† Cryptovaranoides is not a squamate

Cryptovaranoides, Triassic, fossil, Squamata, Archosauromorpha. 38 39 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 3 Introduction. 40 Paleontology has found a new role in the era of widespread genome sequencing of living 41 phylogenetic diversity: providing justification for the placement of fossil calibrations along 42 molecular phylogenies [1–6]. Placing fossils on the Tree of Life has become common practice, 43 and new discoveries [7–10] and reshuffling of hypothesized phylogenetic relationships [11] often 44 revise which fossils are best to use as prior constraints. These factors make the robust placement 45 of potential fossil calibrations essential for calibrating phylogenies to absolute time, which 46 themselves are a foundation of modern evolutionary biology [12]. 47 Recently, Whiteside et al. [13], described Cryptovaranoides microlanius based on a 48 partially articulated skeleton and a collection of referred material from the Carnian [14] to 49 Norian-Rhaetian [13,15–17] (237-201.5 million years ago) fissure fill deposits of England, UK. 50 In a subsequent study, we [18] refuted the affinities of C. microlanius to Anguimorpha as a 51 deeply nested crown squamate that was proposed by Whiteside et al. [13] based on a re-52 examination of the CT scan data of the holotype and referred specimens. This prompted 53 substantial edits to how this taxon was scored in the morphological data matrix used to assess its 54 phylogenetic relationships, finding C. microlanius to be “…either an archosauromorph or an 55 indeterminate neodiapsid…” and not a lepidosaur, much less a crown squamate. In an 56 impassioned response to our study, Whiteside et al. [19] disagreed with many of our anatomical 57 observations and restated their position on the affinities of C. microlanius. Whiteside et al. [19] 58 also referred additional Late Triassic fossils to Cryptovaranoides microlanius and presented 59 putative phylogenetic results that this taxon is a crown group squamate (squamate hereafter). 60 Here we provide point-by-point re-examination of the new evidence and interpretations 61 of Whiteside et al. [19] regarding the anatomy and phylogenetic affinities of C. microlanius. We 62 identify and describe what we consider to be major methodological errors in the comparative 63 anatomical work and phylogenetic analyses of Whiteside et al. [19], and present the results of our 64 reanalysis of their actual data matrices and the recovered synapomorphies ignored by those 65 authors. 66 67 68 69 70 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 4 Results. 71 Errors and Untested Synapomorphies 72 Both Whiteside et al. [13] and Whiteside et al. [19] include numerous comparative anatomy 73 errors that can broadly be grouped into two categories: (i) anatomical interpretation, and (ii) 74 translating these interpretations into scorings in different phylogenetic datasets. In Brownstein et 75 al. [18], we identified 22 errors in the study of Whiteside et al. [13] of type (i) (“Results” in 76 Brownstein et al. [18]) and several more of type (ii) (“Supplementary Material” in Brownstein et 77 al. [18]). In Whiteside et al. [19], the authors claim that there were five observational errors in 78 Brownstein et al. [18]. Four of these are supposed observational errors (type (i)) and one 79 concerns a difference in how Brownstein et al. [18] and Whiteside et al. [19] score a character 80 (type (ii)). In turn, this implies that Whiteside et al. [19] acknowledge that the other 18 type (i) 81 errors produced by their previous study were correctly identified by Brownstein et al. [18]. Yet, 82 Whiteside et al. [19] discuss additional characters in sections of their study and provide different 83 interpretations of the anatomy of Cryptovaranoides microlanius than do Brownstein et al. [18], 84 but without clear justification. 85 In this section we also revisit each alternative interpretation of the anatomy of 86 Cryptovaranoides microlanius provided by Whiteside et al. [19], who discussed 26 characters 87 that they suggest have bearing on the placement of this taxon within Lepidosauria, Pan-88 Squamata, crown Squamata, and successive clades within the crown. We note first that these 89 characters do not correspond to optimized character states in the phylogenies that Whiteside et al. 90 [13] and WEA24 inferred, but instead to an assemblage of character state optimizations 91 presented in various papers in the literature (e.g., [20–22]). This is not an issue per se for a 92 referral of C. microlanius to Squamata, but it does mean that these characters are of unclear 93 relevance to the actual support for the position(s) of C. microlanius among reptiles that 94 Whiteside et al. [13] and Whiteside et al. [19] recovered in the phylogenies that they presented. 95 With this noted, we provide a point-by-point discussion of character interpretations in 96 Brownstein et al. [18] that were challenged by Whiteside et al. [19]. 