{"paper_id":"28efa24f-394e-430e-a59b-dba9a61a7b8d","body_text":"1 \n \nCryptovaranoides is not a squamate 1 \n 2 \nMichael W. Caldwell,1,2* Chase D. Brownstein,3,4 Dalton L. Meyer,5 Simon G. Scarpetta6,7, 3 \nMichael S.Y . Lee8,9, Tiago R. Simões10 4 \n 5 \n1Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada 6 \n2Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada 7 \n3Department of Ecology and Evolutionary Biology, Yale University, New Haven CT 8 \n4Stamford Museum and Nature Center, Stamford, CT 9 \n5 Department of Earth and Planetary Sciences, Yale University, New Haven CT 10 \n6 Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, 11 \nBerkeley, CA 12 \n7Department of Environmental Science, University of San Francisco, San Francisco, CA 13 \n8College of Science and Engineering, Flinders University, Adelaide 5001, Australia 14 \n9Earth Sciences Section, South Australian Museum, North Terrace, Adelaide 5000, Australia. 15 \n10Department of Ecology and Evolutionary Biology, Princeton University, Princeton NJ, 08544, 16 \nUSA 17 \n*Corresponding author: mw.caldwell@ualberta.ca  18 \n 19 \nAbstract.  20 \nAccurate reconstruction of the timescale of organismal evolution requires knowledge of the 21 \nplacement of extinct representatives among living branches. The fossil record has the capacity to 22 \nreframe hypotheses of organismal evolution by producing representatives of clades that predate 23 \npreviously known fossils or node ages. Recently, one fossil with the potential to drastically 24 \nchange current consensus surrounding the timescale of reptile diversification was described from 25 \nTriassic fissure-fill deposits in the United Kingdom. This taxon, Cryptovaranoides microlanius, 26 \nwas originally placed deep within the squamate crown clade, suggesting that many lineages of 27 \nlizards and snakes must have appeared by the Triassic and implying long ghost lineages that 28 \npaleontologists and molecular phylogeneticists have failed to detect using all other available 29 \ndata. Our team questioned this identification and instead suggested Cryptovaranoides had 30 \nunclear affinities to living reptiles, but this alternative interpretation was again challenged by the 31 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n2 \n \nteam that originally described this species. Here, we dissect the morphological character codings 32 \nused to support a crown squamate affinity for Cryptovaranoides microlanius and illustrate 33 \nempirical problems with analyses that hypothesize this taxon to be a crown squamate. Our 34 \nanalyses emphasize the importance of stringency in constructing hypodigms of fossils, 35 \nparticularly when they may be key for proper time calibration of the Tree of Life.  36 \n 37 \nKeywords: Cryptovaranoides, Triassic, fossil, Squamata, Archosauromorpha. 38 \n  39 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n3 \n \nIntroduction. 40 \nPaleontology has found a new role in the era of widespread genome sequencing of living 41 \nphylogenetic diversity: providing justification for the placement of fossil calibrations along 42 \nmolecular phylogenies [1–6]. Placing fossils on the Tree of Life has become common practice, 43 \nand new discoveries [7–10] and reshuffling of hypothesized phylogenetic relationships [11] often 44 \nrevise which fossils are best to use as prior constraints. These factors make the robust placement 45 \nof potential fossil calibrations essential for calibrating phylogenies to absolute time, which 46 \nthemselves are a foundation of modern evolutionary biology [12].  47 \nRecently, Whiteside et al. [13], described Cryptovaranoides microlanius based on a 48 \npartially articulated skeleton and a collection of referred material from the Carnian [14] to 49 \nNorian-Rhaetian [13,15–17] (237-201.5 million years ago) fissure fill deposits of England, UK. 50 \nIn a subsequent study, we [18] refuted the affinities of C. microlanius to Anguimorpha as a 51 \ndeeply nested crown squamate that was proposed by Whiteside et al. [13] based on a re-52 \nexamination of the CT scan data of the holotype and referred specimens. This prompted 53 \nsubstantial edits to how this taxon was scored in the morphological data matrix used to assess its 54 \nphylogenetic relationships, finding C. microlanius to be “…either an archosauromorph or an 55 \nindeterminate neodiapsid…” and not a lepidosaur, much less a crown squamate. In an 56 \nimpassioned response to our study, Whiteside et al. [19] disagreed with many of our anatomical 57 \nobservations and restated their position on the affinities of C. microlanius. Whiteside et al. [19] 58 \nalso referred additional Late Triassic fossils to Cryptovaranoides microlanius and presented 59 \nputative phylogenetic results that this taxon is a crown group squamate (squamate hereafter).  60 \nHere we provide point-by-point re-examination of the new evidence and interpretations 61 \nof Whiteside et al. [19] regarding the anatomy and phylogenetic affinities of C. microlanius. We 62 \nidentify and describe what we consider to be major methodological errors in the comparative 63 \nanatomical work and phylogenetic analyses of Whiteside et al. [19], and present the results of our 64 \nreanalysis of their actual data matrices and the recovered synapomorphies ignored by those 65 \nauthors. 66 \n 67 \n 68 \n 69 \n 70 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n4 \n \nResults. 71 \nErrors and Untested Synapomorphies 72 \nBoth Whiteside et al. [13] and Whiteside et al. [19] include numerous comparative anatomy 73 \nerrors that can broadly be grouped into two categories: (i) anatomical interpretation, and (ii) 74 \ntranslating these interpretations into scorings in different phylogenetic datasets. In Brownstein et 75 \nal. [18], we identified 22 errors in the study of Whiteside et al. [13] of type (i) (“Results” in 76 \nBrownstein et al. [18]) and several more of type (ii) (“Supplementary Material” in Brownstein et 77 \nal. [18]). In Whiteside et al. [19], the authors claim that there were five observational errors in 78 \nBrownstein et al. [18]. Four of these are supposed observational errors (type (i)) and one 79 \nconcerns a difference in how Brownstein et al. [18] and Whiteside et al. [19] score a character 80 \n(type (ii)). In turn, this implies that Whiteside et al. [19] acknowledge that the other 18 type (i) 81 \nerrors produced by their previous study were correctly identified by Brownstein et al. [18]. Yet, 82 \nWhiteside et al. [19] discuss additional characters in sections of their study and provide different 83 \ninterpretations of the anatomy of Cryptovaranoides microlanius than do Brownstein et al. [18], 84 \nbut without clear justification. 85 \nIn this section we also revisit each alternative interpretation of the anatomy of 86 \nCryptovaranoides microlanius provided by Whiteside et al. [19], who discussed 26 characters 87 \nthat they suggest have bearing on the placement of this taxon within Lepidosauria, Pan-88 \nSquamata, crown Squamata, and successive clades within the crown. We note first that these 89 \ncharacters do not correspond to optimized character states in the phylogenies that Whiteside et al. 90 \n[13] and WEA24 inferred, but instead to an assemblage of character state optimizations 91 \npresented in various papers in the literature (e.g., [20–22]). This is not an issue per se for a 92 \nreferral of C. microlanius to Squamata, but it does mean that these characters are of unclear 93 \nrelevance to the actual support for the position(s) of C. microlanius among reptiles that 94 \nWhiteside et al. [13] and Whiteside et al. [19] recovered in the phylogenies that they presented. 