A MORPHOLOGICAL MODEL AND CT ASSESSMENT …palaeo-electronica.org/2005_1/polcyn26/polcyn26.pdf · Palaeontologia Electronica Polcyn, Michael J., Jacobs, Louis L., and Haber, Annat,

Palaeontologia Electronica http://palaeo-electronica.org

Polcyn, Michael J., Jacobs, Louis L., and Haber, Annat, 2005. A Morphological Model and CT Assessment of the Skull of Pachyrhachis Problematicus (Squamata, Serpentes), A 98 Million Year Old Snake with Legs from the Middle East, Palaeontologia Electronica Vol. 8, Issue 1; 26A:24p, 2.9MB; http://palaeo-electronica.org/paleo/2005_1/polcyn26/issue1_05.htm

A MORPHOLOGICAL MODEL AND CT ASSESSMENT OF THE SKULL OF PACHYRHACHIS PROBLEMATICUS (SQUAMATA, SERPENTES),

A 98 MILLION YEAR OLD SNAKE WITH LEGSFROM THE MIDDLE EAST

Michael J. Polcyn, Louis L. Jacobs, and Annat Haber

ABSTRACT

Pachyrhachis problematicus is a snake with well-developed hind limbs knownfrom two specimens from the Cenomanian of the Middle East. One specimen has acomplete and articulated, albeit crushed skull. The second specimen has a disarticu-lated skull crushed beneath the body. Pachyrhachis has recently been at the center ofa debate on the origins and relationships of snakes, specifically whether Pachyrhachisis the sister taxon to all other snakes, or alternatively, a relatively advanced snakeallied with boids and pythonids. Workers using the same specimens arrived at differentinterpretations of the morphology underlying the alternative hypotheses. The mostcomplete skull was resin-embedded and acid-prepared for its original study nearlythree decades ago, rendering the dorsal surface difficult to view using optical tech-niques, and thus significantly hampering later studies. This study utilizes CT scanningand computer reconstruction to test conflicting interpretations of morphology and thusprovides a method to falsify alternative phylogenetic hypotheses. Pachyrhachis isfound to possess an inclined quadrate with a well-developed stylohyal process andlacking a suprastapedial process, no squamosal, and a single mental foramen. Theseparation of exoccipitals above the foramen magnum cannot be demonstrated. Thereis no jugal. Confirmed morphology best supports the phylogenetic hypothesis thatPachyrhachis is a basal macrostomatan snake. Limb retention in a basal macrostoma-tan snake implies that loss of hind limbs occurred multiple times within Serpentes.

Michael J. Polcyn. Department of Geological Sciences, Southern Methodist University, Dallas, Texas 75275, USA [email protected] L. Jacobs. Department of Geological Sciences, Southern Methodist University, Dallas, Texas 75275, USA [email protected] Haber. Department of Geological Sciences, Southern Methodist University, Dallas, Texas 75275, USA [email protected]

KEY WORDS: Cretaceous; Haasiophis; Israel; Macrostomata; Taphonomy

POLCYN, JACOBS, AND HABER: THE SKULL OF PACHYRACHIS

2

PE Article Number: 8.1.26Copyright: Society of Vertebrate Paleontology May 2005Submission: 13 October 2004. Acceptance: 7 April 2005

INTRODUCTION

The Cenomanian snake, Pachyrhachis prob-lematicus, is known from two specimens from lime-stone quarries near 'Ein Yabrud, in the West Bank,north of Jerusalem. One specimen has a completeand articulated, albeit crushed, skull (Haas 1979,1980a). In the second specimen, a disarticulatedskull is crushed below the ribcage (Haas 1980b).Phylogenetic analysis by Caldwell and Lee (1997)places Pachyrhachis as the basal member or sistertaxon of Serpentes. However, that phylogenetichypothesis was tested and falsified by Zaher(1998), who concluded that Pachyrhachis wasinstead a basal macrostomatan allied with boidsand pythonids. Disagreement regarding the phylo-genetic position of Pachyrhachis persisted (Leeand Caldwell 1998; Caldwell 1999, 2000; Zaherand Rieppel 1999b, 2000; Rieppel and Zaher2000a, 2000b), culminating in a seemingly intracta-ble impasse (Rieppel and Kearney 2001). On thebasis of a data set developed independently, Tch-ernov et al. (2000) found Pachyrhachis and a sec-ond taxon from ‘Ein Yabrud, Haasiophis, to bebasal macrostomatans (see also Rieppel et al.2003; Zaher and Rieppel 2002; Lee and Scanlon2002a, 2002b). The same specimens and generalobservational techniques used by all workers led toconflicting interpretations of morphology. Cladisticanalyses based on those interpretations subse-quently yielded different phylogenetic hypotheses.

The source of differing interpretations of mor-phology derives from HUJ [The Hebrew Universityof Jerusalem]-PAL 3659. This specimen is difficultto study due to a number of taphonomic factors,further complicated by preparation techniques.George Haas (1979) of the Hebrew University ofJerusalem originally described Pachyrhachis usingonly HUJ-PAL 3659, which includes the crushedbut beautifully articulated skull originally preservedon a limestone flag. After describing the dorsal sur-face of the skull (Haas 1979; see also Haas 1980a,1980b), the specimen was embedded in resin andthe ventral surface was acid prepared anddescribed (Haas 1980a). Subsequent to Haas’soriginal description, the dorsal surface could onlybe viewed through the embedding resin. Addition-ally, the resin was covered with glass, which atsome point was broken, further obscuring the view.

The glass has since been removed, but the resinremains. The viability of optical techniques forexamination of the morphology of HUJ-PAL 3659 iscompromised due to taphonomic factors includingcrushing, breakage, overlapping elements, dis-placement during preservation, matrix residue frommechanical preparation on the dorsal surface ofthe skull, and to subsequent resin embedding ofthe dorsal surface for acid preparation of the ven-tral surface (Figure 1).

Figure 2 shows three renderings of the dorsalsurface of the articulated skull of Pachyrhachis as

Figure 1. Pachyrhachis problematicus (HUJ-PAL 3659)images demonstrating the state of preservation andconservation at the time of restudy by Caldwell and Lee(1997) and Rieppel and Zaher (1999b). 1.1, resinplaque exposing ventral view of specimen. approxi-mately 18 cm long. 1.2, dorsal surface of the skullviewed through resin. scale in millimeters. 1.3, radio-graph employed by Rieppel and Zaher (1999b), scaleas in 1.2.


3

taken from Haas (1979), Caldwell and Lee (1997),and Zaher and Rieppel (1999b). Given the com-plexity and history of HUJ-PAL 3659, it is not sur-prising that there are some differences in theinterpretations as illustrated in Figure 2, differencesthat contributed to varying phylogenetic placementof Pachyrhachis. Although Haas recognized anumber of diagnostic snake characters, he consid-ered Pachyrhachis a highly derived platynotan orvaranoid lizard. Caldwell and Lee (1997) recog-nized Pachyrhachis as a snake and the sistertaxon to all other snakes, and that clade as the sis-ter taxon to mosasauroids, resurrecting Cope’s(1869) concept of Pythonomorpha (see also Lee1997a, 1997b, 1998; Lee and Caldwell 1998; Cald-well 2000). Zaher (1998) reinterpreted Pachyrha-chis as an advanced snake, specifically a basalmacrostomatan allied with boas and pythons (seealso Zaher and Rieppel 1999a; Rieppel and Zaher2000a, 2000b).

Snakes such as Pachyrhachis, Haasiophis,and Eupodophis, which possess all the bony ele-ments of the hind limb (as opposed to the rudimen-tary limb and girdle elements of modern worm

snakes, boas, and pythons), are primitive in thatattribute. However, the issue of macrostomatanversus more primitive phylogenetic placementhinges in large part on conflicting morphologicalinterpretations of skull elements (Rage andEscuillié 2000; Tchernov et al. 2000; Rieppel et al.2003). The major differences among the threeinterpretations that are important here are: 1) themorphology and orientation of the quadrate; 2) theidentification of the stapes or squamosal; 3) thenumber of mental foramina; 4) the identity of thebones in the circumorbital series; 5) the question ofwhether the exoccipitals contact above the fora-men magnum; and 6) presence of a dorsal prefron-tal process of the maxilla.