97 98 Entepicondylar and ectepicondylar foramen of humerus. The features on the humeri that 99 Whiteside et al. [19] figure and claim are the ente- and ectepicondylar foramina, are in fact, 100 fossae that are filled in with sediment. Although they claim to observe this in yet another referred 101 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 5 humerus, they neither figure the internal structure of the bone nor provide any evidence for its 102 referral to Cryptovaranoides microlanius. Contrary to the assertion of Whiteside et al. [19], CT 103 scans do in fact provide essential information about the structure of these fossae and show that, 104 when infill is removed, foramina are absent (Figure 4 in Brownstein et al. [18]). Further, these 105 structures are in the wrong place to be the claimed foramina. In all diapsids that possess these 106 foramina, they are placed low on the anterior surface (entepicondylar) and high on the distal 107 surface (ectepicondylar) of the humerus (e.g., see [8,21] for examples in squamates, [23] for 108 turtles, and [24,25] for sphenodontians) and are dissimilar in shape and size (the entepicondylar 109 foramen is elongated along the long axis of the humerus; the ectepicondylar foramen is circular). 110 The features that Whiteside et al. [19] figure are similar in shape and size, are placed on the same 111 side of the bone, and differ in placement from humeral foramina observed in other exemplar 112 fossils and living reptile species [8,21,23–25]. The morphology of the fossae observed on the 113 distal end of the humeri referred to C. microlanius by Whiteside et al. [19] are, however, similar 114 in placement, size, and shape to fossae described on the distal ends of the humeri of some 115 archosauromorphs, including the azendohsaurid Puercosuchus traverorum (Figure 8; also see 116 fig.13a in [26]). We further note that, even if WEA24’s interpretation was accurate, the 117 entepicondylar foramen is always absent in all crown squamates [8,21,27]. Among lepidosaurs, 118 the presence of both entepicondylar and ectepicondylar foramina is found only among 119 sphenodontians, stem lepidosaurs, and stem squamates [8,28]. Further, these foramina are also 120 present in many non-lepidosaurian reptiles, including captorhinids (e.g. Captorhinus), 121 younginiforms (e.g., Hovasaurus and Youngina), Claudiosaurus, Acleistorhinidae 122 (Delorhynchus), Mesosaurus, the possible stem turtle Eunotosaurus africanus, and in some 123 sauropterygians (e.g., Serpianosaurus and Lariosaurus)[8,29,30]. If anything, the presence of 124 both foramina would support the assignment of Cryptovaranoides as outside of crown Squamata, 125 not within the clade nor as a squamate synapomorphy. The position taken by Whiteside et al. [13] 126 and Whiteside et al. [19] on this feature is puzzling. 127 128 Absence of jugal posterior process. WEA24 state: “Except for a very few fossil taxa, including 129 two polyglyphanodontians,Tianyusaurus and Polyglyphanodon, … squamates lack a posterior 130 process on the jugal…”. This is entirely incorrect. The two extinct taxa noted by WEA24 here 131 are only unusual among squamates in the fact that they have a complete lower temporal bar, and 132 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 6 thus an elongated jugal posterior process [21,31–33]. However, most families of squamates 133 include species with a jugal posterior process (Figure 1)[8,21,22,32,34], even if a complete lower 134 temporal bar is not present. The high degree of observed variability in the development of the 135 jugal posterior process and lower temporal bar (e.g., Figure 1) means that the placement of 136 Cryptovaranoides microlanius within any pan-lepidosaur clade based on this feature should be 137 viewed with caution. The development and enclosure of the temporal fenestra in reptiles has 138 been linked to the expression of two genes, Runx2 and Msx2, in in vivo studies [35]. We suspect 139 that the variable extent of this feature in many early-diverging lepidosaur and archosauromorph 140 lineages might be an example of the ‘zone of variability’ [36], in which the canalization of 141 development and other constraints (e.g., functionality; see [37]) had not yet completely acted to 142 ‘fix’ the morphology of the posterior process. This hypothesis will of course require further 143 experimental study of living model systems. Together, these observations suggest that the 144 presence of a jugal posterior process was incorrectly scored in the datasets used by WEA24 (type 145 (ii) error). 