanded metatarsal IV.  It's also similar to paravians in the elongate distal caudals and bifurcated chevrons.  Deriving dromaeosaurids from something of Ornitholestes-grade would explain why they are almost unique among derived maniraptorans in having prefrontals, which unlike the dental characters of eudromaeosaurs, are not plausibly due to macropredatory habits.  In this scenario, microraptorians would be convergent with birds in their aerial characters.

Is there any other evidence for this idea?  Don't troodontids show the same pattern as dromaeosaurids, going from Jinfengopteryx/Anchiornis to Mei/Sinovenator to Sinornithoides/Byronosaurus to Troodon?  Maybe not.  Jinfengopteryx and Anchiornis can switch to Avialae easily, and the same may be true for Mei and Sinovenator.  They're often avialans in the in progress Lori matrix, even with Xu et al.'s troodontid characters.  Lori itself emerged sister to Sinornithoides in Hartman et al.'s SVP poster and is Jurassic in age, with serrated teeth.  Maybe that's the basal grade for troodontids, and birds are related but evolved serrationless teeth, long arms, dorsal ischial processes and such on their own branch.

The Jurassic Haplocheirus also supports this idea, since it shows serrated teeth and a general morphology so primitive that Cau's Sumrukia matrix found it to clade with compsognathids.  Note therizinosaurs also have mesial and distal serrations, and that Falcarius has made the clade more basal in most matrices, unlike earlier ideas they were related to oviraptorosaurs.  Maybe coelurosaurs were of the compsognathid-coelurid grade all through their evolution, with ornithomimosaurs, alvarezsaurids, therizinosaurs, dromaeosaurids and troodontids+birds each developing their birdlike and/or herbivorous characters separately.  This idea is kind of anti-Paulian or anti-BCF in nature and has plenty of precedent in the literature.  Ostrom long suggested Ornitholestes as a dromaeosaurid ancestor, and Makovicky (1995) found the two to be sister taxa to the exclusion of birds based on vertebral characters. 

Of course the real test is with cladistic analyses, so how does the idea fare?  The in progress Lori matrix finds a fairly traditional tree with Ornitholestes sister to Maniraptoriformes, microraptorians and Unenlagia basal among dromaeosaurids, and is somewhat unusual in finding troodontids sister to birds.   Constraining Ornitholestes to be a dromaeosaurid and the dromaeosaurid topology 'backwards' from the consensus (Achillobator,Dromaeosaurus(Deinonychus,Velociraptor(Microraptor,Sinornithosaurus))) results in trees 11 steps longer.  Not too bad when you consider enforcing Longrich and Currie's (2009) plausible-seeming traditional dromaeosaurid topology is 7 steps longer than the minimum.

Tuesday, August 9, 2011

And the best paper written about a theropod is...

I'm sure I can come across as a grumpy old carmudgeon thanks to my frequent criticisms of papers, even good ones like Benson et al. (2011).  Critiquing is fun and I think more important than praise when it comes to scientific papers, but for a change, here's a paper I was floored by. 

I was lucky enough to be sent a copy of Dal Sasso and Maganuco's new Scipionyx monograph, and boy does it deliver!  Scipionyx is one of those Science/Nature taxa that's initially described in two pages with a couple figures, then goes for years until a decent description comes out (See how I work criticism into even an article designed to praise, heh.  Btw, of that list, Enantiornis has since been redescribed, and papers on Guanlong, Buitreraptor and Haplocheirus are in the works.  Woo!)  Luckily, the illustrations in Dal Sasso and Signore's 1998 paper were superb and covered all the material, so waiting wasn't as painful as it is for some other taxa.  Even so, if every 'tabloid taxon' were given this good of a treatment once they were redescribed, I'd have no complaint waiting a decade for them.  The monograph is simply unparalleled in every aspect.  Quality diagnosis of autapomorphies.  Huge illustrations and color photos, extensive explanatory diagrams, x-rays, ultraviolet, different angles.  Measurements of everything.  Eleven pages discussing the ontogenetic indicators.  A phylogenetic analysis using a good base (Senter's TWG modification), codes taxa completely, has explicit coding changes based on new papers and most relevent taxa included (exceptions are Proceratosaurus and Bagaraatan).  Then there's the long description of all the soft parts most taxa don't leave us.  And the taphonomy.  And the physiology, discussing Ruben's terrible ideas.  And the quality reconstructions.  And the discussion of diet, given its multiple prey remains.  The tome ends with several life restorations, of which my favorite is Riboli's.  See, that's why I don't write more glowing reviews- saying "x is good, y is good, etc." just gets repetitive and uninteresting.  Sort of like how ancient theologians said much more about the tortures of Hell than the joys of Heaven. ;)