To test conflicting interpretations of morphol-ogy, the articulated skull of Pachyrhachis (HUJ-PAL 3659) was scanned using X-ray computedtomography (CT). Two- and three-dimensionalreconstructions were computer generated toexpose details from viewing perspectives thatcould not be attained using optical techniques. Wealso created a three-dimensional digital model ofthe skull utilizing specific measurements as bound-

Figure 2. Interpretive drawings of the dorsal skull surface of Pachyrhachis problematicus (HUJ-PAL 3659) illustratingconflicts in interpretation of morphology. 2.1, Haas (1979, figure 3). 2.2, Caldwell and Lee(1997, figure 1a). 2.3, Riep-pel and Zaher (1999b, figure 1). Abbreviations used in figures: Haas, 1979 (ang, angular; atna, atlas neural arch; axna,axis neural arch; com, compound bone; co, coronoid; d, dentary; ect, ectopterygoid; f, frontal; mx, maxilla; p, parietal;pmx, premaxilla; porb, postorbital; prf, prefrontal; ptf, postfrontal; pro, prootic; squ, squamosal; qu, quadrate; socc,supraoccipital; spt, septomaxilla; porb, postorbital; squ, squamosal; st, stapes); Caldwell and Lee 1997 (pm, premax-illa; mx, maxilla; de, dentary; prf, prefrontal; fr, frontal; ju, jugal; pof, postorbitofrontal; pa, parietal; com, compoundbone; ec, ectopterygoid; co, coronoid; pro, prootic; sq, squamosal; qa, quadrate; so, supraoccipital; pt, pterygoid; atna,atlas neural arch; axna, axis neural arch; sq, squamosal); Rieppel and Zaher, 1999b (at, atlas neural arch; axna, axisneural arch; com, compound bone; co, coronoid; d, dentary; ect, ectopterygoid; f, frontal; mx, maxilla; n, nasal; p, pari-etal; pm, premaxilla; po, postorbital; prf, prefrontal; q, quadrate; spt, septomaxilla; porb, postorbital; squ, squamosal;st, supratemporal; stp, stapes).


4

aries. By removing distortion due to crushing, wewere able to test the feasibility of the identificationof the most problematic bones of the circumorbitalseries, the ectopterygoid, and the orientation andmorphology of the quadrate. This model then pro-vides a hypothesis of the appearance of the undis-torted skull of Pachyrhachis. The value of digitallymodeling morphology in this case is in providing amore precise identification of structures. It is funda-mentally a taphonomic exercise to remove com-paction, rotation, and distortion.

Agreement among investigators on primaryobservations of morphology is critical to the phylo-genetic understanding of snakes with hind limbs. Amorphological feature either exists, does not exist,or it remains ambiguous or unknown. We intend toelucidate and clarify what can or cannot be seen inthe fossil using optical observation and CT deriveddigital data and provide the basis from which com-peting phylogenetic hypotheses can be tested andfalsified. An independent phylogenetic analysis isbeyond the scope of this study, which is intendedonly to test the data quality of previous primaryobservations and to discover new data.

MATERIALS AND METHODS

CT Scanning

The resin embedded skull (HUJ-PAL 3659)presents the ventral surface exposed on an epoxyresin plaque, retaining traces of the original lime-stone matrix on the surface. The epoxy resin hold-ing the specimen is approximately 17.5 mm thick,75 mm wide, and 195 mm long. The skull wasscanned at the University of Texas at Austin High-Resolution CT Facility (tube voltage 150 kV, 0.16mA, no filter, air wedge, 190% offset, slice thick-ness of 0.24 mm, S.O.D. of 130.0 mm, 1800 views,1 sample per view, interslice spacing of' 0.2 mm,field of reconstruction is 70.0 mm, reconstructionoffset 600, reconstruction scale 75). This resultedin 308 transverse slices at ~137 micron interpixelresolution and a slice thickness of 240 microns;each slice was saved as a 512 X 512 pixel tiffimage in both 16 bit and 8 bit modes (Appendix 1).The sequential 308 slices together form a three-dimensional matrix, and each pixel representing avolume element (voxel) in a three-dimensionalframework. Variations in the value of each voxelrepresent variations in relative X-ray attenuation,which closely mirror compositional variations. Xsignifies the transverse axis, Y the dorsoventralaxis, and Z the longitudinal axis of the CT data set.Voxblast version 3.0 (VayTek 2000) was used tobuild rendered and lighted isosurface and sectionalreconstructions. Voxblast was also used to resam-

ple the original 308 slice stack in the XZ plane, inorder to isolate the 93 slices that contain the speci-men–thus reducing the file size and memoryrequirements for processing, and providing bettersectional illustrations for comparison with isosur-face reconstructions. ImageJ version 1.32i (Ras-band 2003) was used for analysis and tracing ofslices and Adobe Photoshop 6.0 (Adobe Systems,Inc. 2001) for cropping and rotation of the originaldata set as well as increasing voxel density usingthe bicubic method of resampling. The latter pro-cess was used to optimize the isosurface recon-struction abilities of Voxblast, providing a morevoxel-dense volume, thereby minimizing aliasingeffects.

CT scanning and computer reconstructionhave resolving limitations. These are manifested inspatial resolution, X-ray attenuation differentiation,noise artifacts, and reconstruction artifacts. Speci-men geometry greatly influences both the availablespatial resolution and artifacts caused by variationin X-ray scatter and differential absorption due tothe amount and composition of material intersectedby the X-rays at different angular rotations. Idealspecimens are cylindrical and small enough to sitclose to the X-ray source, providing magnificationvia the fan beam projection onto the X-ray detec-tors. In the case of HUJ-PAL 3659, specimen sizeand geometry were less than optimal, presenting along rectangular cross section, with the area ofinterest small relative to the block size, therebyreducing beneficial magnification. Serial sectionsdo not clearly delineate individual elements butshow centers of greater attenuation, allowing ele-ments to be traced through the volume. Addition-ally, software problems encountered during thescanning process forced multiple interruptions andrestarts, resulting in slice misalignment in the ante-rior and midsection of the skull and vertebral col-umn. These misalignments are visible in theisosurface reconstructions as transversely orientedlines on the anterior portion of the skull and verte-bral column. A loss of data in the midsection of theskull occurred during one of the scan interruptions,constituting approximately five slices and amount-ing to about a 1 mm gap, and is represented by thethick black transversely oriented line across themidsection of the skull in the CT reconstructions(Figure 3; see also Appendix 2). The methodsemployed here are not perfect; however, they pro-vide an independent test of previous optical and X-radiograph observations and augment our knowl-edge of the morphology of this specimen. Compar-ison with light photographs demonstrates thesuperiority of CT techniques in eliminating lightingartifacts such as shadow and specularity, and pro-


5

vides a clearer illustration of topology and true mor-phology (Appendix 2). Additionally, the protocolsoutlined retain digital data representing a facsimileof the specimen, and therefore a testable data set(Appendix 1). Moreover the methods describedherein can be duplicated and improved upon if sodesired and therefore presents a superior level oftestability and reproduction of results comparedtooptical examination or X-radiographs alone.

Taphonomic Distortion

Figures 3.1 and 3.2 display isosurfaceimages of the dorsal and ventral surfaces of theskull of Pachyrhachis. The ventral surface isreversed so landmarks can be stacked in order torecognize and remove distortion (Figure 3.1, seealso Appendix 3). A line from the center of thebasioccipital through the parasphenoid rostrumdefines the midline of the skull (Figure 3.1). Theposterior midline of the dorsal surface indicated bythe sagittal crest lies above the ventral midline(Figure 3.2). As the skull was crushed, the snoutrotated to the left, with the right maxilla overlyingthe tip of the right dentary and the left dentary dis-placed laterally but lying on its medial surface. Theskull of Pachyrhachis is crushed dorsoventrally,with individual elements suffering varying degreesof compaction and displacement. The left and rightpostorbitals are symmetrically displaced laterally,

and the coronoid processes of the lower jaws arecollapsed medially on both sides. The symmetry ofstructures and their crushing patterns across theskull are important because they indicate forceapplied orthogonal to the bedding plane on whichthe specimen was preserved.