146 147 Anterior emargination of the maxillary nasal process. Whiteside et al. [19] state that Brownstein 148 et al. [18] “seemingly relied on the anteriorly broken left maxilla” and that “The anterior margin 149 of the maxillary nasal process of the right maxilla tapers anteriorly…with no evidence of the type 150 of emargination suggested”. The character in question (ch. 18 in the dataset used by Whiteside et 151 al. [19]), is one of the original characters from [8], which is the basis for the dataset used by 152 Whiteside et al. [19] [38]. In both datasets, this character is described as “Maxillae, posterior 153 emargination, between nasal and orbital processes”[boldface added], and this character is 154 extensively described in [8]. Therefore, Whiteside et al. [19] incorrectly assessed the anterior 155 margin of the maxilla instead of the posterior margin, which is another type (ii) error. 156 157 Expanded radial condyle of the humerus. Whiteside et al. [19] (p. 3) state that Whiteside et al. 158 [13] “noted an expanded radial condyle on the humerus.” Yet, nowhere in Whiteside et al. [13] 159 do the authors mention or figure such a structure. Whiteside et al. [19] (p.3, fig. 1b) write in their 160 figure caption regarding another isolated fragment: “(b) NHMUK PV 38911 isolated larger 161 specimen of the distal end of left humerus of Cryptovaranoides microlanius in (above) anterior 162 and (below) posterior views showing similar features except the condyle of the capitellum.” 163 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 7 (boldface added). Then, in Whiteside et al. [19] (subsection 2.3), the authors state that this 164 fragment does not have a radial condyle/capitellum of the humerus, which they defend as 165 follows: “This is reinforced by the larger humerus (figure 1b) which is missing the condyle, as is 166 typical in the preservation of fissure lepidosaurs (e.g. Clevosaurus; [12, fig. 29b]) but the cavity 167 in which it sat clearly indicates a substantial condyle in life.” (boldface added). What WEA24 168 highlight is that there is no condyle in this humerus or the holotype specimen and defer it to poor 169 preservation without justification beyond “…as is typical ….of fissure lepidosaurs…” as a reason 170 to conclude the condyle was present and to explain this inconsistency among the bones referred 171 to Cryptovaranoides. Taphonomy and poor preservation cannot be used to infer the presence of 172 an anatomical feature that is absent. Finally, even in the case of the isolated humerus with a 173 preserved capitulum, the condyle illustrated by Whiteside et al. [19] is fairly small compared to 174 even the earliest known pan-squamates, such as Megachirella wachtleri (Figure 4). 175 176 Preservation of the septomaxilla. Whiteside et al. [13] and Whiteside et al. [19] claim that a 177 small, disarticulated piece of bone that is preserved anterolateral to the vomer in the block 178 containing the holotype of Cryptovaranoides microlanius is the septomaxilla. They further 179 suggest that a portion of the medial surface on a maxilla referred to this taxon that is likely from 180 a much larger reptile provides additional support for the presence of a septomaxilla in C. 181 microlanius. Simply put, the CT scans published by Whiteside et al. [13] and Whiteside et al. 182 [19] show that the bone in the holotype is isolated and with no clear morphological affinities to 183 the septomaxillae in squamates (see CT scans in [21]). Whiteside et al. [19] also suggest that the 184 identity of this bone as the septomaxilla is supported by its placement between the maxilla and 185 premaxilla of the holotype but given the level of disarticulation of the holotype and the 186 morphology of the bone fragment, a similar argument could be made that it is a portion of the 187 anterior end of one of the vomers. In any case, we feel it is premature to code C. microlanius for 188 any character related to the morphology of the septomaxilla based on this disarticulated and 189 damaged bone fragment. 190 191 Expanded radial condyle of the humerus. Whiteside et al. [19] provided additional justification 192 of the presence of an expanded radial condyle of the humerus by stating that the projection of the 193 radial condyle above the adjacent region of the distal anterior extremity of Cryptovaranoides 194 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 8 microlanius supports their choice to score the expanded radial condyle as present. This is not the 195 condition specified in either of the morphological character sets that they cite [18,38] – the 196 presence of a distinct condyle that is expanded – and is by their own description not homologous 197 to the condition in other squamates. 198 199 Anterior emargination of the maxillary nasal process. Whiteside et al. [19] flagged our 200 interpretation of the anterior maxillary nasal process as emarginated, which we found united 201 Cryptovaranoides microlanius with archosauromorphs. Although we still interpret this state as 202 such based on the computed tomography scan data, we again note than none of our analyses [18] 203 unambiguously place Cryptovaranoides microlanius within Archosauromorpha and that, while 204 optimized as such, this single character necessarily has limited utility for placing C. microlanius 205 among reptiles. 