Maxillary fenestra - a preview

Last time I described my in progress paper.  While one of the downsides to preparing something for publication is that I have to keep the results to myself until it's out, here's a preview of what the paper will be like, using the classic "maxillary fenestra" character.  So far I've only dealt with the characters and taxa of the first TWG matrix- Norell et al., 2001, NEA01 below).  I list the improved version of the character, the old version, include comments on its original use and other issues, then list the distribution with explicit references (to two specimens if possible).  Note while many of the codings can be backed up by personal observation, the literature references allow other workers to check even without access to the specimens.  Entries with asterisks are those differing from Norell et al.'s codings, which are elaborated upon and figured when a coding is changed to another (unless the original coding was "?").  This makes coding differences explicit and transparent, and will facilitate resolution.

4. Maxilla - lateral surface of antorbital fossa anterior to antorbital fenestra - solid (0); with maxillary fenestra entering maxillary antrum (1).

=4 in NEA01. Pronounced, round accessory antorbital fenestra absent (0) or present (1).

Comments- An extremely commonly used character in theropod analyses, Gauthier first (1984) used it to distinguish tetanurines then included it in a matrix for that purpose in 1986 (character 37).  Note the medial wall of the maxillary antrum may not be fenestrated, leading to the appearance of a maxillary fossa instead of a fenestra as in Byronosaurus (IGM 100/983; Makovicky et al., 2003- fig. 7).  The condition in oviraptorids is interpreted here differently than in most sources.  The basal oviraptorosaur Incisivosaurus shows a large fenestra at the anterior rim of the antorbital fossa and a smaller fenestra posterodorsal to it.  As these match the position of the promaxillary and maxillary fenestrae (respectively) in dromaeosaurids, they are homologized here.  Oviraptorids have the same arrangement of fenestrae, but their promaxillary fenestra is enlarged and maxillary fenestra highly reduced, as exemplified by Citipati.  

Something I threw together to approximate a figure I want in the final paper.  Saurornitholestes maxilla RTMP 94.12.844 (left), Incisivosaurus skull IVPP V13326 (center) and Citipati skull IGM 100/978 (right) showing proposed homology of promaxillary (red) and maxillary (blue) fenestrae.  Incisivosaurus from Balanoff et al. (2009), Citipati from Norell et al. (2002).

0- *Pelecanimimus LH 7777 (Perez-Moreno et al., 1994- fig. 2).  Only one accessory fenestra is reported, which has usually been identified as a maxillary fenestra.  However, its low position at the ventral border of the antorbital fossa matches ornithomimosaur promaxillary fenestrae and it is here identified as such.

Erlikosaurus IGM 100/111 (Clark et al., 1994- figs. 1 and 2). Note that the antorbital fossa wall is incomplete, but any fenestra would have to be positioned more ventrally than in other taxa if it was in the now broken area.

Chirostenotes ROM 43250 (Sues, 1997- fig. 1).  While there are two fossae in the antorbital fossa, both are anterior to the maxillary antrum, which has a solid lateral wall.

*Conchoraptor ZPAL MgD-I/95 (Elzanowski, 1999- fig. 2).  Labeled maxillary foramen is probably the promaxillary as noted above.

0+1- *IGM 100/42.  Present on the left side, but not the right based on photos.  Note Barsbold et al. (1990- fig. 10.1) incorrectly illustrate the area.

1- Sinraptor IVPP V10600 (Currie and Zhao, 1994- fig. 4 as pneumatic opening 8, following Witmer, 1997- 42).

Allosaurus AMNH 600 (Osborn, 1903- fig. 1), USNM 4734 (Gilmore, 1920- fig. 12).

Gorgosaurus CMN 2120 (Lambe, 1917- fig. 8), RTMP 83.35.100 (Witmer, 1997- fig. 30).

Tyrannosaurus AMNH 973 (Osborn, 1912- fig. 22), FMNH PR2081 (Brochu, 2003- fig. 8).

Ornitholestes AMNH 619 (Osborn, 1916- fig. 1).

*Harpymimus IGM 100/29 (Kobayashi and Barsbold, 2005a- 100).

Garudimimus IGM 100/13 (Kobayashi and Barsbold, 2005b- fig. 2).  The authors' identifications are switched, as ornithomimosaurs' ventral fenestra enters the promaxillary recess (Tahara and Larsson, 2011- 130).

*Gallimimus ZPAL MgD-I/1 (Osmolska et al., 1972- pl. 30).  While Norell et al. (2001) coded this differently, the plate seems to show promaxillary and maxillary fenestrae separated by a horizontal bar as in other ornithomimosaurs.  Kobayashi (2004) codes this as polymorphic in his version of the TWG matrix, perhaps indicating some specimens differ from ZPAL MgD-I/1.

Struthiomimus RTMP 90.26.1 (Sereno, 2001- fig. 13).

Caudipteryx BPM 001 (Zhou et al., 2000- pl. 3), NGMC 97-9-A (Ji et al., 1998- fig. 6).

*Rinchenia IGM 100/32A.

Sinornithoides IVPP V9612 (Currie and Dong, 2001- 1754).

Saurornithoides AMNH 6516 (Norell et al., 2009- fig. 3).

Zanabazar IGM 100/1 (Norell et al., 2009- fig. 22).