To quantify the amount of displacement ofeach element, the ventral isosurface reconstructionwas rotated 18.4 degrees relative to the originalscanning axis to approximate the alignment of thecenter of the parasphenoid and the posterior cen-ter of the basioccipital (Figure 3.1) at a referenceangle of 0.0 degrees. The dorsal isosurface wasthen rotated -18.4 degrees to match the alignmentof the ventral surface. By comparing the dorsalsagittal alignment of the parietal to that of thebasioccipital-basisphenoid, it is clear that the brain-case behaved as a single unit with respect tocrushing (Figure 3.2; see also Appendix 3).

The parietal-basicranium midline was used asa reference of 0.0 degrees. In dorsal view the pos-terior terminus of the medial suture of the frontalsis displaced slightly right of center, the sutureangles 15.5 degrees to the left anteriorly. The pre-frontals approximate this displacement to an equiv-alent degree. The right maxilla is preserved in aslightly more anterior position than the left. Thesmall edentulous premaxilla is preserved in placebetween the anterior maxillaries. The right mandi-

Figure 3. Three-dimensional isosurface models derived from CT data and line segment stand-ins to test alignment anddisplacement of cranial elements of Pachyrhachis problematicus (HUJ-PAL 3659). 3.1, Ventral view with lines indicat-ing sagittal plane traced from the median basioccipital to the parasphenoid rostrum and transverse planes indicatinglateral limits of exoccipitals. 3.2, Dorsal view with lines indicating sagittal and transverse planes traced on parietal, andline segments to act as stand-ins for major elements and landmarks. 3.3, Line segment stand-ins, rotated and adjustedto remove translational and rotational distortion of major elements. Abbreviations: d, dentary; gl, glenoid; m, maxilla;pob, postorbital; q, quadrate; sc, sagittal crest; sml, sagittal mid-line; st, supratemporal. Scale bar equals one centime-ter.


6

ble is in articulation with the distal quadrate anddisplaced anteriorly to the left 29.0 degrees, under-lying the skull and invading the natural position ofthe right ectopterygoid. The left mandible is pre-served adjacent to the left side of the skull,embracing the left maxilla.

All relative displacement of elements includingthe snout, frontals, prefrontals, the left mandible,the left supratemporal, and the sagittal crest is left-ward. All rotation of elements is counterclockwise,including the quadrates, with the left displacedmedially and slightly overlapping the anterior verte-bral column.

Morphological Model

The morphological model (Figure 4.1) wasconstructed by building polygon surfaced wire-frame simulation elements using Lightwave 3D,version 8 (Newtek 2004) and employing the three-dimensional isosurface model derived from the CTdata as a guide. Removal of distortion from the ele-ments was somewhat subjective; however, carewas taken to approximate surface areas andlengths of the CT model in the proxy models ofindividual elements. The proxy elements were thenmanipulated to determine best fit to one another.Finally, the elements were distorted to mimic thedistortion present in the CT data representing theactual fossil by manipulating the models (Figure

Figure 4. Morphological model of Pachyrhachis problematicus simulating effects of crushing: (4.1) Uncrushed state,and (4.2) crushed state. 4.3-4.9, oblique (top) and dorsal (bottom) views of taphonomic simulation: 4.3, uncrushedstate; 4.4, initial collapse of dentaries and quadrates; 4.5-4.9, progressive crushing and leftward rotation of snout rela-tive to the braincase due to right dentary underlying right portion of snout, counterclockwise rotation of quadrates, dor-sal portion of postorbitals displaced laterally, and the ventral portion of postorbitals following the position of theanterior ectopterygoids; 4.10, isosurface model of current crushed state based on CT data (of HUJ-PAL 3659) forcomparison to crushed simulation. Note final resting position of ventral portion of postorbital relative to anterior ectop-terygoids; see also Appendix 4 for animation of crushing sequence. The degree of gape in the uncrushed state is sub-jective; however, the position of anterior tips of dentaries as preserved indicate their relatively close proximityanteriorly and the relationship of the mandibles to the quadrate constrains them posteriorly, suggesting the mandibleswere more or less in life position as the carcass came to rest.


7

4.2). The undistorted and distorted reconstructionswere then used as end points in a time sequenceanimation to simulate the interaction of elementsand the relative timing and effects of crushing (Fig-ure 4.3-4.9; see also Appendix 4 for animationsequence).

Institutional Abbreviations

HUJ, Hebrew University of Jerusalem; UCMP,University of California Museum of Paleontology;TMM, Texas Memorial Museum, Austin Texas;CAS, California Academy of Science.

Specimens Examined

Pachyrhachis problematicus HUJ-PAL 3659;Cylindrophis ruffus CAS 231481; Cylindrophis ruf-fus UCMP 136995; Anilius scytale TMM(VPL) M-8281; Xenopeltis unicolor TMM(VPL) M-8276;Xenopeltis unicolor TMM(VPL) M-8277; Pythonregius TMM(VPL) M-8278; Python curtisTMM(VPL)M-8279; Epicrates cenchria TMM (VPL)M-8280.

RESULTS

The computed tomography and computergenerated three-dimensional isosurface recon-struction techniques employed here yield resultscomparable to high fidelity casts enabling viewingof morphology in three axes of rotation. Addition-ally, serial sections illustrate topological relation-ships of individual elements, providing betterunderstanding of those that are obscured by over-lapping elements or matrix residue. Figure 5.1 is alow angle light photograph of the ventral surface ofthe specimen as preserved today. Figure 5.2 is thesame view using the isosurface reconstruction ofthe CT data set. Comparison of Figures 5.1 and 5.2demonstrates the fidelity and therefore the viabilityof computer generated reconstruction of CT datafor illustrative and quantitative purposes and pro-vides a qualitative reference for subsequent dis-cussion of the resin obscured dorsal surface of theskull. The isosurface reconstruction of the resinembedded dorsal surface is represented in Figure5.4 as a stereo pair. Figures 5.3 and 5.5 are inter-pretive line drawings derived from isosurfacereconstructions, photographs, and microscopicstudy of the specimen. Elements that have beenthe subject of conflicting interpretation are indi-cated by ue1 through ue5 (unidentified elements)and are referenced in the following sections.

Orientation and Morphology of the Quadrates

The relationship of the quadrate to thesupratemporal dorsally and the glenoid of the com-pound bone of the lower jaw ventrally is largely

preserved on the right side, but the quadrate isrotated counterclockwise (Figures 3, 6). Caldwelland Lee (1997) reconstructed Pachyrhachis withvertically oriented quadrates with broad lateral fac-ing surfaces. To test this reconstruction, the length,orientation, and position of morphological land-marks were traced on the dorsal surface of theskull, including the maximum length of the mandi-bles as well as the center of the glenoid, maxillae,parietal-supraoccipital midline, snout midline, rightsupratemporal, and right quadrate (Figure 3.2).These tracings were then rotated and adjusted toparallel one another and align the anterior terminusof the premaxillae, maxillae, and mandibles (Figure3.3).

The position of the right supratemporal wasretained and taken to approximate the natural posi-tion for three reasons: 1) the primary force thatcrushed the specimen was orthogonal to the bed-ding plane as previously discussed; 2) this primaryforce also manifested in the leftward displacementof the left supratemporal and the leftward crushingof the sagittal crest (as the result of a leftwardincline of the skull due to the right mandible under-pinning the right side of the skull, which influencedleft lateral but not anterior displacement); and 3)asymmetrical rotation and outward collapse of thequadrates was not likely to have contributed toanterior displacement as evidenced by the fact thatthe quadrates were crushed laterally, not dors-oventrally. This would most likely be the case if thequadrates splayed out prior to the remaining por-tion of the skull being crushed, and thus the resis-tive forces of the quadrates would be moremedially oriented, not anteriorly.