95 \nWith this noted, we provide a point-by-point discussion of character interpretations in 96 \nBrownstein et al. [18] that were challenged by Whiteside et al. [19].  97 \n 98 \nEntepicondylar and ectepicondylar foramen of humerus. The features on the humeri that 99 \nWhiteside et al. [19] figure and claim are the ente- and ectepicondylar foramina, are in fact, 100 \nfossae that are filled in with sediment. Although they claim to observe this in yet another referred 101 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n5 \n \nhumerus, they neither figure the internal structure of the bone nor provide any evidence for its 102 \nreferral to Cryptovaranoides microlanius. Contrary to the assertion of Whiteside et al. [19], CT 103 \nscans do in fact provide essential information about the structure of these fossae and show that, 104 \nwhen infill is removed, foramina are absent (Figure 4 in Brownstein et al. [18]). Further, these 105 \nstructures are in the wrong place to be the claimed foramina. In all diapsids that possess these 106 \nforamina, they are placed low on the anterior surface (entepicondylar) and high on the distal 107 \nsurface (ectepicondylar) of the humerus (e.g., see [8,21] for examples in squamates, [23] for 108 \nturtles, and [24,25] for sphenodontians) and are dissimilar in shape and size (the entepicondylar 109 \nforamen is elongated along the long axis of the humerus; the ectepicondylar foramen is circular). 110 \nThe features that Whiteside et al. [19] figure are similar in shape and size, are placed on the same 111 \nside of the bone, and differ in placement from humeral foramina observed in other exemplar 112 \nfossils and living reptile species [8,21,23–25]. The morphology of the fossae observed on the 113 \ndistal end of the humeri referred to C. microlanius by Whiteside et al. [19] are, however, similar 114 \nin placement, size, and shape to fossae described on the distal ends of the humeri of some 115 \narchosauromorphs, including the azendohsaurid Puercosuchus traverorum (Figure 8; also see 116 \nfig.13a in [26]). We further note that, even if WEA24’s interpretation was accurate, the 117 \nentepicondylar foramen is always absent in all crown squamates [8,21,27]. Among lepidosaurs, 118 \nthe presence of both entepicondylar and ectepicondylar foramina is found only among 119 \nsphenodontians, stem lepidosaurs, and stem squamates [8,28]. Further, these foramina are also 120 \npresent in many non-lepidosaurian reptiles, including captorhinids (e.g. Captorhinus), 121 \nyounginiforms (e.g., Hovasaurus and Youngina), Claudiosaurus, Acleistorhinidae 122 \n(Delorhynchus), Mesosaurus, the possible stem turtle Eunotosaurus africanus, and in some 123 \nsauropterygians (e.g., Serpianosaurus and Lariosaurus)[8,29,30]. If anything, the presence of 124 \nboth foramina would support the assignment of Cryptovaranoides as outside of crown Squamata, 125 \nnot within the clade nor as a squamate synapomorphy. The position taken by Whiteside et al. [13] 126 \nand Whiteside et al. [19] on this feature is puzzling. 127 \n 128 \nAbsence of jugal posterior process. WEA24 state: “Except for a very few fossil taxa, including 129 \ntwo polyglyphanodontians,Tianyusaurus and Polyglyphanodon, … squamates lack a posterior 130 \nprocess on the jugal…”. This is entirely incorrect. The two extinct taxa noted by WEA24 here 131 \nare only unusual among squamates in the fact that they have a complete lower temporal bar, and 132 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n6 \n \nthus an elongated jugal posterior process [21,31–33]. However, most families of squamates 133 \ninclude species with a jugal posterior process (Figure 1)[8,21,22,32,34], even if a complete lower 134 \ntemporal bar is not present. The high degree of observed variability in the development of the 135 \njugal posterior process and lower temporal bar (e.g., Figure 1) means that the placement of 136 \nCryptovaranoides microlanius within any pan-lepidosaur clade based on this feature should be 137 \nviewed with caution. The development and enclosure of the temporal fenestra in reptiles has 138 \nbeen linked to the expression of two genes, Runx2 and Msx2, in in vivo studies [35]. We suspect 139 \nthat the variable extent of this feature in many early-diverging lepidosaur and archosauromorph 140 \nlineages might be an example of the ‘zone of variability’ [36], in which the canalization of 141 \ndevelopment and other constraints (e.g., functionality; see [37]) had not yet completely acted to 142 \n‘fix’ the morphology of the posterior process. This hypothesis will of course require further 143 \nexperimental study of living model systems. Together, these observations suggest that the 144 \npresence of a jugal posterior process was incorrectly scored in the datasets used by WEA24 (type 145 \n(ii) error). 146 \n 147 \nAnterior emargination of the maxillary nasal process. Whiteside et al. [19] state that Brownstein 148 \net al. [18] “seemingly relied on the anteriorly broken left maxilla” and that “The anterior margin 149 \nof the maxillary nasal process of the right maxilla tapers anteriorly…with no evidence of the type 150 \nof emargination suggested”. The character in question (ch. 18 in the dataset used by Whiteside et 151 \nal. [19]), is one of the original characters from [8], which is the basis for the dataset used by 152 \nWhiteside et al. [19] [38]. In both datasets, this character is described as “Maxillae, posterior 153 \nemargination, between nasal and orbital processes”[boldface added], and this character is 154 \nextensively described in [8]. Therefore, Whiteside et al. [19] incorrectly assessed the anterior 155 \nmargin of the maxilla instead of the posterior margin, which is another type (ii) error. 156 \n 157 \nExpanded radial condyle of the humerus. Whiteside et al. [19] (p. 3) state that Whiteside et al. 158 \n[13] “noted an expanded radial condyle on the humerus.” Yet, nowhere in Whiteside et al. [13] 159 \ndo the authors mention or figure such a structure. Whiteside et al. [19] (p.3, fig. 1b) write in their 160 \nfigure caption regarding another isolated fragment: “(b) NHMUK PV 38911 isolated larger 161 \nspecimen of the distal end of left humerus of Cryptovaranoides microlanius in (above) anterior 162 \nand (below) posterior views showing similar features except the condyle of the capitellum.” 163 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n7 \n \n(boldface added). Then, in Whiteside et al. [19] (subsection 2.3), the authors state that this 164 \nfragment does not have a radial condyle/capitellum of the humerus, which they defend as 165 \nfollows: “This is reinforced by the larger humerus (figure 1b) which is missing the condyle, as is 166 \ntypical in the preservation of fissure lepidosaurs (e.g. Clevosaurus; [12, fig. 29b]) but the cavity 167 \nin which it sat clearly indicates a substantial condyle in life.” (boldface added). What WEA24 168 \nhighlight is that there is no condyle in this humerus or the holotype specimen and defer it to poor 169 \npreservation without justification beyond “…as is typical ….of fissure lepidosaurs…” as a reason 170 \nto conclude the condyle was present and to explain this inconsistency among the bones referred 171 \nto Cryptovaranoides. Taphonomy and poor preservation cannot be used to infer the presence of 172 \nan anatomical feature that is absent. Finally, even in the case of the isolated humerus with a 173 \npreserved capitulum, the condyle illustrated by Whiteside et al. [19] is fairly small compared to 174 \neven the earliest known pan-squamates, such as Megachirella wachtleri (Figure 4). 