Byronosaurus IGM 100/974 (Bever and Norell, 2009- fig. 7), IGM 100/983 (Makovicky et al., 2003- fig. 3).

Troodon CMN 12392 (Currie, 1985- fig. 2), MOR 246-11 (Varricchio et al., 2002- 566).

Sinornithosaurus IVPP V12811 (Xu and Wu, 2001- fig. 2).

*Saurornitholestes RTMP 94.12.844 (Currie and Varricchio, 2004- fig. 4.2).

Tsaagan IGM 100/1015 (Norell et al., 2006- fig. 3).

Velociraptor AMNH 6515 (Sues, 1977- fig. 1), IGM 100/25 (Barsbold and Osmolska, 1999- fig. 1).

Deinonychus YPM 5232 (Ostrom, 1969- fig. 6).

Achillobator FR.MNUFR-15 (Perle et al., 1999- fig. 2).

Archaeopteryx JM SoS 2257 (Paul, 2002- pl. 7), WDC-CSG-100 (Mayr et al., 2007- fig. 5).

*Confuciusornis GMV-2130 (Chiappe et al., 1999- fig. 15), GMV-2131 (Chiappe et al., 1999- fig. 16).  While Norell et al. (2001) scored this feature as absent, the single accessory fenestra is here identified as a maxillary fenestra due to its posterior placement and the lack of a dorsal maxillary process which could contain a promaxillary recess.

?- Shuvuuia.  Both Chiappe et al. (2002- 92, fig. 4.3) and Sereno (2001- fig. 12) identified maxillary fenestrae in IGM 100/977.  However, the right maxillary fenestra in Chiappe et al.'s figure 4.3 is located far anterior to the left, and Sereno's figure 10 shows it is a break in the maxilla anterior to the antorbital fenestra.  Sereno also places the maxillary fenestra anteriorly, and his reconstruction differs from the material in having a defined dorsal edge to an antorbital fossa anterior to the antorbital fenestra.  While there at first glance does appear to be a well defined ventral edge, this is more probably caused by dorsoventral crushing which ventromedially displaced the portion of the maxilla anterior to the fenestra.  This is confirmed by IGM 100/1001 (Chiappe et al., 2002- fig. 4.5), which shows no fossa anterior to the antorbital fenestra.  The supposed left maxillary fenestra of Chiappe et al. is defined posteriorly by an anteriorly curved structure with a flared base, which does not contact the maxilla dorsally.  This is congruent with a palatine, but not part of the maxilla.  As Chiappe et al. (2002- 92) note, no specimen preserves a medial antorbital fossa wall, so the presence of a maxillary fenestra is unknown.

*Oviraptor (coded 1 by Norell et al., 2001).  Norell et al. coded this based on what is here identified as the promaxillary fenestra.  While there is a hole in the proper position for a maxillary fenestra in the left maxilla (AMNH 6517, Clark et al., 2002- fig. 11), numerous other holes are also present which are caused by damage.

"Ingenia" (coded 0 by Lu, 2004).  As Lu identifies the promaxillary fenestra of oviraptorids as a maxillary fenestra, his statement "Ingenia" lacks the opening is here applied to the promaxillary fenestra. 

First publication submitted, second in progress

And it's been a while again.  Why, you ask?  One reason is two weeks ago, I finally got my first paper submitted with David Marjanovic as coauthor.  Unlike blog posts, manuscripts require a ton of double-checking and tweaking, so that took quite a while.  Now for the peer review process...

And now that my first paper is in the system, I've been working on my second.  This one is a detailed reanalysis of the Theropod Working Group matrix.  Back on the DML I once praised invertebrate zoologist Ronald Jenner for his paper on how flawed current cladistic practices are.  Unfortunately, as you would have gathered from my posts, things have only gotten worse since then.  Jenner notes "Rather than representing occasional lapses of judgement, most of the identified errors are symptomatic of a generally cavalier attitude towards character study. A major aim of future cladistic analyses of the Metazoa must therefore be the correction of the many errors through a more detailed and explicit approach to character study."  And "It is a striking observation that none of the recent cladistic studies of the Metazoa comprehensively support all data matrix entries with source citations."  These are both just as true for theropod analyses.

I figure what better place to start than the TWG matrix?  It's accurate in general, uses species-level OTUs, covers a wide and controversial swath of taxa, and most importantly is used by the majority of coelurosaur workers when they describe a new taxon.  Over thirty papers have used variants, including over 120 taxa.  The goal is not to make a new analysis, since that's a huge long-term project.  Instead, the TWG characters (including those from all derivative analyses) will be discussed and refined, but kept as close to their original intent as possible.  States will be explicitly and quantitatively defined, and codings will be defended with references to exact specimens or literature.  The resulting trees will then be discussed with an emphasis on how parsimonious various alternative topologies are, and how much of the proposed evidence has been incorporated into the dataset.

This way future workers will have a better dataset to plug their taxa into, and any coding disagreements can be more easily resolved.  It will also give us a better idea of the current state of coelurosaur phylogenetics and provide suggestions for which characters should be added in future modifications to further our understanding. 

Eodromaeus thoughts

I just added Eodromaeus to the Database and noted a few things.

- PVSJ 563 was listed as a paratype, but this is a typo (Sereno, pers. comm.).