The supratemporals in Pachyrhachis are longrelative to other snakes. As preserved, the poste-rior free-ending extensions of the supratemporalcomprise approximately one-third their total length.The anterior ends reach anterior to the anterior ter-minus of the prootic. In Recent snakes thesupratemporal does not extend anterior to theanterior terminus of the prootic, and in that respectmay justify a more posterior reconstruction. How-ever, reconstruction of the supratemporals in amore posterior position would in fact exaggeratethe macrostomatan condition of the distal exten-sion of the supratemporal beyond the skull roof.The supratemporal and the parietal are develop-mentally part of the dermatocranium whereas theprootic is a part of the chondocranium and thus donot share obvious developmental relationships thatwould preclude the supratemporal anterior termi-nus exceeding that of the prootic. Given the tapho-nomic affects discussed and in absence ofdevelopmental constraints, the proportionality ofsutured versus free-end of the supratemporal and


8

the position of the anterior terminus relative to theanterior extent of the prootic is deemed reason-able.

Taking the length of the quadrate along itsmidline, the right quadrate requires 19 degrees ofinclination to achieve articulation with both themandibular glenoid posteroventrally and thesupratemporal anterodorsally. The degree of incli-nation is of course controlled by both the position

of the supratemporal and the position of the mandi-ble. Therefore, the mandibular articulation surfaceof the quadrate was examined and compared witha number of alethinophidian and macrostomatansnakes to determine if the trochanter morphologycould be used to determine orientation of the artic-ulation. In specimens examined that possess avertical or nearly vertical quadrate (e.g., Cylindro-phis ruffus, Anilius scytale, Xenopeltis unicolor,

Figure 5. Photograph and computer reconstructions derived from CT data, and interpretive line drawings of Pachyrha-chis problematicus (HUJ-PAL 3659). 5.1, light photograph of ventral surface as currently conserved; 5.2, computerreconstructed isosurface model derived from CT data. Note resolution and fidelity of surface reconstruction as com-pared with light photograph. 5.3, interpretive drawing of ventral surface; 5.4, stereopair of dorsal surface from com-puter reconstructed surface model derived from CT data; 5.5, interpretive drawing of dorsal surface. Abbreviations: a,angular; atn, atlas neural arch; ax, axis vertebra; bs, basisphenoid; bo, basioccipital; c, compound bone; cor, coronoid;d, dentary; ect, ectopterygoid; ex, exoccipital; f, frontal; m, maxilla; p, parietal; pm, premaxilla; pob, postorbital; pf, pre-frontal; pl, palatine; pt, pterygoid; q, quadrate; s, stapes; so, supraoccipital; sp, splenial; st, supratemporal, ue1-5; uni-dentified elements; v3-v4, 3rd and 4th cervical vertebra. (See also Appendices 2, 3.) Scale bar equals one centimeter.


9

Figure 6. Stereopairs of quadrates of HUJ-PAL 3659, from computer reconstructed isosurface model derived from CTdata and associated interpretive line drawings: 6.1-6.3, right quadrate in (6.1) medial, (6.2) lateral, and (6.3) posteriorview; 6.4-6.6, left quadrate in (6.4) medial, (6.5) lateral, and (6.6) posterior view. Abbreviations: c, compound bone;cor, coronoid; pt, pterygoid; q, quadrate; s, stapes; st, supratemporal; stl, stylohyal process; V3-V4, 3rd and 4th cervicalvertebra. (See also Appendix 5 for animated reconstruction sequence.)


10

Python regius ), the trochanter was symmetrical inlateral view. In specimens possessing a slightlyposteroventrally inclined quadrate (e.g, Epicratescenchria) the trochanter was asymmetrical with themajority of the trochanter restricted to the anteriorportion. In Pachyrhachis, the trochanter isobscured on the right quadrate, but a well-definedtrochanter is present on the anteroventral surfaceof the left quadrate (Figure 6.4), but not on the pos-teroventral surface (Figure 6.5). Thus, the articulat-ing surface was predominantly restricted to theanterior portion of the distal quadrate, and there-fore, the quadrate was not vertical in Pachyrhachis,but inclined to a moderate degree. This condition isconsistent with the position and length of thesupratemporal.

The quadrates in Pachyrhachis are preservedwith a broad lateral profile due to crushing. Thecrushed state of the quadrate was apparently inter-preted by Caldwell and Lee (1997) as the true mor-phology as addressed in their description andreconstruction. We disagree with this interpreta-tion. During crushing, the distal portion of the quad-rates was rotated relative to the cephalic condylesyielding the broad surface as preserved. In snakesthe quadrate articulation with the supratemporalwhere present is in para-sagittal plane and themandibular condyle long axis is oriented orthogo-nal to the mandibular axis. Removal of distortionintroduced by crushing was achieved by aligningthe cephalic condyle with the sagittal plane androtating the mandibular condyle to bring it roughlyorthogonal to the sagittal plane, distributing therotation linearly along the length of the quadrate(see Appendix 5 for details of reconstruction).

Stapes

The elements that Haas (1979) referred to assquamosals are the supratemporals as recognizedby later authors. The tentative squamosal of Cald-well and Lee (1997) is the proximal portion of theright stapes as identified by Zaher and Rieppel(2002). The distal end of the stapes was correctlyidentified by Caldwell and Lee (1997) but incor-rectly identified as the opisthotic paroccipital pro-cess by Zaher and Rieppel (2002). The element inquestion is sandwiched between the posteriorpterygoid quadrate ramus, the distal supratempo-ral, and the quadrate (Figure 6.1-6.3). Apparently,the right stapes is broken or bent along its shaft.Our identification of this element as the stapes issupported by tracing it in serial sections 180 to 240and 280 to 305 (Figure 7). The shafts representingboth the proximal and distal portions of the rightstapes are visible in the same plane. The stylohyalprocess of the quadrate is visible in Figure 6.3, 6.6.

The reconstructed length of the stapes is consis-tent with the distance from the stylohyal process tothe inferred position of the fenestra ovalis (Figure4). Comments. The supratemporal is extremelyreduced or absent in scolecophidians (Zaher andRieppell 2002) and the quadrate abuts the sidewallof the braincase. In alethinophidians examined(e.g., Cylindrophis ruffus, Anilius scytale), thesupratemporal is relatively short and the quadrateis supported by both the supratemporal and thebraincase and the stapes articulates with a posteri-orly directed suprastapedial process of the quad-rate via a separate intervening calcified cartilage(extracolumella or stylohyal) as is the case in Dinil-ysia (Rieppell 1979, figure 4 A, B; see also Cald-well and Albino 2002 for discussion of Dinilysia). Inmacrostomatans examined (e.g., Python regius,Python curtis, Epicrates cenchria), the supratem-porals project posteriorly and provide sole supportof the quadrate (see also Rieppell 1979, figure 4C),and the stapes articulates with the middle to distalmedial quadrate shaft via a fused calcified carti-lage, the stylohyal. In all macrostomatan speci-mens examined the quadrate shaft exhibits amedial protuberance at the point of articulation withthe stapes, the stylohyal process. Pachyrhachis isfound to lack a suprastapedial process and isshown to possess a stylohyal process on the distalmedial quadrate shaft (Figure 6.3). Thus, evidenceprovided by the free-ending supratemporal, pres-ence of a stylohyal process, correction of the orien-tation of the cephalic and distal condyles andresulting morphology of the quadrate, and the pos-teroventral inclination of the quadrate from thesupratemporal to the articular agree best with thecondition in macrostomatan snakes (see Appendix5 for reconstruction of quadrate).

Number of Mental Foramina

A single mental foramen is visible in both isos-urface and sectional views. The second foramenillustrated by Caldwell and Lee (1997, figure 1A;see also Figure 2.2 this paper) is an artifact ofcrushing into the void formed by the Meckel’sgroove anterior to the anterior terminus of the sur-angular (Figure 8.1, 8.4-8.7, arrow 3; see alsoAppendix 2). Tracing through the slices, it is appar-ent the depression opens into the Meckel’s groove.Also, a third depression on the antrolateral surfaceof the left dentary superficially resembles a fora-men (Figure 8.1, arrow 1). However, this structurelies within a crushed and distorted area and ismerely an artifact of preservation. In life, the ante-rior tips of the dentaries curved sharply medially,approximating the dorsal outline of the maxillae.