175 \n 176 \nPreservation of the septomaxilla. Whiteside et al. [13] and Whiteside et al. [19] claim that a 177 \nsmall, disarticulated piece of bone that is preserved anterolateral to the vomer in the block 178 \ncontaining the holotype of Cryptovaranoides microlanius is the septomaxilla. They further 179 \nsuggest that a portion of the medial surface on a maxilla referred to this taxon that is likely from 180 \na much larger reptile provides additional support for the presence of a septomaxilla in C. 181 \nmicrolanius. Simply put, the CT scans published by Whiteside et al. [13] and Whiteside et al. 182 \n[19] show that the bone in the holotype is isolated and with no clear morphological affinities to 183 \nthe septomaxillae in squamates (see CT scans in [21]). Whiteside et al. [19]  also suggest that the 184 \nidentity of this bone as the septomaxilla is supported by its placement between the maxilla and 185 \npremaxilla of the holotype but given the level of disarticulation of the holotype and the 186 \nmorphology of the bone fragment, a similar argument could be made that it is a portion of the 187 \nanterior end of one of the vomers. In any case, we feel it is premature to code C. microlanius for 188 \nany character related to the morphology of the septomaxilla based on this disarticulated and 189 \ndamaged bone fragment.  190 \n 191 \nExpanded radial condyle of the humerus. Whiteside et al. [19] provided additional justification 192 \nof the presence of an expanded radial condyle of the humerus by stating that the projection of the 193 \nradial condyle above the adjacent region of the distal anterior extremity of Cryptovaranoides 194 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n8 \n \nmicrolanius supports their choice to score the expanded radial condyle as present. This is not the 195 \ncondition specified in either of the morphological character sets that they cite [18,38] – the 196 \npresence of a distinct condyle that is expanded – and is by their own description not homologous 197 \nto the condition in other squamates.  198 \n 199 \nAnterior emargination of the maxillary nasal process. Whiteside et al. [19] flagged our 200 \ninterpretation of the anterior maxillary nasal process as emarginated, which we found united 201 \nCryptovaranoides microlanius with archosauromorphs. Although we still interpret this state as 202 \nsuch based on the computed tomography scan data, we again note than none of our analyses [18] 203 \nunambiguously place Cryptovaranoides microlanius within Archosauromorpha and that, while 204 \noptimized as such, this single character necessarily has limited utility for placing C. microlanius 205 \namong reptiles.  206 \n 207 \nSubdivision of the metotic fissure. Whiteside et al. [19] claim that the division of the metotic 208 \nfissure into the vagus foramen and recessus scala tympani by the crista tuberalis, a key squamate 209 \nfeature, can be scored for Cryptovaranoides microlanius, yet paradoxically suggest the presence 210 \nof this condition is only inferable based on other observations of the anatomy of the holotype and 211 \nreferred specimens. In fact, Whiteside et al. [19] argue that because another character relating to 212 \na different part of the structure of the metotic fissure can be inferred based on the presence of the 213 \ncrista tuberalis, that the division of the metotic fissure may also be inferred by the presence of the 214 \ncrista tuberalis. This logic would imply that no reptile taxon should exist that possesses solely 215 \neither a crista tuberalis or a subdivided metotic fissure, even when this is an observed state 216 \ncombination in squamates scored for the matrices that both our teams have used to analyze the 217 \nphylogenetic position of Cryptovaranoides microlanius [8,38]. Thus this inference lacks 218 \njustification. To verify that C. microlanius possessed a vagus foramen, Whiteside et al. [19] state 219 \nthat they searched for isolated otoccipital fragments from the same locality and found an 220 \notoccipital fragment with a vagus foramen that they refer to C. microlanius without other 221 \njustification. It is unclear to us how Whiteside et al. [19] accounted for confirmation bias when 222 \nconducting this collections search, or on what basis they refer this isolated bone to C. 223 \nmicrolanius. In any case, the presence of the lateral opening of the recessus scala tympani is not 224 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n9 \n \nfigured in the fragment, and thus the division of the metotic fissure is not demonstrated in the 225 \nreferred fragment.   226 \n 227 \nFusion of exoccipitals and opisthotics. As Whiteside et al. [19] note, we concur with their 228 \nidentification of an otoccipital in Cryptovaranoides microlanius formed by the fusion of the 229 \nexoccipitals with the opisthotics. Our concern is with the use of this feature to assign C.  230 \nmicrolanius to Squamata. Whiteside et al. [19] cite de Queiroz and Gauthier [20], who list the 231 \npresence of an otoccipital as a distinguishing feature of squamates. However, Whiteside et al. 232 \n[19] fail to provide any phylogenetic evidence supporting the optimization of this feature as a 233 \nsquamate synapomorphy in phylogenies including C. microlanius, nor do they recognize that an 234 \notoccipital is present in numerous non-squamate reptiles, including numerous archosauromorphs 235 \n[26,39,40]. For these reasons, the presence of an otoccipital alone cannot be used to assign C. 236 \nmicrolanius to Squamata or even Lepidosauria instead of Archosauromorpha or other clades of 237 \nreptiles known from the Permo-Triassic, except to distinguish the turtle total clade 238 \n(Eunotosaurus africanus possesses unfused exoccipitals and opisthotics [41]). We acknowledge 239 \nthat with respect to a character state widespread among reptiles, optimization along a phylogeny 240 \nis what is of primary importance for referring taxa to a particular clade. To this end, we reiterate 241 \nthat Whiteside et al. [19] did not show that the presence of an otoccipital optimizes as an 242 \nambiguous or unambiguous synapomorphy of Lepidosauria, Pan-Squamata, or Squamata in any 243 \nof their phylogenies. For characters that show evidence of homoplastic evolution like the 244 \npresence of an otoccipital (and indeed, the presence of a jugal posterior process; see above), 245 \nphylogenetic character optimization is essential.  246 \n 247 \nEnclosed vidian canal exiting anteriorly at base of each basipterygoid process. In our restudy of 248 \nthe holotype of Cryptovaranoides microlanius, we were unable to verify the presence of an 249 \nenclosed vidian canal exiting the sphenoid via the base of the corresponding basipterygoid 250 \nprocess. Whiteside et al. [19] take issue with our interpretation of this region of the braincase and 251 \nsuggest that a larger, abraded, and isolated sphenoid that they refer to C. microlanius also 252 \nsupports their interpretation of the anatomy of this region of the braincase. Yet, they stated that 253 \nthis fragment is of limited informativeness and appear to agree with us that the best course of 254 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n10 \n \naction is to score this character as missing data when including C. microlanius in phylogenetic 255 \nanalyses. 