- Eodromaeus specimens were thought to be Eoraptor until 2000, but Sereno (pers. comm.) confirms there are indeed several specimens besides the holotype correctly referred to Eoraptor that await description.

- Several of Eodromaeus' listed autapomorphies are shared with Herrerasaurus, such as the ventrally convex maxillary alveolar margin (more poorly developed in Sanjuansaurus), large distal carpal 5 overlapping distal carpal 4 with a posteroventral heel (note Sereno misidentified carpal 5 as 4 in 1993- Ezcurra, 2010), and pubic apron with sinuous lateral margin (in Sanjuansaurus too, but not developed much in Staurikosaurus).  Of course Eodromaeus specimens are adult so it's not a synonym, but these might be saurischian/theropod plesiomorphies.

- The supposed small herrerasaurid forelimb MACN-PV 18.649a mentioned by Ezcurra and Novas (2007, 2008) may be referrable to Eodromaeus.  It was referred to Herrerasauridae due to- enlarged distal carpal V; manual phalanx I-1 longer than metacarpal I; strongly curved manual unguals; metacarpals IV-V ventral to the others.  All of these are present in Eodromaeus as well.  Ezcurra (2010) states that it differs from Herrerasaurus in having manual phalanx II-1 with a conspicuous longitudinal ridge on its proximolateral border.  Eodromaeus does have a marked proximolateral projection on II-1, but whether this is a ridge or not is not described.  Ezcurra's (2010) matrix could be checked for further information on the forelimb's morphology, which could then be compared to Eodromaeus.

- In Martinez et al.'s (2011) cladogram, Tawa is the basalmost coelophysoid.  In this case, Avepoda contains Tawa and other coelophysoids under ACCTRAN character optimization, but excludes Coelophysoidea under DELTRAN optimization.  Gotta love apomorphy-based definitions...

References- Ezcurra and Novas, 2007. New dinosaur remains (Saurischia: Herrerasauridae) from the Ischigualasto Formation (Carnian) of NW Argentina. Ameghiniana. 44, 17R.

Ezcurra and Novas, 2008. A review of the dinosaur diversity of the Ischigualasto Formation (Carnian, NW Argentina): Insights on early dinosaur evolution. in Langer, Bittencourt and Castro (eds.). Boletim de Resumos, VI Simposio Brasileiro de Paleontologia de Vertebrados, Paleontologia, Edicao especial. Universidad de Sao Pablo: Ribeirao Preto. 88-89.

Ezcurra, 2010. A new early dinosaur (Saurischia: Sauropodomorpha) from the Late Triassic of Argentina: A reassessment of dinosaur origin and phylogeny. Journal of Systematic Palaeontology. 8(3), 371-425.

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

Halfway back to theropods with sauropodomorph Eoraptor

When Eodromaeus was described, much was said about the analysis placing Eoraptor in Sauropodomorpha.  What nobody did was elaborate on why Martinez et al. (2011) placed it there and how strong the evidence is.  So I made a NEXUS file from Martinez et al.'s matrix to extract the character evidence.

The first thing to note is that the characters listed as multistate don't correspond to those with more than two states in the matrix, which also means the characters said to be ordered aren't those that should be.  So I ordered 51, 69, 70, 76 (though nothing is coded with state 2, making ordering useless), 102 and 117.  In addition, the definitions of some multistate characters have problems.  "Premaxillary tooth number: 4 (0); 3 (1); 5 or 6 (2)" should ideally be ordered, but states 0 and 1 need to be switched so that the intermediate state is in the middle.  "Maxillary/dentary crowns, shape: recurved (0); subtriangular (1); lanceolate (2)" artificially separates the morphology of sauropodomorph and ornithischian teeth, which are after all both triangular and lanceolate in both clades.  The current coding doesn't let the reduced curvature group them together.  "Ilium, preacetabular process, shape: tab-shaped (0); strap-shaped (1); subtriangular (2); semicircular (3)" is problematic since the next character deals with preacetabular length, and the only difference between "strap-shaped" and the other choices is length.  "Ilium, bevis[sic] fossa, shape and orientation: broad laterally-open depression (0); shallow groove or absent (1); arched ventrally-opening ovate or parallel-sided depression (2); arched ventrally-opening posteriorly-expanding to a width approximately 50% of its length (3)" combines a lot of independant variables.  There's depth (already partly covered by another character), orientation, proportional width and posterior expansion.  Oddly, lagerpetonids and Marasuchus are coded inapplicable, despite their correct state of "absent" being covered by state 1.  So given those issues, I ran the matrix and found similar results to Martinez et al.- 3 MPTs of 247 steps each, CI of .615 compared to his 3 MPTs 246 steps each with a CI of .618.  The topology is identical.  If you don't constrain the outgroups to be in the order (hypothetical(Lagerpetonidae(Marasuchus(Silesauridae,ingroup)))), then you get a lot more trees, sometimes with non-dinosauriform sauropodomorphs, and/or ornithischian silesaurids and/or Marasuchus, presumably because characters supporting more basal nodes weren't included.