11

The main body of each dentary is preserved nearlyperpendicular to its anatomical position causing theanterior medial portion to deform, twisting nearly90 degrees, resulting in an area of crushing andfractures that can be seen in serial section (Figure8.2-8.7). One of the foramina (Figure 8.1, arrow 2)can be traced into unfractured bone, has well-defined edges, and is interpreted here as a singleand only true mental foramen. A single mental fora-

men is characteristic of Serpentes (Rieppel et al.2003; Lee and Caldwell 1998).

Circumorbital Series

All authors agree on the identification of thepostorbitals lying symmetrically on either side ofthe skull. Medial extensions (Figure 5, ue4 andue5) of the postorbitals, overlying the anterior pari-etal as illustrated by Caldwell and Lee (1997),gives them a lizard-like appearance (Figure 2.2).

Figure 7. Computer generated views of the skull of Pachyrhachis problematicus specimen (HUJ-PAL 3659) in (7.1)ventral and (7.2) dorsal views; 7.3, serial sections of the area indicated by highlighted section of surface model, repre-senting every tenth slice from 150 through 320 to illustrate the topological relationships of elements in the posteriorportion of the skull. Abbreviations: atn, atlas neural arch; ax, axis vertebra; bs, basisphenoid; bo, basioccipital; c, com-pound bone; cor, coronoid; ex, exoccipital; psc, parietal sagittal crest; pt, pterygoid; q, quadrate; s, stapes; so, supraoc-cipital; st, supratemporal. Scale bar equals one centimeter.


12

Figure 8. Skull of Pachyrhachis problematicus (HUJ-PAL 3659) in dorsal view and serial sections, illustrating mentalforamen path and crushed regions. 8.1, dorsal view, computer generated reconstruction. Arrow 3 indicates depressionidentified by Caldwell and Lee (1997) as a second mental foramen. Arrow 1 indicates similar crushed region superfi-cially resembling mental foramen; arrow 2 points to true mental foramen. 8.2 and 8.3, serial sections illustrating therelationship of the anterior crushed region, manifested in the superficial anterior depression in 8.1, arrow 1; 8.4-8.7,sequential serial sections demonstrating the relationship of external morphology to internal crushed regions. In serialsection 8.7, the foramen indicated by arrow 2 can be traced through the sections without interruption; however, thesuperficial depressions mimicking foramina directly overlay crushed regions. Arrow 3 overlies the area weakened bythe void of the Meckel’s groove below and the anterior surangular suture above, and arrow 1 overlies the anteriorcrushed region formed by coronal rotation of the anterior dentaries. Scale bar equals one centimeter.


13

However, Zaher and Rieppel (1999) did not figurethe medial structure as part of the postorbital butdid indicate topographical relief in their interpretivedrawing on the left side of the skull (Figure 2.3). Itis unclear from the isosurface reconstruction (Fig-ure 5.4, 5.5; see also Appendix 2) if the medialextensions were ever in contact with the undis-puted portion of the postorbitals. However, it isclear that they are now topologically displaced anddiscontinuous with the postorbitals. The structureslie in a portion of the parietal table that is crushedand distorted. The structures themselves may beartifacts caused by crushing on top of the basip-terygoid processes (Figure 5.4, 5.5). In any eventthe identity of these structures is ambiguous atbest.

The most controversial elements in the skullof Pachyrhachis are those variably referred to aspostfrontals by Haas (1979), as jugals by Caldwelland Lee (1997), and the broken anterior ectoptery-goids by Zaher and Rieppel (1999). They areshown here in Figure 5.5 (elements labeled ue1and ue2). These elements are in close proximity tothe distal terminus of the undisputed postorbitalslying somewhat symmetrically on the suborbitalprocess of the maxillae. We are reticent about pre-cisely identifying ue1 and ue2 as postfrontals,ectopterygoids, or jugals, because the evidence foreach is the same, namely where they lie.

No recent author agrees with Haas’s (1979)identification of these elements as postfrontals.Given that the apparent force vector responsiblefor the crushing was dorsoventral, it is unlikely thatthe postfrontals would settle in the oblique positionof these bones.

Supporting the argument of Zaher and Riep-pel (1999b) that ue2 is a broken fragment of anectopterygoid, is the fact that the right dentary isrotated under the skull, interrupting the naturalposition of the right ectopterygoid relative to themaxilla and pterygoid (Figure 5.1-5.5) and poten-tially causing breakage. The right pterygoid is dis-placed anteriorly and rotated to overlap slightly theparasphenoid (Figure 5.3). Thus it could haveapplied anteriorly directed force to the ectoptery-goid and possibly caused breakage and displace-ment. Given the foreshortening of the left side ofthe skull and the leftward rotation of the snout, theectopterygoid could have compressed in its longaxis, retaining its natural anterior articulation withthe maxilla, the broken posterior portion rotatingclockwise and medially, coming to rest in its currentposition.

Arguing against identification as an ectoptery-goid is Haas’s (1979) correct (in our opinion) identi-fication of the ectopterygoid on the left side and the

otherwise consistent symmetry of other elementsof the skull. Element ue3 lies medial to the dentaryand is identified here as anterior right ectoptery-goid (Figure 5.5; see also Appendix 2 and 3 forillustration of topological and dorsoventral relation-ships). Additionally, element ue1 on the left sideand ue2 on the right are more or less symmetricallydisplaced (Figure 5.4 and 5.5). However, the leftmandible could not have applied the same amountand direction of force on the left ectopterygoid ason the right, because the left mandible now lies lat-eral to and does not interfere with the natural posi-tion of the left ectopterygoid. It is also unlikely thatsufficient force could be applied to the ectoptery-goids to cause the pattern of breakage and dis-placement preserved in ue1 and ue2. We reject thehypothesis that the elements are displaced brokenectopterygoids on the basis of identification of theintact ectopterygoids and taphonomic interpreta-tions.

Caldwell and Lee‘s (1997) identification of theelements ue1 and ue2 as jugals is topologicallyplausible in part. However, their interpretation pre-sents three issues. First, there is no clear anddefinitive justification for the presence of a jugalexcept topological position in relation to the maxil-lae, but, given the taphonomic affects identifiedherein, that same evidence is applicable andequally compelling with respect to the other alter-natives. Second, the element’s relationship to thepostorbitals and maxillae as preserved is problem-atic as there is no clear articulation facet or suturewith either element (Appendix 3). Additionally, theposition of the right and left elements relative to themaxillae are different. The medial portion of the leftelement is in contact with the maxilla whereas thelateral portion of the right element overlies themaxilla. Therefore, other than proximity to the pos-torbitals, there is no clear indication of articulationwith the maxillae. Third, the morphology of the ele-ment is inconsistent with the morphology of thejugal in any known squamate in that it is merely aflat piece of bone that widens anteriorly and thusdisplays no morphology that clearly defines it as ajugal. Jugals have been reported as present inDinylisia (Estes et al. 1970), but their presence wassubsequently contradicted by Caldwell and Albino(2002). Jugals are unknown in all other snakes. Wereject the hypothesis that Pachyrhachis had jugalson the basis of its morphology, topological relation-ships, and taphonomic considerations.

The identity of the elements ue1 and ue2 ismost parsimoniously explained as the ventral por-tion of elongate postorbitals. The undisputed pos-torbitals are in fact the dorsal portion of thepostorbitals and share a long articulation with the


14

anterolateral parietal, and likely contacted the fron-tal as in some macrostomatans (Lee and Scanlon2002b, figure 2 d,e,f). This is supported by multiplelines of evidence: 1) the anterior portions of both ofthe ectopterygoids are visible in dorsal view; 2) theventral ends of both ue1 and ue2 are in contactwith the anterior ends of the ectopterygoids; 3) thedorsal ends are in contact with the undisputed pos-torbitals; 4) the combined length of the undisputedportion of the postorbitals and their ventral counter-parts is accommodated by the anterolaterally elon-gate parietal; and 5) taphonomic affects evidencedin the distortion of other morphology suggest pre-dominantly dorsoventral forces acted upon the fos-sil and thus would reasonably produce theresultant configuration of the postorbitals, ue1, andue2. Figure 4 illustrates the effects of crushing onHUJ-PAL 3659 (See also Appendix 4 for animationsequence of crushing).