As for negatives, Scipionyx and Orkoraptor are grouped together based on the supposed caudal pleurocoels of the former.  Yet those are so small they look more like nutrient foramina to me, which have caused similar confusion in Acrocanthosaurus and some therizinosauroids.  But Dal Sasso and Maganuco correctly discuss how the Senter matrix does not include relevent taxa and characters from Benson et al.'s study, and that the latter does not include enough coelurosaur information.  Also, I would disagree with a couple coding choices for ontogenetically variable characters in Scipionyx, which are discussed in Appendix 5.  But hey, what other papers even mention why they code ontogenetically variable characters in young specimens?  So really, even the few problems were elaborated on to the point that I can't count them against the authors.  The work is simply a masterpiece.

Anyone who wants to write a description of a theropod, look at what Dal Sasso and Maganuco created, and copy its format and scope to the best of your ability.

Dal Sasso and Maganuco, 2011. Scipionyx samniticus (Theropoda: Compsognathidae) from the Lower Cretaceous of Italy: Osteology, ontogenetic assessment, phylogeny, soft tissue anatomy, taphonomy, and palaeobiology. Memorie della Società Italiana di Scienze Naturali e del Museo Civico di Storia Naturale di Milano. 281 pp.

Saturday, August 6, 2011

Pneumatic disappointment

Benson et al. have a new paper out on theropod postcranial pneumaticity which I was extremely excited about, but the paper itself came as quite the disappointment.  Not the general conclusions, which I agree with, but the data collection.  The abstract reads "We review recent work on the significance of pneumaticity for understanding the biology of extinct ornithodirans, and present detailed new data on the proportion of the skeleton that was pneumatised in 131 non-avian theropods and Archaeopteryx."  With supposed pneumatic ilia in Piatnitzkysaurus and others, Buitreraptor's pneumatic furcula, Shixinggia's pneumatic femur and other recent records, examining 131 theropods for postcranial pneumaticity would be quite enlightening.  It's one of those features that is easily missed unless looked for, not often described, and rarely apparent in photos or illustrations.  This is especially true for coelurosaurs, since most of the reported unusual pneumatic bones have been from them.  All of the authors (Benson, Butler, Carrano and O'Connor) have done excellent detailed work before, so my expectations were high.

The meat of the paper is appendix S1, which contains all of the primary data.  It's available here for those who are interested.  The first problem is that it's all axial, so there goes my hope of getting some real info on how common appendicular pneumaticity is.  More disappointing though is that only 12 of the 99 coelurosaurs are coded from seeing real specimens.  The rest is all from the literature.  Not that I'm one to frown on using literature, since that's where much of my data comes from too.  And Benson et al. are usually good at determining which data can be coded from the literature and noting when information is from a figure, data matrix, etc..  But the information is basically what I could (and have) accumulated myself, with a few new additions thanks to personal communications with Balanoff and Brusatte, but then again I have my own sets of unpublished photos and AMNH observations with data not used by Benson et al..  I suppose I should be happy since this backs up my thesis that papers covering many taxa usually rely mostly on the literature and that my own upcoming paper explicitly describing codings in coelurosaurs is comparable in this measure to one written by four professional leaders in the field.  But this time I was hoping for something more, akin to what Nesbitt et al. (2009) did for theropod furculae.

Benson, Butler, Carrano and O'Connor, 2011. Air-filled postcranial bones in theropod dinosaurs: Physiological implications and the 'reptile'-bird transition. Biological Reviews. DOI: 10.1111/j.1469-185X.2011.00190.x

Tuesday, July 26, 2011

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.

Friday, July 15, 2011

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.

Tuesday, June 28, 2011

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.