So that's the matrix, but what about Eoraptor's sauropodomorph position?  It's supported by the following characters-

2. external naris size large, expanded narial margin.
The plesiomorphic state specifies a tapered snout, but some taxa coded 0 like Herrerasaurus, Eodromaeus and Ceratosaurus certainly don't have tapered snouts.  If you measure Eoraptor's naris compared to its skull length, then yes it looks large.  But that's because it has a short snout.  If you measure naris length compared to some more neutral value such as skull height at the orbit, its naris is actually smaller than any other taxon in the matrix.  Also, Panphagia does not preserve a premaxilla, so cannot be coded, contra the matrix.

19. nasal posterolateral process present.
This is actually unknown in silesaurids and Tawa (Nesbitt et al., 2009), though Panphagia has it (Martinez and Alcober, 2009).  It is also present in Coelophysis (Downs, 2000), Megapnosaurus (Downs, 2000) and "M." kayentakatae (Tykoski, 1998).

24. squamosal, ventral process a slender prong 3 or more times basal width.
This is actually present in Silesaurus (Dzik and Sulej, 2007), Lesothosaurus (Sereno, 1991), Saturnalia (Langer and Benton, 2006), "M." kayentakatae (Tykoski, 1998) and Coelophysis (Colbert, 1989). It is polymorphic in Sauropodiformes because one of Martinez et al.'s two examplars (Massospondylus- Sues et al., 2004) lacks it.  The condition in Megapnosaurus is unknown (Raath, 1977).

45. dentary tooth 1 inset.
Oddly, silesaurids are coded as inapplicable, even though this is one of their distinctive characters.  If anything ornithischians should be coded unknown, in case their predentary is homologous to the anterior dentary. 

43. maxillary and dentary crowns lanceolate.
As noted above, there's no difference between Martinez et al.'s triangular and lanceolate shapes, as can be seen by the near identical shape of the supposed triangular tooth of Silesaurus (Dzik, 2003 fig. 5H) and the supposed lanceolate tooth of Panphagia (Martinez and Alcober, 2006 fig. 5B). 

69. deltopectoral crest 45% or more of humeral length.
Eoraptor's crest has previously been reported to be 35% of humeral length (Langer and Benton, 2006).  Note that in this and other cases where I claim Martinez et al.'s codings for Eoraptor are incorrect, it's with the caveat that they are redescribing the taxon and may be shown to be right with the publication of their monograph.  Genasaurs' should be polymorphic, since Scutellosaurus (Colbert, 1964) has a short crest.  Ceratosaurus also has a short crest (Galton, 1982).

76. manus phalanx I-1, rotation of axis through distal condyles 45° ventromedially.
Martinez et al.'s own figure only labels Eoraptor's torsion as 35 degrees. 

79. preacetabular process subtriangular.
As noted above "strap-shaped" should be deleted and the taxa coded to reflect their distal shape, not their length.  In that case, Heterodontosaurus' is tab-shaped (Santa Luca, 1980), Lesothosaurus' is broken (Thulborn, 1972; Sereno, 1991) and Genasauria's is rounded (Colbert, 1964; Galton, 1974).  Panphagia's is also broken (Martinez and Alcober, 2009), while Saturnalia's is tab-shaped (Langer, 2003).  Staurikosaurus' is rounded (Bittencourt and Kellner, 2009).  Among theropods, Megapnosaurus' is tab-shaped (Raath, 1990), "M." kayentakatae's is unpreserved (Tykoski, 1998), Dilophosaurus' is tab-shaped (Tykoski, 2005) and Ceratosaurus' is unpreserved (Gilnmore, 1920). 

81. preacetabular process, attachment scar present.
Also present in Marasuchus (Novas, 1996), Saturnalia (Langer, 2003), Herrerasaurus (Novas, 1993), Staurikosaurus (Bittencourt and Kellner, 2009).  Absent in Sauropodiformes (Cooper, 1981; Huene, 1926).  Unknown in "M." kayentakatae (Tykoski, 1998) and Ceratosaurus (Gilmore, 1920).

90. ischial mid shaft cross-sectional shape subtriangular.
This is absent in Panphagia (Martinez and Alcober, 2009).  It is also present in Lesothosaurus (Thulborn, 1972), Herrerasaurus (Langer, 2003) and "M." kayentakatae (Tykoski, 1998). 

122. astragalus fibular facet, primary orientation lateral.
The condition in Lagerpeton (Sereno and Arcucci, 1993) and Lesothosaurus (Thulborn, 1972) is unknown.  Genasauria (Scutellosaurus- Langer and Benton, 2006) and Herrerasaurus (Langer and Benton, 2006) have a laterally oriented facet.  Megapnosaurus (Langer and Benton, 2006) and "M." kayentakatae (Tykoski, 2005) lack it. 

125. astragalus anteromedial corner shape (dorsal view)- anteriorly projecting at least 25% width of the medial side of the astragalus.
Martinez and Alcober (2009) state this is absent in Eoraptor.  It's present in Megapnosaurus (Langer and Benton, 2006), "M." kayentakatae (Tykoski, 2005) and Dilophosaurus (Tykosaki, 2005).  The condition in Lesothosaurus (Thulborn, 1972) is unknown.  

Additionally, Martinez et al. found Eoraptor to be closer to Panphagia and Saturnalia than sauropodiforms based on-

83. ventral acetabular flange of ilium present.
Lesothosaurus lacks a flange (Sereno, 1991).