Exoccipitals

The exoccipitals are compact and project onlya short lateral distance (Figure 9.2). The areaabove the basioccipital preserves the supraoccipi-tal but obscures the foramen magnum (Figure 9.1).There is evidence of' slight crushing parasagittallyon the dorsal surface of the supraoccipital, indicat-ing weak support from below and allowing the pos-sibility of separation of the exoccipitals. However,this character remains inconclusive and must betreated as unknown in Pachyrhachis. Exclusion ofthe supraoccipital from the foramen magnum bycontact of the exoccipitals has long been consid-ered a synapymorphy of Serpentes (Underwood

1967; Rieppel 1979; Estes et al. 1988), but Zaherand Rieppel (2002) indicate this character appearsto be variable within Macrostomata.

Dorsal Laminae of Maxillae

Haas (1979) mistook the left prefrontal for thefrontal. Caldwell and Lee (1997) correctly identifiedprefrontals and frontals but reconstruct an ascend-ing process of the maxillae, overlapping the pre-frontal. Zaher and Rieppel (1999b) illustrate thestructure as a portion of the prefrontal. The area inquestion is separated from the maxillae on both theright and left sides and is displaced ventrally rela-tive to the preserved dorsal surface of the maxillae.Light photographs demonstrate artifacts of shadowand surface irregularity that obfuscate morphologywhen compared with surfaces derived from CTdata as evidenced in Appendix 2. Comparing thelight photographs and the CT renderings, it is clearthese bones are separate from both the maxillaeand the prefrontals, albeit not in a uniform way. Thenarial margin in Pachyrhachis can be traced up toand including the prefrontals, but unambiguousdelineation of where the prefrontals end and themaxillae begin is difficult. However, the more pos-terior portion of the external nares curve mediallyas preserved and thus would indicate at least amoderate development of the dorsal laminae of themaxillae and that interpretation is accepted here.Some alethinophidians retain a modest dorsal lam-ina of the maxilla at the point of articulation with theprefrontal as in Cylindrophis (Lee and Caldwell2002, figure 4B). The presence of dorsal laminae

Figure 9. Stereopairs and line drawings of posterior portion of skull of Pachyrhachis problematicus (HUJ-PAL 3659),from computer reconstructed surface model derived from CT data in (9.1) dorsal and (9.2) ventral views. Abbrevia-tions: atn, atlas neural arch; ax, axis vertebra; bs, basisphenoid; bo, basioccipital; cor, coronoid; ex, exoccipital; p,parietal; pt, pterygoid; q, quadrate; s, stapes; so, supraoccipital; st, supratemporal; V3, 3rd cervical vertebra.


15

does not exclude interpretation of Pachyrhachis atleast at the level of Alethinophia.

Summary of Characters

Of the six characters examined all have beenshown to: 1) have been misinterpreted; 2) possessthe Serpentes, the alethinophidian, or the macros-tomatan condition; or 3) be absent or ambiguous.Table 1 summarizes the interpretations of thisstudy in comparison to previous studies. The quad-rate lacks a suprastapedial process. A stylohyalprocess is present on the ventral medial shaft. Theposteriorly projecting supratemporal provides solesupport for the quadrate, which is inclined.Pachyrhachis is shown to possess an elongate andslender stapes and a single mental foramen. Ajugal is absent, and the elements referred to hereinas ue1 and ue2 are considered the ventral portionof the postorbital. The exoccipital contact abovethe foramen magnum is unknown. The maxillaepossess a moderately developed ascending pro-cess.

The presence of a single mental foramen andloss of the jugal is diagnostic of Serpentes (Leeand Caldwell 1998; Tchernov et al. 2000). A dorsallamina of the maxilla is present in alenthinophidi-ans but is reduced in Recent macrostomatans. The

dorsal laminae of Pachyrhachis are primitive. How-ever, in Pachyrhachis the supratemporal providessole support of the quadrate, the quadrate has areduced suprastapedial process and a well-devel-oped distomedial stylohyal process, and the stapesis long and slender. Thus, in respect to the quad-rate suspensorium and morphology, Pachyrhachisdisplays the condition in macrotomatan snakesabove the level of Loxemus and Xenopeltis (Tcher-nov et al. 2000). In the absence of characters elim-inating Pachyrhachis from Serpentes and in thepresence of skull characteristics otherwise diag-nosing the macrostomatan condition as notedabove, better support is found for the hypothesisplacing Pachyrhachis problematicus as a basalmacrostomatan (sensu Tchernov et al. 2000). Fig-ure 10 illustrates our revised reconstruction of theskull of Pahyrhachis problematicus.

DISCUSSION AND CONCLUSIONS

Perhaps the most widely acknowledged char-acter of snakes is the loss of limbs. However, onlyin derived macrostomatans is the loss of limbstotal. Scolecophideans, pythons, and boas allretain vestiges of hind limbs or girdle elements.With the demonstration that Pachyrhachis and

Table 1. Comparison of interpretation of selected morphology from previous and current studies of Pachyrhachis prob-lematicus. Ue1-ue5 refer to the elements illustrated in figure 5 of this study. See Figure 2 for illustrations and interpreta-tions of previous studies.

Haas 1979, 1980a Caldwell and Lee 1997Zaher and Rieppel,

1999b This StudyPostfrontals Jugals Broken displaced anterior

ectopterygoidsVentral portion of postorbitals (ue1&ue2)

Not applicable Postfrontal fused to postorbital Crushed frontalis decensus

Anterior portion of ectopterygoid (ue3)

Anterior portion of left ectopterygoid

Posterior left maxilla Not applicable Anterior portion of left ectopterygoid

Posterior portion of left ectopterygoid

Ectopterygoid Not applicable Posterior portion of left ectopterygoid

Right ectopterygoid Posterior right maxilla Posterior right maxilla Posterior right maxilla

Not applicable Medial processes of postorbital

Not part of postorbital Possibly crushing of parietal table (ue4&ue5)

Stapes Tentative squamosal Stapes Stapes

Not applicable Stapes Paroccipital process of opisthotic

Stapes

Not applicable Vertically oriented quadrate Posterventrally inclined quadrate

Posteroventrally inclined quadrate

Not applicable Two mental formina One mental foramen One mental foramen

Not applicable Broad lateral profile of quadrate

No suprastapedial process of quadrate

No suprastapedial process of quadrate

Not applicable Broad lateral profile of quadrate

More Macrostomatan-like quadrate

Stylohyal process on ventral medial margin

Not applicable Exoccipitals do not contact Unknown Unknown


16

Haasiophis are macrostomatans (Tchernov et al.2000), the occurrence of hind limbs with a com-plete bony complement attains added significance.Although Tchernov et al. (2000; see also Zaher andRieppel 1999) entertained the possibility (on thebasis of parsimony analysis) that legs may have re-evolved in macrostomatans, that possibility nowseems remote. In and of itself, the loss and re-attainment of a complex element or characterwithin a specific monophyletic group is always lessparsimonious than a single loss. The interpretationof limb reacquisition as more parsimonious is pos-sible only in the context of tree topology based onother characters not related to the one in question,and on the acceptance of reduced limbs as a basalsynapomorphy within Serpentes.

Tree topology is accepted on the basis of par-simony. Character interpretation as homoplasy,synapomorphy, or symplesiomorphy is guided bythe test of congruence. But neither parsimony anal-

ysis nor interpretations of characters based ontests of congruence are explicitly accompanied byan understanding of genetic, developmental, orother biological processes involved with the loss orgain of a character. Therefore, analysis and inter-pretation of character distribution should, whenpossible, be performed in the context of an under-standing of biological processes rooted in empiricalevidence and experimentation.