256 \n 257 \nDevelopment of the choanal fossa of the palatine. Squamata includes multiple instances where 258 \nthe complexity of the bony palate increases dramatically, an innovation that is related to 259 \nchemosensory evolution and the integration of different bones that form this region of the skull 260 \n[21,21,22,34,42–46]. One feature recognized as phylogenetically informative is the development 261 \nof the choanal fossa on the ventral surface of the palatine (also known as the palatine sulcus) 262 \n[18,21,34,47]. Whiteside et al. [19] claim that the development of the palatine choanal fossa in 263 \nCryptovaranoides microlanius is comparable to the development of this feature in living 264 \nsquamates, and cite the living iguanian genus Ctenosaura as an example of a squamate with 265 \nsimilar anteroposterior development of this feature as C. microlanius. Importantly, most 266 \niguanians appear to show the plesiomorphic condition where the choanal fossa is anteriorly 267 \nrestricted on the palatine [21]; this feature has contributed to debates about whether Iguania 268 \nforms the living sister group of all other crown squamates (as found in many morphological 269 \ncharacter-based phylogenies; [21,22]) or is deeply nested within the crown clade and secondarily 270 \nconvergent with rhynchocephalians (as implied by phylogenies made using DNA sequence data 271 \n[48–54] and some made using morphological data [8]). As such, this comparison is not salient to 272 \nthe discussion about whether the development of the choanal fossa in C. microlanius represents 273 \nthe squamate condition. Secondly, Whiteside et al. [19] take issue with our contention that the 274 \npalatine fossa is present, albeit variably, across a wide swath of reptilian diversity, including 275 \nmany early-diverging archosauromorph clades. They explicate this concern by distinguishing 276 \nbetween the narrow channel found in taxa like Tanystropheus (figure 1l in Whiteside et al. [19]) 277 \nand the wider fossa found in C. microlanius. We agree that the fossa in C. microlanius is more 278 \ndeveloped than in some early-diverging lepidosaurs, such as Marmoretta oxoniensis [55]. 279 \nHowever, it is clear that the feature in Cryptovaranoides falls within the variation in the choanal 280 \nfossa length and depth (Figure 2; Figure 3) that represents the ancestral condition in lepidosaurs 281 \n[21] and is exemplified across archosauromorph (see, for example [26]) and indeed diapsid [56–282 \n58] diversity. Finally, Whiteside et al. [19] cite the discovery of a large, isolated palatine that they 283 \nstate confirms the presence of a “squamate-type” choanal fossa in C. microlanius, except they 284 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n11 \n \nprovide no justification for why this isolated bone should be referred to this species. In any case, 285 \nthe morphology of that bone is also unlike those of squamates (Figure 2).   286 \n 287 \nVomer ventral ridges and dentition. Whiteside et al. [19] reiterated their earlier characterization 288 \n[13] of the vomer of Cryptovaranoides microlanius as ridged, and suggest that the morphology 289 \nof the vomerine ridges and vomerine teeth in C. microlanius is comparable to the condition in the 290 \nanguid anguimorph Pseudopus apodus. We dispute this on the basis that the vomer of C. 291 \nmicrolanius as figured by Whiteside et al. [19] shows no clear ridges equivalent to those in 292 \nPseudopus apodus [59] or other squamates with ridged vomers, including extinct forms such as 293 \nEoscincus ornatus [34] (Figure 4). Instead, the new photograph of the holotype specimen of C. 294 \nmicrolanius provided in Whiteside et al. [19] shows that the vomer is indeed toothed, but no 295 \nridges are figured or visible. We once again reexamined the CT scan data and failed to find any 296 \nstructure resembling the ridges present in some anguimorphs, although we acknowledge that the 297 \nnature of the scan data (43 microns per segment) means that the vomer surface on the scan 298 \nsegmentations is coarse. In any case, no ridges equivalent in shape or size to those found in 299 \nanguimorph squamates are present in the holotype of C. microlanius. The presence of teeth on 300 \nthe vomer is itself rare among squamates; only in the pan-scincoid Eoscincus ornatus [34] and 301 \nsome [59] anguid and varanoid [60] species are vomerine teeth documented. Whiteside et al. 302 \n[13,19] appear to suggest that the presence of vomerine ridges and a row of vomerine teeth 303 \ntherefore allies C. microlanius with anguimorphs. The structure of the vomer in C. microlanius, 304 \nhowever, is fundamentally unlike those of anguimorph squamates, which are elongate and 305 \npossess pronounced ridges that are placed medially on the ventral surface of the main body of 306 \neach vomer and each house only one row of teeth along their posterior third [59,61]. In contrast, 307 \nthe condition that Whiteside et al. [19] figure for C. microlanius shows multiple, parallel rows of 308 \nvomerine teeth on either side of the vomer that run across the entire length of the bone. This 309 \nmorphology is even unlike that observed in the only squamate known where multiple vomerine 310 \ntooth rows are present, Eoscincus ornatus [34] (Figure 4). In that species, all vomerine teeth are 311 \nrestricted to a raised surface at the posterior end of the ventral surface of the vomer main body 312 \n[34]. Thus, Whiteside et al. [19] have provided no evidence that vomerine ridges are present in 313 \nC. microlanius. We note again that vomerine teeth are widespread across neodiapsid diversity 314 \noutside Squamata [62] and appear in many lineages of Triassic archosauromorphs. 315 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n12 \n \n 316 \nLacrimal arches dorsally over lacrimal duct and floors lacrimal duct with medial process 317 \nposteriorly. We argued that this feature was unobservable in the holotype of  Cryptovaranoides 318 \nmicrolanius [18]. Whiteside et al. [19] dispute this by suggesting that the CT scan data does not 319 \nreliably show the feature, and instead provide a photograph of the holotype skull that was stated 320 \nto show this morphology (figure 2a-c in [19]). This figure shows no curvature to the lacrimal, 321 \nwhich appears as a flat element, whereas an arch dorsally and a floor ventrally would indicate the 322 \npresence of a foramen. Whiteside et al. [19] did not code this feature (dorsal arcuation of the 323 \nlacrimal over the lacrimal duct, which is posteriorly floored by the medial process of the 324 \nlacrimal) for C. microlanius, but still use it to refer C. microlanius to Anguimorpha based on 325 \noptimization as a plesiomorphy of that clade in phylogenetic analyses that place C. microlanius 326 \nwithin Anguimorpha. This appears to suggest that, despite never conducting an analysis where 327 \nthis feature is coded as ‘present’ for C. microlanius, Whiteside et al. [19] used the presence of the 328 \nfeature to ally C. microlanius with Anguimorpha, not as a recovered synapomorphy, but stating 329 \nthat it was so. This action would be an arbitrary unification of a species with a clade based on a 330 \nselected character state and would deny the equal possibility that this character state is absent 331 \ndue to secondary reversal in C. microlanius. In sum, the use of lacrimal morphology to ally C. 332 \nmicrolanius with anguimorphs is apparently not based on direct character state optimization, i.e., 333 \na test of congruence. 334 \n 335 \nDistinct quadratojugal absent. The quadratojugal cannot be located in the holotype of 336 \nCryptovaranoides microlanius [13,19]. We argued that this might be due to postmortem 337 \ndisarticulation and damage to the skull, and also noted that a complete ontogenetic series would 338 \nideally be required to test whether the quadratojugal is modified throughout ontogeny [18]. 339 \nWhiteside et al. [19] focused on our comment about the ideal situation of having an ontogenetic 340 \nseries for C. microlanius to assess the development of the quadratojugal, which we restate would 341 \nbe helpful to understand how this bone transforms through ontogeny given the complex 342 \nrestructuring to this region of the skull that occurs throughout the evolution of lepidosaurs [63]. 