88. brevis fossa an arched ventrally-opening ovate or parallel-sided depression.
This was discussed above as being a composite character and miscoded in the outgroup (also in Staurikosaurus- Bittencourt and Kellner, 2009).  Regardless, Eodromaeus has the same state as Eoraptor, so the combination is not unexpected in a basal theropod.

95. ischial antitrochanter, anteroposterior length less than adjacent length of the articular surface for the ilium (also in coelophysoids).
This is actually absent in Panphagia (Martinez and Alcober, 2009), Saturnalia (Langer, 2003), Coelophysis (Padian, 1986), Megapnosaurus (Raath, 1990), "M." kayentakatae (Tykoski, 2005) and Dilophosaurus (Tykoski, 2005).  This is also present in Lagerpeton (Sereno and Arcucci, 1993, coded inapplicable by Martinez et al.), Heterodontosaurus (Santa Luca, 1980), Herrerasaurus (Novas, 1993) and Staurikosaurus (Bittencourt and Kellner, 2009).  Makes me wonder if Martinez et al. reversed the states on accident.  Silesaurus (Dzik, 2003), Lesothosaurus (Sereno, 1991), Genasauria (Colbert, 1964) and Tawa (Nesbitt et al., 2009) do not seem to have significant ischial antitrochanters.

When all of the above are changed in the matrix, Eoraptor is the basalmost theropod.  An additional question to ask is how many previously suggested theropod characters of Eoraptor are in the matrix?  In particular, how many of the characters suggested to link it with Tawa+Avepoda are included?  As listed in the Database, the previously suggested characters are as follows.  Those included in Martinez et al.'s matrix are in bold.

Tykoski (2005)- subnarial process of premaxilla narrow and rod-like; maxilla anterodorsally concave; nasal contacts antorbital fossa; lacrimal inverted L-shape; lacrimal at least equal to orbital height and reaches orbit's ventral rim; antorbital fossa exposure on lacrimal large, with triangular fossa on ventral process; vertebra 25 (dorsosacral) incorporated into sacrum (not actually present in Eoraptor, contra Tykoski); humerus twisted; metacarpal I distal condyles strongly asymmetrical; preacetabular process thin and blade-like; postacetabular process longer than acetabulum (not actually present in Eoraptor- Ezcurra, 2010); pubic fenestra (incorrectly coded absent in Eoraptor); distal ischium <3 times minimum width of shaft; subrectangular distal tibia with posterolateral extension (incorrectly coded absent in Eoraptor).
Ezcurra (2006)- lateral surface of premaxillary body pierced by a single neurovascular foramina above the second premaxillary tooth; maxillary antorbital fossa rostral to internal antorbital fenestra broad and rostrocaudally well extended; medial wall of the antorbital fossa extends through the entire ventral border of the internal antorbital fenestra as a very narrow lamina; lateral lamina of bone of the lacrimal with no interruption of the lacrimal antorbital fossa and restricted to the caudal margin of the ventral ramus along its dorsoventral extension; rostral process of jugal excluded from the internal antorbital fenestra, bluntly squared rostrally; ventral process of the squamosal length forms more than half of the caudal border of the infratemporal fenestra (absent in Eoraptor); humerus length subequal or shorter than 0.6 of the length of the femur; extensor pits on the dorsal surface of the distal end of metacarpals deep, well developed; shaft of metacarpal IV in relation to that of metacarpals I-III significantly narrower (incorrectly coded absent in Eoraptor); metacarpal IV and fourth digit: proximal portion set lateral to Mc III (idem Mc V) and with only one or lacking phalanges; supraacetabular crest and lateroventral border of the postacetabular process (lateral brevis shelf) continuous as a weakly developed ridge; cnemial crest on proximal tibia moderately developed; caudal cleft between medial part of the proximal end of the tibia and fibular condyle present.
Nesbitt et al. (2009)- premaxilla-maxilla, subnarial gap between the elements (absent in Eoraptor); nasal possesses a posterolateral process that envelops part of the anterior ramus of the lacrimal; ilium, ischiadic peduncle orientation well expanded posteriorly to the anterior margin of the postacetabular embayment.
Ezcurra (2010)- posterior part of premaxillary alveolar margin edentelous, resulting in an interruption of the upper tooth row (absent in Eoraptor); anterior margin of maxillary antorbital fossa squared; dorsoventrally compressed ridge on lateral surface of maxilla, forming the ventral border of the antorbital fossa (alveolar ridge) (incorrectly coded absent in Eoraptor); orientation of the lacrimal orbital margin erect and close to vertical; supraacetabular crest of ilium flares lateroventrally to form a hood-like overhang that hides anterodorsal half of acetabulum in lateral view (coded absent in Eoraptor); well developed brevis fossa with sharp margins on the ventral surface of the postacetabular process of the ilium present, being directly ventrally facing; well developed tibiofibular crest on distal femur.

Of course some of these are only supportive of a theropodan Eoraptor given the proper outgroup/ingroup arrangement and some are absent in Eoraptor, showing their own matrices have problems.  But of the 31 characters present (as far as I can tell) in Eoraptor, only 11 are included, and of those 11 at least 4 are incorrectly coded as absent.  Enforcing a placement for Eoraptor closer to avepods than herrerasaurids in this modified matrix is 13 steps longer, but the you have to wonder how many of the proposed characters for placing Eoraptor outside Herrerasaurus+Avepoda were included and how correctly they are coded.  It's all outside the scope of this post.

