Thursday, April 28, 2011

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. 

Tuesday, April 26, 2011

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.