343 \nHowever, Whiteside et al. [19] state “we argue based on juvenile and adult specimens and the 344 \nabsence of a quadratojugal facet on the quadrate.” First, the region of the quadrate that would 345 \narticulate with the quadratojugal is not preserved in the holotype of C. microlanius, so it is 346 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n13 \n \nimpossible to tell whether a facet for the quadratojugal is present. Second, Whiteside et al. [19] 347 \nfail to provide any justification for the referral of the isolated partial quadrate NHMUK PVR 348 \n37606 to C. microlanius. Third, Whiteside et al. [19] did not identify the quadratojugal facet on 349 \nthis isolated quadrate when they figure this bone; indeed, based on the figure the process that 350 \nwould have housed the quadratojugal facet is also missing from this quadrate (NHMUK PVR 351 \n37606). It is impossible to tell whether C. microlanius lacked a quadratojugal based on the 352 \ncurrent data. Instead, all that can be said is that a quadratojugal is not preserved in the holotype 353 \nof C. microlanius, and the region housing the articular facet for the quadratojugal is not 354 \npreserved in either the holotype or referred quadrate. 355 \n 356 \nPterygoid/quadrate overlap. Whiteside et al. [19] restate the interpretation of Whiteside et al. 357 \n[13] that the pterygoid and quadrate have a short overlap in Cryptovaranoides microlanius.  358 \nWhiteside et al. [19] only compared the morphology of the quadrate in Cryptovaranoides 359 \nmicrolanius, which they agree is damaged, to the morphology present in rhynchocephalians, and 360 \nsuggest based on this comparison that their interpretation is correct. We restate that this is not 361 \npossible to verify without more complete, articulated or semi-articulated palates assignable to 362 \nCryptovaranoides microlanius based on apomorphic character states and combinations. 363 \n 364 \nFusion of the premaxillae and single median tooth. Whiteside et al. [19] suggest that Brownstein 365 \net al. [18] incorrectly characterized the nature of fusion of the premaxillae into a single median 366 \nelement in Cryptovaranoides microlanius. However, we reiterate that no justification has been 367 \ngiven in any paper [13,19] for referring these isolated premaxillae to C. microlanius. Whiteside 368 \net al. [19] focus on differentiating these isolated large premaxillae from the premaxillae of two 369 \nother fissure fill lepidosaurs, Gephyrosaurus bridensis and Diphydontosaurus avonis, without 370 \nconsidering the possibility that additional taxa are present in the assemblage. Scoring fused 371 \npremaxillae as present for C. microlanius despite the presence of unfused, paired premaxillae in 372 \nthe holotype defines (1) ontogenetic character state transformations solely based on the relative 373 \nsize of the holotype and larger isolated bones referred without justification and (2) which 374 \ncharacter state among those present in ontogeny is the phylogenetically informative one. 375 \nDefining both of these requires a robust ontogenetic series, which is not available for C. 376 \nmicrolanius at present. Observations of the development of living squamates also suggest that 377 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n14 \n \nthese larger fused premaxillae should not be referred to C. microlanius. In crown squamates with 378 \na median premaxilla, the premaxilla is invariably a single element upon first appearance very 379 \nearly in embryonic development [64–68]. In contrast, the holotype of C. microlanius, which is 380 \nvery clearly a juvenile and not an embryonic specimen, possesses paired premaxillae. The 381 \nontogenetic series that Whiteside et al. [19] suggest for C. microlanius therefore differs from any 382 \nknown squamate with a single median premaxilla. 383 \n 384 \nPeg-in-notch articulation of quadrate with rod-shaped squamosal. Whiteside et al. [19] suggest 385 \nthat both our teams are in agreement about the presence of a peg-in-notch articulation between 386 \nthe quadrate and squamosal. We reiterate that we believe the presence of this type of articulation 387 \nis unclear based on the available data for the holotype, as these bones are both damaged in the 388 \nrelevant sections and disarticulated (Figure 5). 389 \n 390 \nFrontal underlaps parietal laterally on frontoparietal suture. Whiteside et al. [19] confirm that 391 \nthe presence of this feature in Cryptovaranoides microlanius is based on the morphology of a 392 \nreferred isolated frontal that they state matches the corresponding articular portion of the 393 \nprefrontal in the holotype. However, we do not understand how this bone could possibly match 394 \nthe corresponding articular surface unless it was from the same individual or an animal of 395 \nexactly the same size. Unless Whiteside et al. [19] were actually able to articulate these bones, it 396 \nis unclear how this inference can be made. Finally, we note that the posterior process of the 397 \nprefrontal is broken off in the holotype of Cryptovaranoides microlanius. In squamates and other 398 \nlepidosaurs, this process abuts the lateral surface of the frontal along its anteroposterior axis. 399 \nSeveral of us (C.D.B. and D.L.M.) worked to rearticulated the holotype of Eoscincus ornatus, 400 \nwhich involved rearticulating the prefrontal and frontal. Rearticulating these bones is simply 401 \nimpossible without the complete posterior process of the prefrontal, as the orientation of this 402 \nprocess must match the curvature of the lateral margin of the frontal. Because the isolated frontal 403 \nis not figured in either paper by Whiteside et al. [13,19], it is impossible for us to verify whether 404 \nthis bone actually matches the corresponding articulation surface on the prefrontal in the 405 \nholotype. In any case, we regard it a best practice to exclude this isolated frontal from 406 \ndiscussions of the affinities of C. microlanius. 407 \n 408 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n15 \n \nMedial process of the articular and prearticular. Whiteside et al. [19] revise their initial [13] 409 \ncharacterization of the medial process and refer to it as ‘rudimentary,’ scoring it as unobservable. 410 \nWe determined that this process is absent [18] and offer no further comment besides that it 411 \nappears the distinction between our interpretation of this feature and that of Whiteside et al. [19] 412 \nis, as they explicate, largely arbitrary.    413 \n 414 \nBicapitate cervical ribs and cervical ribs with an anteriorly oriented process.  Whiteside et al. 415 \n[19] took issue with our characterization of the morphology of the cervical ribs in 416 \nCryptovaranoides microlanius, and compared the bicapitate morphology of the cervical ribs in 417 \nC. microlanius to two anguimorph squamates, Pseudopus apodus and Varanus spp. However, the 418 \ncervical ribs of P . apodus are not bicapitate, as shown by the very figure from [69] that Whiteside 419 \net al. [19] cited. Similarly, the ribs of Varanus are unicapitate, not bicapitate, as shown in [70]. 420 \nWe assume that Whiteside et al. [19] referred to the morphology of the cervical rib head in P . 421 \napodus because of the presence of a posterior process on the rib head [69]. This is not the 422 \nbicapitate condition and is not homologous with the morphology of the cervical rib heads  423 \nin either C. microlanius or archosauromorphs, where an anterior process is offset from the 424 \nprocess formed by the capitulum and tuberculum [39,71]. We reiterate that the condition in C. 425 \nmicrolanius is identical to that in archosauromorphs (figure 2c, figure 3 in [18]); the comparisons 426 \nmade by Whiteside et al. [19] are across non-homologous structures and result from a 427 \nmisinterpretation of cervical rib anatomy. 