206 207 Subdivision of the metotic fissure. Whiteside et al. [19] claim that the division of the metotic 208 fissure into the vagus foramen and recessus scala tympani by the crista tuberalis, a key squamate 209 feature, can be scored for Cryptovaranoides microlanius, yet paradoxically suggest the presence 210 of this condition is only inferable based on other observations of the anatomy of the holotype and 211 referred specimens. In fact, Whiteside et al. [19] argue that because another character relating to 212 a different part of the structure of the metotic fissure can be inferred based on the presence of the 213 crista tuberalis, that the division of the metotic fissure may also be inferred by the presence of the 214 crista tuberalis. This logic would imply that no reptile taxon should exist that possesses solely 215 either a crista tuberalis or a subdivided metotic fissure, even when this is an observed state 216 combination in squamates scored for the matrices that both our teams have used to analyze the 217 phylogenetic position of Cryptovaranoides microlanius [8,38]. Thus this inference lacks 218 justification. To verify that C. microlanius possessed a vagus foramen, Whiteside et al. [19] state 219 that they searched for isolated otoccipital fragments from the same locality and found an 220 otoccipital fragment with a vagus foramen that they refer to C. microlanius without other 221 justification. It is unclear to us how Whiteside et al. [19] accounted for confirmation bias when 222 conducting this collections search, or on what basis they refer this isolated bone to C. 223 microlanius. In any case, the presence of the lateral opening of the recessus scala tympani is not 224 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 9 figured in the fragment, and thus the division of the metotic fissure is not demonstrated in the 225 referred fragment. 226 227 Fusion of exoccipitals and opisthotics. As Whiteside et al. [19] note, we concur with their 228 identification of an otoccipital in Cryptovaranoides microlanius formed by the fusion of the 229 exoccipitals with the opisthotics. Our concern is with the use of this feature to assign C. 230 microlanius to Squamata. Whiteside et al. [19] cite de Queiroz and Gauthier [20], who list the 231 presence of an otoccipital as a distinguishing feature of squamates. However, Whiteside et al. 232 [19] fail to provide any phylogenetic evidence supporting the optimization of this feature as a 233 squamate synapomorphy in phylogenies including C. microlanius, nor do they recognize that an 234 otoccipital is present in numerous non-squamate reptiles, including numerous archosauromorphs 235 [26,39,40]. For these reasons, the presence of an otoccipital alone cannot be used to assign C. 236 microlanius to Squamata or even Lepidosauria instead of Archosauromorpha or other clades of 237 reptiles known from the Permo-Triassic, except to distinguish the turtle total clade 238 (Eunotosaurus africanus possesses unfused exoccipitals and opisthotics [41]). We acknowledge 239 that with respect to a character state widespread among reptiles, optimization along a phylogeny 240 is what is of primary importance for referring taxa to a particular clade. To this end, we reiterate 241 that Whiteside et al. [19] did not show that the presence of an otoccipital optimizes as an 242 ambiguous or unambiguous synapomorphy of Lepidosauria, Pan-Squamata, or Squamata in any 243 of their phylogenies. For characters that show evidence of homoplastic evolution like the 244 presence of an otoccipital (and indeed, the presence of a jugal posterior process; see above), 245 phylogenetic character optimization is essential. 246 247 Enclosed vidian canal exiting anteriorly at base of each basipterygoid process. In our restudy of 248 the holotype of Cryptovaranoides microlanius, we were unable to verify the presence of an 249 enclosed vidian canal exiting the sphenoid via the base of the corresponding basipterygoid 250 process. Whiteside et al. [19] take issue with our interpretation of this region of the braincase and 251 suggest that a larger, abraded, and isolated sphenoid that they refer to C. microlanius also 252 supports their interpretation of the anatomy of this region of the braincase. Yet, they stated that 253 this fragment is of limited informativeness and appear to agree with us that the best course of 254 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 10 action is to score this character as missing data when including C. microlanius in phylogenetic 255 analyses. 