In the end, I don't think the evidence for placing Eoraptor in Sauropodomorpha is strong.  Of the 12 characters, 4 seem absent in Eoraptor, 2-3 of the others seem present basally in avepods, 3 of the others are present in Herrerasaurus, and all have high homoplasy.  Even the toothless dentary tip and lanceolate teeth are complicated by their presence in silesaurids and/or ornithischians.  With so much homoplasy among basal dinosauromorphs, it's necessary to include fragmentary but important taxa like Lewisuchus, Guaibasaurus, Chindesaurus and Pisanosaurus. Only then and when we incorporate all suggested conflicting character data can we hope to have meaningful results.

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

The Sauropodomorph Database is online!

Go check it out, in its bare bones form.  As for me, I'm getting some sleep...

The Sauropodomorph Database Approacheth- "Yibinosaurus" and "Sugiyamasaurus"

The Sauropodomorph Database is almost ready to debut, but first here's a couple more entries to illustrate why I'm making the website.  The first is "Yibinosaurus", whose usual online information is limited to what Olshevsky wrote on the DML in 2001.  The other is "Sugiyamasaurus", which no one seems to have connected to Fukuititan yet. 

"Yibinosaurus" Ouyang vide anonymous, 2001
"Y. zhoui" Ouyang vide anonymous, 2001
Toarcian, Early Jurassic
Dongyuemiao Member of Ziliujing Formation, Sichuan, China
Material- (Chongqing Museum of Natural History coll.) specimen including dorsal vertebrae
Comments- This name originally appeared in a guidebook, with the taxon stated to be under study by Ouyang. Ouyang (2003) later mentioned it in his thesis as a new genus, which he places in an eponymous subfamily within Vulcanodontidae. As he also includes the more basal Gongxianosaurus in Vulcanodontidae, Ouyang's conception of the family may be more of a grade. Ouyang further notes the anterior dorsal neural spines are transversely expanded, which he believes indicates a possible relationship to taxa with bifurcated spines like Datousaurus. As Ouyang states "Yibinosaurus" is from the same locality as Gongxianosaurus, the dorsal vertebrae, 51 articulated caudal vertebrae, scapulae and ilium mentioned by Luo and Wang (1999) as Gongxianosaurus sp. nov. may be the "Yibinosaurus" material.
References- Luo and Wang, 1999. New discovery on dinosaur fossils from Early Jurassic, Sichuan, China. Chinese Science Bulletin. 44(23), 2182-2188.
Anonymous, 2001. Dinosaur Fossils from Chongqing Natural History Museum.
Ouyang, 2003. Skeletal characteristics of Mamenchisaurus youngi and the systematics of mamenchisuarids. PhD thesis. Chengdu University of Technology. 176 pp.

Titanosauriform tooth (FPDM coll.) from the Kitadani Formation, probably Fukuititan and/or "Sugiyamasaurus".  Scale = 10 mm.  After Goto et al. (2002).