428 \n 429 \nCervical and dorsal vertebral intercentra. Whiteside et al. [19] suggest that we inferred the 430 \npresence of cervical and dorsal intercentra in Cryptovaranoides microlanius; however, we did 431 \nnot propose this in our paper. In fact, Whiteside et al. [13] state in their original paper that there 432 \n“are gaps between the vertebrae indicating that intercentra were present (but displaced in the 433 \nspecimen) on CV3 and posteriorly. Some images of bones on the scans are identified as 434 \nintercentra” (p. 11, [13]). The statement in [19] consequently represents an incorrect attribution 435 \nand an incorrect characterization of our reexamination, as we determined that no cervical and 436 \ndorsal intercentra were preserved or present in the holotype. Whiteside et al. [19] justify their 437 \nposition that cervical intercentra are present in C. microlanius based on the morphology of 438 \nanother isolated bone that they refer to this taxon. In any case, the absence of dorsal intercentra is 439 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n16 \n \nnot a distinguishing feature of squamates because several lineages of squamates, including 440 \nlacertids, xantusiids, gekkotans, and the stem-squamate Bellairsia gracilis all possess cervical 441 \nand dorsal intercentra [38,72,73].  442 \n 443 \nAnterior dorsal vertebrae, diapophysis fuses to parapophysis. Whiteside et al. [19] concur with 444 \nBrownstein et al. [18] that the diapophyses and parapophyses are unfused in the anterior dorsals 445 \nof the holotype of Cryptovaranoides microlanius, and restate that fusion of these structures is 446 \nbased on the condition they observed in isolated vertebrae that they again refer to C. microlanius 447 \nwithout justification. As such, this feature should not be scored as present for C. microlanius. 448 \n 449 \nZygosphene–zygantrum in dorsal vertebrae. Whiteside et al. [19] again claim that the 450 \nzygosphene-zygantrum articulation is present in the dorsal series of Cryptovaranoides 451 \nmicrolanius based on the presence of  ‘rudimentary zygosphenes and zygantra’ in isolated 452 \nvertebrae that they again refer to this species without justification. The structures that Whiteside 453 \net al. [19] label as the zygosphenes and zygantra (figure 3 in [19]) are clearly not, however, 454 \nzygosphenes and zygantra, as the former is by definition a centrally located wedge-like process 455 \nthat fits into the zygantrum, which is a fossa on the following vertebra. The structures labeled 456 \nzygosphenes and zygantra by Whiteside et al. [19] are the dorsal surfaces of the 457 \nprezygopophyses and the medial margins of the postzygapophyses. 458 \n 459 \nAnterior and posterior coracoid foramina/fenestra. Whiteside et al. [19] use isolated coracoids 460 \nreferred to Cryptovaranoides microlanius to support their claim that the upper ‘fenestra’ 461 \n(foramen) of the coracoid in the holotype specimen is indeed a foramen. Confusingly, Whiteside 462 \net al. [19] label this feature as the ‘primary coracoid fenestra’ in their figure 3i-j, even though it is 463 \nclearly the coracoid foramen. Whiteside et al. [19] appear to have confused the coracoid 464 \nforamen, which is completely bounded by bone and placed inside the coracoid, with the coracoid 465 \nfenestra, which is bounded in part by the coracoid (the coracoid margin is curved to form part of 466 \nthe bounding region in species with the coracoid fenestra) but also by the interclavicle (see 467 \nfigures in [18,21]. The coracoid fenestra is not contained within the coracoid. This feature is also 468 \nnot shown to be optimized as a pan-squamate synapomorphy in any phylogeny including 469 \nCryptovaranoides microlanius [13,19], so its bearing on the identification of C. microlanius as a 470 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n17 \n \npan-squamate is unclear to us. Finally, we note here that Whiteside et al. [19] appear to have 471 \nlabeled a small piece of matrix attached to a coracoid that they refer to C. microlanius as the 472 \nsupracoroacoid [sic] foramen in their figure 3, although this labeling is inferred because only 473 \n“suc, supracoroacoid [sic]” is present in their figure 3 caption.  474 \n 475 \nAtlas pleurocentrum fused to axis pleurocentrum. Whiteside et al. [19] reiterate their claim that 476 \nthe atlas and axis pleurocentra are present in Cryptovaranoides microlanius based on their 477 \nidentification of an isolated, globose bone fragment as the atlas intercentrum, but provide no 478 \nadditional justification for this identification and refer the reader to their original paper for a 479 \nfigure of this bone [13], which is only visible on CT scans due to its entombment within the 480 \nmatrix that includes the holotype. To this end, Whiteside et al. [19] revise their initial 481 \ninterpretation of the what they identify as the preserved atlas-axis region, but again without any 482 \njustification or figures detailing how they reidentified a bone fragment that they had initially 483 \nbelieved was a cervical intercentrum as the atlas centrum and intercentrum 2. Thus, Whiteside et 484 \n[19] do not provide any additional description of how they reidentified these bones or a figure 485 \nillustrating their revised interpretation, and so we cannot comment on the strength of their 486 \nrevised interpretation. Again, we note that we were not able to identify the morphology of the 487 \natlas and axis with any confidence in the holotype of C. microlanius, and so we again believe any 488 \nrelevant characters should be scored as missing data for this taxon. 489 \n 490 \nMidventral crest of presacral vertebrae. Whiteside et al. [19] appear to agree with our assertion 491 \nthat a midventral crest is not present on the presacral vertebrae [18]. We never challenged their 492 \nscoring of keels on the caudal centra as missing data. Rather, we stated that keels are clearly 493 \npresent on the cervical vertebrae [18]. 494 \n 495 \nAngular does not extend posteriorly to reach articular condyle. Whiteside et al. [19] state that 496 \nthe posterior portion of the angular is present medially on the right mandible in the holotype, and 497 \nprovide an interpretation of the anatomy of this region. They cite figure 3a in Whiteside et al. 498 \n[19], but this shows the mandible in lateral view and only a small portion of the angular is 499 \nvisible. As such, it is not clear to us what they interpret to be the posterior portion of the angular. 500 \nIn any case, we could not identify anywhere on the CT scans or on the accessible portions of the 501 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n18 \n \nreal specimen (e.g., figure 2b in [19]) the feature that Whiteside et al. [19] consider to be the 502 \nposterior angular extent. Whiteside et al. [19] describe the posterior extent of the angular as a 503 \n‘contoured feature,’ but we are entirely unclear about what this actually describes.  504 \n 505 \nUlnar patella. The only disagreement between our interpretation [18] and that made by 506 \nWhiteside et al. [13,19] concerns whether the ulnar patella is absent due to the ontogenetic state 507 \nor preservation status of the holotype [13,19] or an ontogenetically invariable feature of the 508 \nanatomy of Cryptovaranoides microlanius [18]; we suggested the latter based on our observation 509 \nthat the forelimb of the holotype is articulated and mostly complete.   