Independent of limb development, the mor-phological interpretation of the skull presented hereis consistent with a phylogenetic placement ofPachyrhachis as a basal macrostomatan. Reten-tion of limbs in a relatively advanced snake hasimplications for the developmental model of limb-lessness and axial patterning as presented byCohn and Tickle (1999) who studied the geneticcontrol and developmental process of limb loss insnakes. Their model accepted Pachyrhachis as thesister taxon to Serpentes and thus favored loss of

Figure 10. A-D. Morphological model of Pachyrhachis problematicus in (10.1) lateral view, (10.2) dorsal view, (10.3)ventral view, and (10.4) oblique view. This varies from Caldwell and Lee (1997) in the reconstruction and orientation ofthe quadrate, the ectopterygoid, and the circumorbital series. The nasals are conjectural as they are not preserved inthe specimen. Discussion of the reconstruction of the quadrate and circumorbital bones is detailed in the text. Caldwelland Lee’s (1997) reconstruction of the ectopterygoid is implausible as it would interfere with the natural position of thecoronoid and not allow the jaws to be shut. Therefore, we reconstructed the ectopterygoids in a more medial positionnear the maxilla, allowing passage of the coronoid.


17

distal limb elements in basal Serpentes, and totalloss in advanced snakes. In that study, fibroblastgrowth factors were grafted to Python limb budsand successfully stimulated outgrowth. They wereunable to stimulate apical ridge development, butdid demonstrate polarizing potential by grafting thePython limb buds to the wing area of mutant wing-less chicken embryos. The development of limbs intreated wingless chicken embryos demonstratedthat Python hind limb mesenchyme conserves cod-ing for limb development and polarization, and thatsuppression of limb development in Python is dueto absence of apical ridge development.

Hind limbs occasionally occur in whales as inthe humpback whale specimen documented byAndrews (1921) that possessed a cartilaginousfemur, osseous tibia, cartilaginous tarsus, andosseous metatarsal. Reduction of hind limbs inwhales is the result of arrested limb bud develop-ment (Bejder and Hall 2002). In humpback whaleslimb bud development persists longer than in odon-tocetes, partially explaining the more frequentexpression in humpbacks. Presumably the loss ofhind limbs in whales is accomplished by similardevelopmental and genetic processes as in otherlimbless vertebrates. However, the occasionaloccurrence of hind limbs in whales is a variantwithin a species and is quantitatively different fromthe fixed presence of hind limbs implicit inPachyrhachis and Haasiophis. The variable pres-ence of hind limbs in whales speaks to the processof limb loss, and does not necessarily speak to thegenetic or developmental processes of reacquisi-tion unless the assumption is made that the pro-cesses and controls elucidated by Cohn and Tickle(1999) are easily reversed. There is no direct sup-porting evidence to suggest that reacquisition oflimbs after loss has ever occurred.

In insects, the reacquisition of wings hasrecently been hypothesized (Whiting et al. 2003).That study, based on molecular phylogenetic anal-ysis, suggested the reacquisition (versus multipleloss of wings) based on parsimony analysis, similarto the situation we face with limb presence in basalmacrostomatans. However, the conclusion thatwings re-evolved after loss is again based on theparsimony analysis and tests of congruence ofcharacter distribution, a distribution that may havenothing to do with the genetic control, develop-ment, or other fundamental biological attributes ofwings. In that case, one could reasonably predictthat with further acquisition and analysis of charac-ter data, the hypothesis of re-evolution of insectwings will be falsified.

Clearly, expansion of the thoracic identity inthe axial skeleton, most likely controlled by Hox

gene expression domains, is an early developmentin snake evolution. Additionally, Hox gene expres-sion related to apical ridge development in hindlimb buds may control further limb loss. The recog-nition of the derived nature of Pachyrhachis dem-onstrates that leg loss under such a model is morevariable in snakes than recognized previouslybecause the hind limb skeleton of Pachyrhachis isbetter developed than in either boas and pythonsor worm snakes (scolecophideans). However, thisvariation merely implies that hind limb loss insnakes is more complicated than a progressivedecrease in development through time, and thathind limbs were reduced separately in more thanone clade. This also appears to be the case in arecent study of limblessness in anguid lizards(Wiens ands Slingluff 2001). Given the hypothesisthat snakes are evolved from within Squamata,retention of hind limbs, a plesiomorphic structure intetrapods, is not surprising nor is it informative in acladistic sense.

The interpretation of limb retention inPachyrhachis and related forms implies multiplelimb reductions in scolecophidians, alethinophidi-ans, and within macrostomatans. This scenarioappears likely given our current understanding ofdevelopmental mechanisms controlling limbexpression, does not require an additional ad hochypothesis of biological processes controlling rede-velopment, and is therefore a more parsimoniousconclusion compared to reacquisition. The totalelimination of hind limb specification and its skele-tal remnants is characteristic of advanced macros-tomatan snakes only.

Various interpretations of observed morphol-ogy placed Pachyrhachis in a more primitive andbasal position among snakes, or in a derived phy-logenetic position as a macrostomatan. Computedtomography allows a more thorough examinationof Pachyrhachis problematicus than previouslyavailable and therefore provides for revised recon-struction and modeling of the skull, especially withrespect to the morphology and position of thequadrates, the identity of the circumorbital bones,and the identity and position of the ectopterygoid.There is no compelling evidence for retention of asquamosal, a jugal, vertical orientation of the quad-rate, or retention of multiple mental foramina. Thisanalysis confirms the presence of a posterior free-ending projection of the supratemporals with distalexpansion providing sole support of the quadrates,quadrate with no suprastpedial process but with astylohyal process. The contact of the exoccipitalsabove the foramen magnum is ambiguous. Ouranalysis favors the phylogentic hypothesis thatPachyrhachis is a basal macrostomatan, consis-


18

tent with the conclusions of Zaher (1998; see alsoZaher and Rieppel 1999b; Tchernov et al. 2000).

ACKNOWLEDGMENTS

We would like first to acknowledge WillDowns, to whose memory we dedicate this work.Will had a quick and creative mind and was alwaysanxious to look at interesting fossils in ways thatshed new light. Thanks to R. Ketchum of the Uni-versity of Texas at Austin High Resolution CT facil-ity for scanning services and advice. Thanks to K.Newman, D. Winkler, and D. Vineyard for assis-tance in many aspects of this project. C. Bell pro-vided access to comparative specimens. We thankG. Bell for useful comments and discussion of ear-lier versions of this work. Thanks to O. Rieppel andM. Caldwell for thorough and constructive reviewsof this paper. This project was supported by theNational Geographic Society and the Institute forthe Study of Earth and Man at Southern MethodistUniversity. Finally we would like to remember EitanTchernov. We will miss his friendship and enthusi-asm for our joint studies of the fossils of ‘EinYabrud.

REFERENCES

Adobe Systems Inc. 2001. Adobe Photoshop version6.0.1. Adobe Systems Incorporated, San Jose, Cali-fornia,USA.

Andrews, R.C. 1921. A remarkable case of external hindlimbs in a humpback whale. American Museum Novi-tates, 9:1–6.

Bejder, L. and Hall, B.K. 2002. Limbs in whales and limb-lessness in other vertebrates: mechanisms of evolu-tionary and developmental transformation and loss.Evolution & Development, 4:445–458.

Caldwell, M.W. 1999. Squamate phylogeny and the rela-tionships of snakes and mosasauroids. ZoologicalJournal of the Linnean Society, 125:115–147.

Caldwell, M.W. 2000. On the phylogenetic relationshipsof Pachyrhachis within snakes: a response to Zaher(1998). Journal of Vertebrate Paleontology, 20:187–190.

Caldwell, M.W. and Lee, M.S.Y. 1997. A snake with legsfrom the marine Cretaceous of the Middle East.Nature, 386:705–709.

Caldwell, M.W. and Albino, A. 2002. Exceptionally pre-served skeletons of the Cretaceous snake Dinilysiapatagonica Woodward, 1901. Journal of VertebratePaleontology, 22:861–866.