256 257 Development of the choanal fossa of the palatine. Squamata includes multiple instances where 258 the complexity of the bony palate increases dramatically, an innovation that is related to 259 chemosensory evolution and the integration of different bones that form this region of the skull 260 [21,21,22,34,42–46]. One feature recognized as phylogenetically informative is the development 261 of the choanal fossa on the ventral surface of the palatine (also known as the palatine sulcus) 262 [18,21,34,47]. Whiteside et al. [19] claim that the development of the palatine choanal fossa in 263 Cryptovaranoides microlanius is comparable to the development of this feature in living 264 squamates, and cite the living iguanian genus Ctenosaura as an example of a squamate with 265 similar anteroposterior development of this feature as C. microlanius. Importantly, most 266 iguanians appear to show the plesiomorphic condition where the choanal fossa is anteriorly 267 restricted on the palatine [21]; this feature has contributed to debates about whether Iguania 268 forms the living sister group of all other crown squamates (as found in many morphological 269 character-based phylogenies; [21,22]) or is deeply nested within the crown clade and secondarily 270 convergent with rhynchocephalians (as implied by phylogenies made using DNA sequence data 271 [48–54] and some made using morphological data [8]). As such, this comparison is not salient to 272 the discussion about whether the development of the choanal fossa in C. microlanius represents 273 the squamate condition. Secondly, Whiteside et al. [19] take issue with our contention that the 274 palatine fossa is present, albeit variably, across a wide swath of reptilian diversity, including 275 many early-diverging archosauromorph clades. They explicate this concern by distinguishing 276 between the narrow channel found in taxa like Tanystropheus (figure 1l in Whiteside et al. [19]) 277 and the wider fossa found in C. microlanius. We agree that the fossa in C. microlanius is more 278 developed than in some early-diverging lepidosaurs, such as Marmoretta oxoniensis [55]. 279 However, it is clear that the feature in Cryptovaranoides falls within the variation in the choanal 280 fossa length and depth (Figure 2; Figure 3) that represents the ancestral condition in lepidosaurs 281 [21] and is exemplified across archosauromorph (see, for example [26]) and indeed diapsid [56–282 58] diversity. Finally, Whiteside et al. [19] cite the discovery of a large, isolated palatine that they 283 state confirms the presence of a “squamate-type” choanal fossa in C. microlanius, except they 284 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 11 provide no justification for why this isolated bone should be referred to this species. In any case, 285 the morphology of that bone is also unlike those of squamates (Figure 2). 286 287 Vomer ventral ridges and dentition. Whiteside et al. [19] reiterated their earlier characterization 288 [13] of the vomer of Cryptovaranoides microlanius as ridged, and suggest that the morphology 289 of the vomerine ridges and vomerine teeth in C. microlanius is comparable to the condition in the 290 anguid anguimorph Pseudopus apodus. We dispute this on the basis that the vomer of C. 291 microlanius as figured by Whiteside et al. [19] shows no clear ridges equivalent to those in 292 Pseudopus apodus [59] or other squamates with ridged vomers, including extinct forms such as 293 Eoscincus ornatus [34] (Figure 4). Instead, the new photograph of the holotype specimen of C. 294 microlanius provided in Whiteside et al. [19] shows that the vomer is indeed toothed, but no 295 ridges are figured or visible. We once again reexamined the CT scan data and failed to find any 296 structure resembling the ridges present in some anguimorphs, although we acknowledge that the 297 nature of the scan data (43 microns per segment) means that the vomer surface on the scan 298 segmentations is coarse. In any case, no ridges equivalent in shape or size to those found in 299 anguimorph squamates are present in the holotype of C. microlanius. The presence of teeth on 300 the vomer is itself rare among squamates; only in the pan-scincoid Eoscincus ornatus [34] and 301 some [59] anguid and varanoid [60] species are vomerine teeth documented. Whiteside et al. 302 [13,19] appear to suggest that the presence of vomerine ridges and a row of vomerine teeth 303 therefore allies C. microlanius with anguimorphs. The structure of the vomer in C. microlanius, 304 however, is fundamentally unlike those of anguimorph squamates, which are elongate and 305 possess pronounced ridges that are placed medially on the ventral surface of the main body of 306 each vomer and each house only one row of teeth along their posterior third [59,61]. In contrast, 307 the condition that Whiteside et al. [19] figure for C. microlanius shows multiple, parallel rows of 308 vomerine teeth on either side of the vomer that run across the entire length of the bone. This 309 morphology is even unlike that observed in the only squamate known where multiple vomerine 310 tooth rows are present, Eoscincus ornatus [34] (Figure 4). In that species, all vomerine teeth are 311 restricted to a raised surface at the posterior end of the ventral surface of the vomer main body 312 [34]. Thus, Whiteside et al. [19] have provided no evidence that vomerine ridges are present in 313 C. microlanius. We note again that vomerine teeth are widespread across neodiapsid diversity 314 outside Squamata [62] and appear in many lineages of Triassic archosauromorphs. 