510 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n19 \n \nOverarching Empirical Problems in Whiteside et al. [19].  511 \nUnassignable specimens and “hypodigm inflation.” Whiteside et al. [13] and Whiteside et al. 512 \n[19] describe and defend their addition of isolated elements to fill in gaps in the holotype concept 513 \nof Cryptovaranoides to build, in our view, an unjustifiably inflated hypodigm. WEA24 (p. 15) 514 \ntry to ameliorate this problem in their Section (5.5) where they state that: “We emphasize that we 515 \nalways match isolated bones with their equivalents on the holotype…” and then state in 516 \ncontradiction that: “We consider it remiss not to include isolated bones as they provide details 517 \nwhich no scan can. Furthermore, as the holotype is a juvenile, they give additional information 518 \nfrom larger, and presumably older individuals, on characters of the holotype otherwise 519 \nunavailable or uncertain.” (boldface added). In summary, Whiteside et al. [19] claimed to only 520 \nmatch isolated bones with equivalent ones in the holotype but also acknowledged use of 521 \nelements that are not comparable with the ones in the holotype. This lack of consistency is a 522 \nserious empirical issue. 523 \n 524 \nApomorphic characters not empirically obtained. Whiteside et al. [19] discussed nearly 30 525 \nanatomical characters (Sections 2-6), most of which are used to support their core hypothesis that 526 \nCryptovaranoides is a squamate. Yet, none of these 30 characters or conditions are actually 527 \nfound by Whiteside et al. [19] to be synapomorphies of Squamata in their various phylogenetic 528 \nanalyses. In other words, they did not present the results of their Tests of Congruence, but rather 529 \nsimply elected to argue that untested interpretations of anatomy were apomorphies, 530 \nsynapomorphies, or shared characters.This is a non-trivial substantive methodological flaw in 531 \nWhiteside et al. [13], that was perpetuated in Whiteside et al. [19], and that nullifies the bulk of 532 \nthe arguments presented repeatedly in both studies. 533 \nIn Section 6, Whiteside et al. [19] (p. 16) indicate they modified the datasets of 534 \nBrownstein et al. [18] and [38], but preferred the results of [11] and performed two different 535 \nanalyses based on [38]: one using only morphological data, and one using morphological data 536 \nwith several constraints from a molecular backbone. The former was tested using maximum 537 \nparsimony and the latter using Bayesian inference. What is not clear from either Section 6 or 7, 538 \nis which phylogenetic analysis was used by WEA24 to “review the apomorphy distribution”. But 539 \nthis uncertainty is inconsequential as the apomorphy distributions discussed in Section 7 of 540 \nWhiteside et al. [19] were not derived from their phylogenetic analyses. Instead, Whiteside et al. 541 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n20 \n \n[19] (p. 19) exclusively extracted characters from the literature to support their identification of 542 \nCryptovaranoides as a squamate, rather than basing this inference primarily on their own 543 \nphylogenetic analyses. These literature sourced characters include “two diagnostic characters of 544 \nSquamata (=crown-clade Squamata)” and “…further eight squamate synapomorphies” listed by 545 \nWEA24 (Section 7, p. 19). As stated by the authors, “we give the citation for the squamate 546 \nsynapomorphy at the end of each character”— indicating that these diagnostic characters or 547 \nsynapomorphies were picked from the literature and not derived from ancestral state 548 \nreconstructions based on their phylogenetic results. 549 \nIn order to check the characters listed by Whiteside et al. [19] (p.19) as “two diagnostic 550 \ncharacters” and “eight synapomorphies” in support of a squamate identity for Cryptovaranoides, 551 \nwe conducted parsimony analysis of the revised version of the dataset [38] provided by WEA24 552 \nin TNT v 1.5 [74]. We used Whiteside et al.’s [19] own data version—e.g., with (0) scored for 553 \ncharacter 1 and not including character 383. We recovered eight apomorphies at the squamate 554 \nnode of which only three were recovered as unambiguous synapomorphies (boldface indicates 555 \nthe state as scored by Whiteside et al. [19]for Cryptovaranoides): 556 \nCh. 138. Basisphenoid (or fused parabasisphenoid), ventral aspect, shape, concavity: 557 \nsingle (0)/divided (1)/ absent (2). 0 -> 2 558 \nCh. 142. Prootics, alar crest: absent (0)/ present (1). 0->1 559 \nCh. 347. Prefrontal/palatine antorbital contact: absent (0) / narrow forming less than 1/3 560 \nthe transverse distance between the orbits (1) / contact broad, forming at least 1/2 the distance 561 \nbetween the orbits (2). 01->2 562 \nThe eight features described by Whiteside et al. [19] (p.19) as synapomorphies for 563 \nCryptovaranoides + Squamata were also not inferred at their recovered crown squamate node 564 \nfrom their own results. Rather, they were copied nearly verbatim from principally two sources 565 \n[21,75] and presented as if they were recovered as synapmorphies by Whiteside et al. [19] (p. 566 \n19). In Table 1, the italicized text is from Whiteside et al. [19] (p.19), including their literature 567 \nsource for the supposed synapomorphy. The non-italicized text is the character number and state 568 \nfrom [11] as recovered by us from the TNT analysis conducted for this reassessment of 569 \nWhiteside et al. [19]. We also include where in our phylogeny the character state is recovered as 570 \nsynapomorphic (Table 1).  571 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n21 \n \nOur reanalysis shows that Whiteside et al. [19] did not diagnose Cryptovaranoides + 572 \ncrown Squamata based on synapomorphies found by their own analyses as there were only three 573 \n(see our results above). Instead, Whiteside et al. [19] provided ad hoc mischaracterizations of 574 \ndiagnostic features of crown Squamata from studies that did not include Cryptovaranoides and 575 \nthen discussed and reviewed synapomorphies of Squamata from these sources [21,75]. Because 576 \neach additional taxon has the possibility of inducing character reoptimization, an empirical 577 \nanalysis of character optimization that includes a given new taxon is necessary to support 578 \nreferring said taxon to any particular clade. If Cryptovaranoides was indeed a Triassic crown 579 \nsquamate, it could plausibly show character distributions not previously sampled among known 580 \nmembers of the crown or stem group.  581 \n 582 \nDiscussion and Conclusions. 583 \nAs we noted above and in Brownstein et al. [18], the anatomy of Cryptovaranoides is 584 \nsimilar to many Late Triassic neodiapsid reptiles. For example, the quadrates of 585 \nCryptovaranoides are closely comparable to those of archosauromorphs such as Prolacerta [76], 586 \nMacronemus [77] and Malerisaurus [78], with which Cryptovaranoides shares the presence of a 587 \nnotch on the quadrate for an immobile articulation with the squamosal. Furthermore, WEA24’s 588 \ninference that the quadrate, the notch, and the articulation with the squamosal was mobile, i.e., 589 \nstreptostylic as in squamates, is unfounded. 590 \nSimilarly, the vertebrae and cervical ribs of the holotype of Cryptovaranoides do not 591 \nresemble those of squamates, but in fact share important features with non-squamate 592 \nneodiapsids, especially archosauromorphs (a point left unaddressed by Whiteside et al. [19]). For 593 \nexample, whereas fusion of the neural arches to the centra occurs during embryonic ossification 594 \nin squamates [79], in Cryptovaranoides unfused bony neural arches and centra are present, as 595 \ncommonly observed in archosaurs and other non-lepidosauromorph neodiapsids [80,81]—we 596 \nprovide a long-form review of these and other features in Cryptovaranoides that compare 597 \nfavorably with non-squamate reptiles in Supplementary Material.   