Fukuititan Azuma and Shibata, 2010
?= "Sugiyamasaurus" Lambert, 1990
F. nipponensis Azuma and Shibata, 2010
Barremian, Early Cretaceous
Kitadani Formation of the Akaiwa Subgroup of the Tetori Group, Japan
Holotype- (FPDM V8468) three teeth, incomplete cervical neural arch, three distal caudal vertebrae (30 mm), proximal scapula, incomplete humeri (~910 mm), incomplete radii (~600 mm), metacarpal IV (295 mm), incomplete ischia, partial femur (~1.14 m), partial tibia, fibula, pedal phalanx (130 mm), fragments
Referred- ?(Sugiyama-ryu; "Sugiyamasaurus") three teeth (Azuma, 1991)
? five teeth (Azuma, 1991)
?(FPDM 1080417) tooth (Goto et al., 2002)
?(FPDM 1080417-A) tooth (Goto et al., 2002)
?(FPDM 1080757) tooth (Goto et al., 2002)
?(FPDM 1080920) tooth (Goto et al., 2002)
?(FPDM 1080942) tooth (Goto et al., 2002)
?(FPDM 1080944) tooth (Goto et al., 2002)
Diagnosis- (after Azuma and Shibata, 2010) tooth crowns asymmetrical and elongated with weak or absent labial groove and no lingual concavity; stalk-like cervical epipophyses; humerus proximal width 32% of length; metacarpal IV 48% of radial length; ischia slightly expanded distally.
Comments- The holotype was discovered in 2007 and described as a basal titanosauriform, though it has yet to be included in an analysis.
Teeth were first discovered from the quarry in 1989. Three teeth were informally called "Sugiyama-ryu", as found in Azuma (1991) and referred to Camarasauridae by this author and Dong et al. (1990). Lambert (1990) inappropriately made it into a genus name, listing it as "Sugiyamasaurus" in a childrens' book. Azuma (1991) lists five additional sauropod teeth as family indet. A and B, but he later (2003) placed all the teeth in Brachiosauridae. Kobayashi et al. (2006) referred the specimens to Titanosauriformes indet. based on near identical morphology to teeth from the Kuwajima Formation. Goto et al. (2002) illustrate a tooth. As the "Sugiyamasaurus" teeth are generally similar to Fukuititan's in morphology (D-shaped section; wrinkled enamel; parallel mesial and distal edges- Kobayashi et al., 2006) and found in the same quarry, they may belong to the same taxon. They should be examined for Fukuititan's supposed dental autapomorphies, which should be checked for positional variation and compared to other taxa as well.
References- Dong, Hasegawa and Azuma, 1990. The Age of Dinosaurs in Japan and China. Fukui, Japan: Fukui Prefectural Museum. 65 pp.
Lambert, 1990. The Dinosaur Data Book. New York: Avon Books, 66. ISBN 0-380-75896-3.
Azuma, 1991. Early Cretaceous Dinosaur Fauna from the Tetori Group, central Japan. Research on Dinosaurs from the Tetori Group (1). Professor S. Miura Memorial Volume, 55-69.
Azuma, Kawagoshi and Miyagawa, 1995. Dinosaurs of the Tetori Group in Japan. Fukui Prefectural Museum. 158 pp.
Azuma and Tomida, 1995. Early Cretaceous dinosaur fauna of the Tetori Group in Japan. in Sun and Wang (eds.). Sixth Symposium on Mesozoic Terrestrial Ecosystems and Biota, Short Papers. China Ocean Press, Beijing. 125-131.
Goto, Yabe and Sano, 2002. The research report of the Dinosaur Fossil Exploratory Excavation held by Fukui Prefecture in 2001. Memoir of the Fukui Prefectural Dinosaur Museum. 1, 102-118.
Azuma, 2003. Early Cretaceous vertebrates from Katsuyama City, Fukui Prefecture, Japan. Memoir of the Fukui Prefectural Dinosaur Museum. 2, 17-21.
Kobayashi, Manabe, Ikegami, Tomida and Hayakawa, 2006. Dinosaurs from Japan. in Lu, Kobayashi, Huang and Lee (eds.). Papers from the 2005 Heyuan International Dinosaur Symposium. Geological Publishing House, Beijing. 87-102.
Shibata and Goto, 2008. Report of the 3rd Dinosaur Excavation Project in Katsuyama, Fukui, 2007. Memoir of the Fukui Prefectural Dinosaur Museum. 7, 109-116.
Azuma and Shibata, 2010. Fukuititan nipponensis, a new titanosauriform sauropod from the Early Cretaceous Tetori Group of Fukui Prefecture, Japan. Acta Geologica Sinica. 84(3), 454-462.

Sauropodomorph phylogenetic analyses - The list

The first step to starting your own analysis is compiling the data from past analyses.  Here's all of the quantitative cladistic sauropodomorph analyses I know of, in chronological order, with the subsequent modifications listed indented afterwards.  Ones I don't have copies of are in bold.  If anyone has them, I'd be thankful for a pdf of course.  A 'u' in front of the entry means the supporting matrix was not presented.  Also, if there are any I missed, I'd love to know.

uYou, 1990 (SVP abstract)

            You, 1993 (Diplodocus thesis)

Russell and Zheng, 1993 (Mamenchisaurus sinocanadorum)

Upchurch, 1993 (Sauropoda phylo thesis)

            uUpchurch, 1995 (Sauropoda phylo)

Calvo and Salgado, 1995 (Limaysaurus)

uGauffre, 1995 (SVP abstract)

            Gauffre, 1996 (new riojasaurid thesis)

Zheng, 1996 (Shunosaurus and Camarasaurus thesis)

Salgado et al., 1997 (titanosaur postcrania)

            uKellner and Azevedo, 1999 (Gondwanatitan)

Upchurch, 1998 (Sauropoda phylo)

            Upchurch, 1999 (Nemegtosauridae)

            Upchurch and Martin, 2002 (Cetiosaurus)

            Alifanov and Averianov, 2003 (Ferganasaurus)

            Sander et al., 2006 (Europasaurus)

uWilson and Sereno, 1994 (SVP abstract)

            Wilson and Sereno, 1998 (Sauropoda phylo)

            Sereno, 1999 (Sauropoda)

            Upchurch and Martin, 2002 (Cetiosaurus)

Sanz et al., 1999 (Lirainosaurus)

Sereno, 1999 (Prosauropoda)

            Leal, 2001 (Unaysaurus thesis)

            Barrett et al., 2005 (Lufengosaurus)

            Barrett et al., 2007 (Yunnanosaurus)

Benton et al., 2000 (Thecodontosaurus)

Casanovas et al., 2001 (Losillasaurus)

Curry Rogers, 2001 (titanosaur thesis)

            Curry Rogers, 2005 (Titanosauria)
            Csiki et al., 2010 (Paludititan)

            Mannion, 2010 (Mongolosaurus)

Curry Rogers and Forster, 2001 (Rapetosaurus)

            O'Leary et al., 2004 (Mali titanosaur)

Smith et al., 2001 (Paralititan)

Hinic, 2002 (Massospondylus thesis)

Wilson, 2002 (sauropod phylo)

            Barco Rodriguez, 2003 (Galveosaurus thesis)

            Harris and Dodson, 2004 (Suuwassea)

            O'Leary et al., 2004 (Mali titanosaur)

            Rauhut et al., 2005 (Brachytrachelopan)

            Barco et al., 2006 (Galveosaurus)

            Ksepka and Norell, 2006 (Erketu)

            Rauhut, 2006 (Canadon Calcareo brachiosaurid)