315 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 12 316 Lacrimal arches dorsally over lacrimal duct and floors lacrimal duct with medial process 317 posteriorly. We argued that this feature was unobservable in the holotype of Cryptovaranoides 318 microlanius [18]. Whiteside et al. [19] dispute this by suggesting that the CT scan data does not 319 reliably show the feature, and instead provide a photograph of the holotype skull that was stated 320 to show this morphology (figure 2a-c in [19]). This figure shows no curvature to the lacrimal, 321 which appears as a flat element, whereas an arch dorsally and a floor ventrally would indicate the 322 presence of a foramen. Whiteside et al. [19] did not code this feature (dorsal arcuation of the 323 lacrimal over the lacrimal duct, which is posteriorly floored by the medial process of the 324 lacrimal) for C. microlanius, but still use it to refer C. microlanius to Anguimorpha based on 325 optimization as a plesiomorphy of that clade in phylogenetic analyses that place C. microlanius 326 within Anguimorpha. This appears to suggest that, despite never conducting an analysis where 327 this feature is coded as ‘present’ for C. microlanius, Whiteside et al. [19] used the presence of the 328 feature to ally C. microlanius with Anguimorpha, not as a recovered synapomorphy, but stating 329 that it was so. This action would be an arbitrary unification of a species with a clade based on a 330 selected character state and would deny the equal possibility that this character state is absent 331 due to secondary reversal in C. microlanius. In sum, the use of lacrimal morphology to ally C. 332 microlanius with anguimorphs is apparently not based on direct character state optimization, i.e., 333 a test of congruence. 334 335 Distinct quadratojugal absent. The quadratojugal cannot be located in the holotype of 336 Cryptovaranoides microlanius [13,19]. We argued that this might be due to postmortem 337 disarticulation and damage to the skull, and also noted that a complete ontogenetic series would 338 ideally be required to test whether the quadratojugal is modified throughout ontogeny [18]. 339 Whiteside et al. [19] focused on our comment about the ideal situation of having an ontogenetic 340 series for C. microlanius to assess the development of the quadratojugal, which we restate would 341 be helpful to understand how this bone transforms through ontogeny given the complex 342 restructuring to this region of the skull that occurs throughout the evolution of lepidosaurs [63]. 343 However, Whiteside et al. [19] state “we argue based on juvenile and adult specimens and the 344 absence of a quadratojugal facet on the quadrate.” First, the region of the quadrate that would 345 articulate with the quadratojugal is not preserved in the holotype of C. microlanius, so it is 346 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 13 impossible to tell whether a facet for the quadratojugal is present. Second, Whiteside et al. [19] 347 fail to provide any justification for the referral of the isolated partial quadrate NHMUK PVR 348 37606 to C. microlanius. Third, Whiteside et al. [19] did not identify the quadratojugal facet on 349 this isolated quadrate when they figure this bone; indeed, based on the figure the process that 350 would have housed the quadratojugal facet is also missing from this quadrate (NHMUK PVR 351 37606). It is impossible to tell whether C. microlanius lacked a quadratojugal based on the 352 current data. Instead, all that can be said is that a quadratojugal is not preserved in the holotype 353 of C. microlanius, and the region housing the articular facet for the quadratojugal is not 354 preserved in either the holotype or referred quadrate. 355 356 Pterygoid/quadrate overlap. Whiteside et al. [19] restate the interpretation of Whiteside et al. 357 [13] that the pterygoid and quadrate have a short overlap in Cryptovaranoides microlanius. 358 Whiteside et al. [19] only compared the morphology of the quadrate in Cryptovaranoides 359 microlanius, which they agree is damaged, to the morphology present in rhynchocephalians, and 360 suggest based on this comparison that their interpretation is correct. We restate that this is not 361 possible to verify without more complete, articulated or semi-articulated palates assignable to 362 Cryptovaranoides microlanius based on apomorphic character states and combinations. 