Cohn, M.J. and Tickle, C. 1999. Developmental basis oflimblessness and axial patterning in snakes. Nature,399:474–479.

Cope, E.D. 1869. On the reptilian orders Pythonomorphaand Streptosauria. Proceedings of the Boston Soci-ety of Natural History, 12:250–266.

Estes, R., Frazzetta, T.H. and Williams, E.E. 1970. Stud-ies on the fossil snake Dinilysia patagonica Wood-ward. Part I. Cranial morphology. Bulletin of theMuseum of Comparative Zoology, 140:25–74.

Estes, R., de Queiroz, K., and Gauthier, J. 1988. Phylo-genetic relationships within Squamata. In Estes, R.and Pregill, G. (eds), Phylogenetic Relationships ofthe Lizard Families: Essays commemorating CharlesL. Camp. Stanford University Press: Stanford, Cali-fornia, pp. 119-270.

Haas, G. 1979. On a new snakelike reptile from theLower Cenomanian of Ein Jabrud, near Jerusalem.Bulletin du Muséum national d’Histoire naturelle,Paris (Series 4), 1:51–64.

Haas, G. 1980a. Pachyrhachis problematicus Haas,snakelike reptile from the Lower Cenomanian: ven-tral view of the skull. Bulletin du Muséum nationald’Histoire naturelle, Paris (Series 4), 2:87–104.

Haas, G. 1980b. Remarks on a new ophiomorph reptilefrom the lower Cenomanian of Ein Jabrud, Israel, p.177–192. In Jacobs, L.L. (ed.), Aspects of VertebrateHistory, Museum of Northern Arizona Press, Flag-staff, Arizona.

Lee, M.S.Y. 1997a. On snake-like dentition in mosasau-rian lizards. Journal of Natural History, 31: 303-314.

Lee, M.S.Y. 1997b. The phylogeny of varanoid lizardsand the affinities of snakes. Philosophical Transac-tions of the Royal Society of London B 352: 53-91.

Lee, M.S.Y. and Caldwell, M.W. 1998. Anatomy and rela-tionships of Pachyrhachis problematicus, a primitivesnake with hindlimbs. Philosophical Transactions ofthe Royal Society of London B, 352:1521–1552.

Lee, M.S.Y. and Scanlon, J.D. 2002a. The Cretaceousmarine squamate Mesoleptos and the origin ofsnakes. Bulletin of the Museum of Natural History,London, 68(2):131–142.

Lee, M.S.Y. and Scanlon, J.D. 2002b. Snake phylogenybased on osteology, soft anatomy and ecology. Bio-logical Reviews. 77:333–401.

Newtek Inc. 2004. Lightwave 3D. Newtek Incorporated.San Antonio, Texas.

Rage, J.C. and Escuillie´, F. 2000. Un nouveau serpentbipède du Cénomanien (Crétacé). Implicationsphylétiques. Comptes Rendus de l’Académie desSciences de Paris, Sciences de la Terre et desPlanètes, 330:513–520.

Rasband, W. 2003. ImageJ version 1.31. National Insti-tutes of Health. Bethesda, Maryland, USA.

Rieppel, O. and Kearney, M. 2001. The origin of snakes:limits of a scientific debate. Biologist. 48:100–114.

Rieppel, O. 1979. A cladistic classification of primitivesnakes based on skull structure. Z. Zool. Syst. Evolu-tionsforsch. 17:140-150.

Rieppel, O. and Zaher, H. 2000a. The intramandibularjoint in squamates, and the phylogenetic relation-ships of the fossil snake Pachyrhachis problematicusHaas. Fieldiana, Geology, 43:1–69.

Rieppel, O. and Zaher, H. 2000b. The braincases ofmosasaurs and Varanus, and the relationships ofsnakes. Zoological Journal of the Linnean Society,129:489–514.


19

Rieppel, O., Zaher, H., Tchernov, E., and Polcyn, M.J.2003. The anatomy and relationships of Haasiophisterrasanctus, a fossil snake with well-developed hindlimbs from the mid-Cretaceous of the Middle East.Journal of Paleontology, 77(3):536–558.

Tchernov, E., Rieppel, O., Zaher, H., Polcyn, M.J., andJacobs, L.L. 2000. A fossil snake with limbs. Sci-ence, 287:2010–2012.

Underwood, G. 1967. A contribution to the classificationof snakes. British Museum (Natural History), 653:1–179.

Vaytek, 2000. Voxblast 3.0. Image Analysis Facility. Uni-versity of Iowa, Ames, Iowa, USA.

Whiting, M.F., Bradler, S., and Maxwell, T. 2003. Lossand recovery of wings in stick insects. Nature,421:264–267.

Wiens, J.J. and Slingluff, J.L. 2001. How lizards turn intosnakes: A phylogenetic analysis of body-form evolu-tion in anguid lizards. Evolution, 55(11):2303–2318.

Zaher, H. 1998. The phylogenetic position of Pachyrha-chis within snakes (Squamata, Lepidosauria). Jour-nal of Vertebrate Paleontology, 18:1–3.

Zaher H, and Rieppel O. 1999a. Tooth implantation andreplacement in squamates, with special reference tomosasaur lizards and snakes. American MuseumNovitates 3271: 1-19.

Zaher, H. and Rieppel, O. 1999b. The phylogenetic rela-tionships of Pachyrhachis problematicus, and theevolution of limblessness in snakes (Lepidosauria,Squamata). Comptes Rendus de l´Académie desSciences de Paris, Sciences de la Terre et desPlanètes, 329:831–837.

Zaher, H. and Rieppel, O. 2000. A brief history ofsnakes. Herpetological Review, 31:73–76.

Zaher, H. and Rieppel, O. 2002. On the phylogeneticrelationships of the Cretaceous snakes with legs,with special reference to Pachyrhachis problematicus(Squamata, Serpentes) Journal of Vertebrate Pale-ontology, 2002, 22(1):104-109


20

Appendix 1. CT data set of Pachyrhachis problematicus (HUJ-PAL 3659). 1.1, Original data set; 1.2, data set alignedand resampled in the XZ axis.

1.1 1.2


21

Appendix 2. Comparison of light photograph of the anterior dorsal portion of Pachyrhachis problematicus (HUJ-PAL3659) and CT reconstruction of densities represented as a surface model. Note artifacts introduced by lighting condi-tions and differences in apparent surface fractures, morphology, and sutures when comparing the light photograph andthe density derived model. For example, crushing into the Meckel’s groove previously interpreted as a second mentalforamen, morphology of purported medial process of postorbital, the relationship of the maxillae to the prefrontals, andthe posterior margin of the parietal table.


22

Appendix 3. Comparison of dorsal and ventral CT reconstructions illustrating alignment of dorsal and ventral struc-tures. Note the position of ventral portion of the postorbitals (ue1 and ue2 in Figure 5) in relation to the anterior portionof the ectopterygoids (left ectopterygoid and ue3 in Figure 5).


23

Appendix 4. Animation sequence illustrating taphonomic affects on the preservation of Pachyrhachis problematicus(HUJ-PAL 3659).


24

Appendix 5. Digital reconstruction of the quadrate of Pachyrhachis problematicus. Animation sequence showingextraction of region of interest, rotation of region of interest, removal of elements other than quadrate, removal ofcrushing of the quadrate, and rotation of restored quadrate. Removal of crushing was accomplished by alignment ofthe cephalic condyle long axis with the sagittal axis of the skull and alignment of the mandibular condyle orthogonal tothe manidibular long axis. A crack apparently due to extensional forces was eliminated by a slight anterior rotation ofthe distal portion of the quadrate. Note the lack of suprastapedial process and the presence of a stylohyal process onthe distal medial shaft.

Documents

A MORPHOLOGICAL MODEL AND CT ASSESSMENT …palaeo-electronica.org/2005_1/polcyn26/polcyn26.pdf · Palaeontologia Electronica Polcyn, Michael J., Jacobs, Louis L., and Haber, Annat,