598 \nSeveral errors in Whiteside et al. [13] identified in Brownstein et al. [18], and subsequent 599 \nerrors in Whiteside et al. [19] that were discussed above result in the incorrectly interpreted 600 \nneodiapsid and lepidosaur anatomy of Cryptovaranoides and consequently provide erroneous 601 \nscorings for Cryptovaranoides for morphological character matrices. Whiteside et al. [19] also 602 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n22 \n \nmake additional errors on an alpha taxonomic level, such as the unjustified inflation of the 603 \nCryptovaranoides hypodigm based on contradictory arguments pertaining to the assignment of 604 \nfragmentary and isolated elements to the holotype. Finally, we highlight here that where 605 \nWhiteside et al. [13] and Whiteside et al. [19] should have reported their own recovered 606 \nsynapomorphies, that is, the actual results of their phylogenetic analyses, rather than listing a 607 \nsubstantive number of supposed apomorphies that the authors argue support the squamate 608 \naffinities of Cryptovaranoides broadly, and anguimorph affinities more specifically. On a 609 \nmethodological and analytical level, we do not consider that manually selecting apomorphic 610 \ncharacters supporting their preferred placement of Cryptovaranoides instead of using characters 611 \nempirically obtained from phylogenetic ancestral state reconstruction of their phylogenetic 612 \nresults, stands as valid support of a phylogenetic hypothesis. 613 \nWe end with a perspective on the fossil record of neodiapsid evolution. The anatomies 614 \nand morphologies that diagnose crown group squamates are many and varied, and except for a 615 \nfew features, hardly universally distributed amongst the living and fossil members of the crown. 616 \nThey are themselves the product of some 250 million years of evolutionary time and would not 617 \nhave evolved in a linear fashion. Rather, phylogenetic analyses of diverse extinct and living 618 \nreptile clades have shown that the squamate bauplan originated in the context of extensive 619 \nmosaic and homoplastic osteological character evolution [8,30,34,47,58]. We do not doubt that 620 \nmembers of Pan-Squamata were present during the Triassic; this is supported by the fossil record 621 \n[8] as well as numerous time-calibrated phylogenies based on genomic [48,49] morphological 622 \n[34,38,47] and total-evidence [8,30] data. However, Whiteside et al. 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(doi:10.1111/brv.12666) 855 \n 856 \n 857 \n 858 \n 859 \n 860 \n 861 \n 862 \n 863 \n 864 \n 865 \n  866 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n30 \n \nFigures 867 \n 868 \n 869 \n 870 \nFigure 1. Comparison of jugal morphologies among living lepidosaurs. Note the variability in 871 \nthe presence and development of the posterior process, as well as the presence of an ossified 872 \njugal itself. CT scan images are from digimorph.org.  873 \n 874 \n 875 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n31 \n \n 876 \nFigure 2. Comparison of palatine morphologies. Blue shading indicates choanal fossa. Top 877 \nimage of Cryptovaranoides referred palatine is from Whiteside et al. [19].  878 \n 879 \n 880 \n 881 \n 882 \n 883 \n 884 \n 885 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n32 \n \n 886 \nFigure 3. Choanal fossa character scoring. 887 \n  888 \n 889 \nProminent choanal fossa on anterior margin of ventral surface of palatine \nSphenodon punctatus\nafter Gauthier et al. (2012)\n†Eoscincus ornatus \nafter Brownstein et al. (2022)\n0: absent 2: present and extending\nover halfway along palatine\nconsidered “prominent” by WEA24 1: present, limited to\nanterior third of palatine\n†Helioscopos dickersonae\nafter Meyer et al. (2023)\n†Cryptovaranoides \nHolotype\n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n33 \n \n 890 \nFigure 4. Comparison of vomer morphologies. Top image is Eoscincus ornatus from Brownstein 891 \net al. (2022). Note that the rows of vomerine teeth are posteriorly placed, and the vomerine 892 \nridges are large and laterally placed. Bottom image of Cryptovaranoides holotype is from 893 \nWhiteside et al. [19]. 894 \n 895 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n34 \n \n 896 \n 897 \nFigure 5. Quadrate-squamosal articulation character scoring.  898 \n 899 \n 900 \n 901 \nFigure 6. Anterior articulation of vomer and maxilla character scoring.  902 \n 903 \n 904 \nCephalic head of (mobile) quadrate with notch for the squamosal, peg-in-notch articulation\n0: absent 1: present\nSphenodon punctatus\nafter Gauthier et al. (2012)\nAmphiglossus splendidus\nafter Gauthier et al. (2012)\n†Cryptovaranoides \nHolotype\nconsidered “present” by WEA24 \nfeature WEA24 identify as notch\nnotchsquamosal\nquadrate\nVomer and maxilla meet at anterior margin of fenestra exochoanalis \n0: absent 1: present considered “present” by WEA24 \nSphenodon punctatus\nafter Gauthier et al. (2012)\npremaxilla\nvomer\nmaxilla\nPogona vitticeps\nafter Gauthier et al. (2012)\n†Cryptovaranoides \nHolotype\ndamaged\n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n35 \n \n 905 \nFigure 7. Presence of a medially positioned posterior mylohyoidal foramen on the mandible. As 906 \nshown, there is no identifiable foramen on the mandible of Cryptovaranoides. Bottom image of 907 \nCryptovaranoides holotype skull is from Whiteside et al. [19].  908 \n 909 \n 910 \n 911 \nCelestus enneagrammus\nafter Gauthier et al. (2012)\n†Cryptovaranoides \nHolotype\nposition of foramen \naccording to WEA24\n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n36 \n \n 912 \n 913 \n 914 \n 915 \n 916 \nFigure 8. Comparison of the humerus of Cryptovaranoides microlanius to Puercosuchus 917 \ntraverorum [26]. Left image of Cryptovaranoides holotype humerus is from Whiteside et al. 918 \n[19].  919 \n 920 \n 921 \n 922 \n  923 \n†Cryptovaranoides \nHolotype\n†Peurcosuchus traverorum \nafter Marsh et al. (2022)\n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint \n\n \n \n37 \n \nTable 1. 924 \n 925 \nCharacter Number in Tałanda \net al. (2022) \nStudy Cited in \nWEA24  \nSynapomorphy of Unambiguous \nOptimization \nCephalic head of (mobile) \nquadrate with notch for the \nsquamosal, peg-in-notch \narticulation with rod-\nshaped squamosal \n \n123 de Queiroz and \nGauthier (2020) \nPan-Squamata 1→0 \nV omer and maxilla meet at \nanterior margin of fenestra \nexochoanalis \n371 Gauthier et al. \n(2012) \nN/A N/A \nProminent choanal fossa \non anterior margin of \nventral surface of palatine \n100 Gauthier et al. \n(2012) \nLepidosauria N/A \nSubdivision of embryonic \nmetotic fissure by the \ncrista tuberalis into vagus \n(jugular) foramen and \nrecessus scala tympani \n382 Simões et al. \n(2018); de \nQueiroz and \nGauthier (2020) \nN/A N/A \nNo quadrate foramen 118 Gauthier et al. \n(2012) \nLepidosauria 1→0 \nMedially positioned \nposterior mylohyoidal \nforamen on mandible \n163 Gauthier et al. \n(2012) \nN/A N/A \nFusion of exoccipitals and \nopisthotics forming an \notoccipital \n151 Gauthier et al. \n(2012); de \nQueiroz and \nGauthier (2020) \nN/A N/A \nTrunk vertebrae lack \nintercentra \n237 de Queiroz and \nGauthier (2020) \nPan-Unidentata 1→0 \n 926 \n 927 \n 928 \n 929 \n 930 \n.CC-BY 4.0 International licenseavailable under a \nwas not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made \nThe copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint","source_license":"CC-BY-4.0","license_restricted":false}