            Remes, 2006 (Tornieria)

            Sander et al., 2006 (Europasaurus)

            You et al., 2006 (Huanghetitan)

            Lovelace et al., 2007 (Supersaurus)

            Lu et al., 2007 (Huanghetitan)

            Rose, 2007 (Paluxysaurus)

            Allain and Aquesbi, 2008 (Tazoudasaurus)

            Canudo et al., 2008 (Tastavinsaurus)

            Santucci, 2008 (Uberaba titanosaur)

            Hocknull et al., 2009 (Australian titanosaurs)

            Remes et al., 2009 (Spinophorosaurus)

            Royo-Torres et al., 2009 (Turiasaurus)

            Upchurch and Mannion, 2009 (Qingshan somphospondylan)

            Wilson and Upchurch, 2009 (Euhelopus)

            Carballido and Pol, 2010 (Amygdalodon)

            Chure et al., 2010 (Abydosaurus)
            Csiki et al., 2010 (Paludititan)

            Ksepka and Norell, 2010 (Erketu)

            Mannion, 2010 (Mongolosaurus)

            Suteethorn et al., 2010 (Phuwiangosaurus)
            Mateus et al., 2011 (Angolatitan)

            Zaher et al., 2011 (Tapuiasaurus)

Calvo and Gonzalez Riga, 2003 (Rinconsaurus)

Gonzalez Riga, 2003 (Mendozasaurus)

Yates, 2003 (Pantydraco)

            Leal et al., 2004 (Unaysaurus)

            Sues et al., 2004 (Massospondylus)

            Barrett et al., 2007 (Yunnanosaurus)

Yates and Kitching, 2003 (Antetonitrus)

            Yates, 2004 (Anchisaurus)

            uYates, 2004 (Gryponyx)

            Barrett et al., 2005 (Lufengosaurus)

            Fedak, 2006 (Nova Scotia massospondylid thesis)

            Fedak and Galton, 2007 (Anchisaurus)

            Kutty et al., 2007 (Indian taxa)

            Upchurch et al., 2007 (Chinshakiangosaurus)

            Lu et al., 2010 (Chuxiongosaurus)

Galton and Upchurch, 2004 (Dinosauria 2)

            Barrett et al., 2005 (Lufengosaurus)

            Royo-Torres et al., 2006 (Turiasaurus)

            Barrett et al., 2007 (Yunnanosaurus)

            Kutty et al., 2007 (Indian taxa)

            Upchurch et al., 2007 (Chinshakiangosaurus)

Salgado et al., 2004 (Limaysaurus)

Upchurch et al., 2004 (Apatosaurus)

Upchurch et al., 2004 (Dinosauria 2)

            Sander et al., 2006 (Europasaurus)

            Santucci, 2008 (Uberaba titanosaur)

            Upchurch and Mannion, 2009 (Qingshan somphospondylan)

            Wilson and Upchurch, 2009 (Euhelopus)
            Csiki et al., 2010 (Paludititan)

            Mannion, 2010 (Mongolosaurus)
            Mateus et al., 2011 (Angolatitan)

Gallina and Apesteguia, 2005 (Cathartesaura)

Harris, 2005 (Suuwassea thesis)

            Harris, 2006 (Suuwassea)

            Taylor and Naish, 2007 (Xenoposeidon)

            You et al., 2008 (Daxiatitan)

            Taylor, 2009 (Brachiosaurus)

            Mo et al., 2010 (Liubangosaurus)
            Taylor et al., 2011 (Brontomerus)

Bonaparte et al., 2006 (Ligabuesaurus)

Salgado et al., 2006 (Zapalasaurus)

Calvo et al., 2007 (Muyelensaurus)

            Calvo et al., 2007 (Futalognkosaurus)
            Csiki et al., 2010 (Paludititan)

            Filippi et al., 2011 (Narambuenatitan)

Sereno et al., 2007 (Nigersaurus)
            Fernandez-Baldor et al., 2011 (Demandasaurus)

Upchurch et al., 2007 (sauropodomorph phylo)

            Martinez, 2009 (Adeopapposaurus)

            Bandyopadhyay et al., 2010 (Barapasaurus)

            Sekiya, 2010 (Xixiposaurus)

            Sertich and Loewen, 2010 (Seitaad)

            Yates et al., 2010 (Aardonyx)

            Rowe et al., 2011 (Sarahsaurus)

Yates, 2007 (Eucnemesaurus)

            Smith and Pol, 2007 (Glacialisaurus)

            Yates, 2007 (Melanorosaurus)

            Ezcurra, 2010 (Chromogisaurus)

            Knoll, 2010 (Ignavusaurus)

            Sertich and Loewen, 2010 (Seitaad)

            Yates, 2010 (Anchisaurus)

            Yates et al., 2010 (Aardonyx)
            Pol et al., 2011 (Leonerasaurus)

            Rowe et al., 2011 (Sarahsaurus)

Lang, 2008 (cetiosaur thesis)

Gonzalez Riga et al., 2009 (Malarguesaurus)

            Hocknull et al., 2009 (Australian titanosaurs)

Carballido et al., 2011 (Chubutisaurus)

Gallina and Apesteguia, 2011 (Bonitasaura skull)

Whitlock, 2011 (Diplodocoidea)