363 364 Fusion of the premaxillae and single median tooth. Whiteside et al. [19] suggest that Brownstein 365 et al. [18] incorrectly characterized the nature of fusion of the premaxillae into a single median 366 element in Cryptovaranoides microlanius. However, we reiterate that no justification has been 367 given in any paper [13,19] for referring these isolated premaxillae to C. microlanius. Whiteside 368 et al. [19] focus on differentiating these isolated large premaxillae from the premaxillae of two 369 other fissure fill lepidosaurs, Gephyrosaurus bridensis and Diphydontosaurus avonis, without 370 considering the possibility that additional taxa are present in the assemblage. Scoring fused 371 premaxillae as present for C. microlanius despite the presence of unfused, paired premaxillae in 372 the holotype defines (1) ontogenetic character state transformations solely based on the relative 373 size of the holotype and larger isolated bones referred without justification and (2) which 374 character state among those present in ontogeny is the phylogenetically informative one. 375 Defining both of these requires a robust ontogenetic series, which is not available for C. 376 microlanius at present. Observations of the development of living squamates also suggest that 377 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 14 these larger fused premaxillae should not be referred to C. microlanius. In crown squamates with 378 a median premaxilla, the premaxilla is invariably a single element upon first appearance very 379 early in embryonic development [64–68]. In contrast, the holotype of C. microlanius, which is 380 very clearly a juvenile and not an embryonic specimen, possesses paired premaxillae. The 381 ontogenetic series that Whiteside et al. [19] suggest for C. microlanius therefore differs from any 382 known squamate with a single median premaxilla. 383 384 Peg-in-notch articulation of quadrate with rod-shaped squamosal. Whiteside et al. [19] suggest 385 that both our teams are in agreement about the presence of a peg-in-notch articulation between 386 the quadrate and squamosal. We reiterate that we believe the presence of this type of articulation 387 is unclear based on the available data for the holotype, as these bones are both damaged in the 388 relevant sections and disarticulated (Figure 5). 389 390 Frontal underlaps parietal laterally on frontoparietal suture. Whiteside et al. [19] confirm that 391 the presence of this feature in Cryptovaranoides microlanius is based on the morphology of a 392 referred isolated frontal that they state matches the corresponding articular portion of the 393 prefrontal in the holotype. However, we do not understand how this bone could possibly match 394 the corresponding articular surface unless it was from the same individual or an animal of 395 exactly the same size. Unless Whiteside et al. [19] were actually able to articulate these bones, it 396 is unclear how this inference can be made. Finally, we note that the posterior process of the 397 prefrontal is broken off in the holotype of Cryptovaranoides microlanius. In squamates and other 398 lepidosaurs, this process abuts the lateral surface of the frontal along its anteroposterior axis. 399 Several of us (C.D.B. and D.L.M.) worked to rearticulated the holotype of Eoscincus ornatus, 400 which involved rearticulating the prefrontal and frontal. Rearticulating these bones is simply 401 impossible without the complete posterior process of the prefrontal, as the orientation of this 402 process must match the curvature of the lateral margin of the frontal. Because the isolated frontal 403 is not figured in either paper by Whiteside et al. [13,19], it is impossible for us to verify whether 404 this bone actually matches the corresponding articulation surface on the prefrontal in the 405 holotype. In any case, we regard it a best practice to exclude this isolated frontal from 406 discussions of the affinities of C. microlanius. 407 408 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 15 Medial process of the articular and prearticular. Whiteside et al. [19] revise their initial [13] 409 characterization of the medial process and refer to it as ‘rudimentary,’ scoring it as unobservable. 410 We determined that this process is absent [18] and offer no further comment besides that it 411 appears the distinction between our interpretation of this feature and that of Whiteside et al. [19] 412 is, as they explicate, largely arbitrary. 413 414 Bicapitate cervical ribs and cervical ribs with an anteriorly oriented process. Whiteside et al. 415 [19] took issue with our characterization of the morphology of the cervical ribs in 416 Cryptovaranoides microlanius, and compared the bicapitate morphology of the cervical ribs in 417 C. microlanius to two anguimorph squamates, Pseudopus apodus and Varanus spp. However, the 418 cervical ribs of P . apodus are not bicapitate, as shown by the very figure from [69] that Whiteside 419 et al. [19] cited. Similarly, the ribs of Varanus are unicapitate, not bicapitate, as shown in [70]. 420 We assume that Whiteside et al. [19] referred to the morphology of the cervical rib head in P . 421 apodus because of the presence of a posterior process on the rib head [69]. This is not the 422 bicapitate condition and is not homologous with the morphology of the cervical rib heads 423 in either C. microlanius or archosauromorphs, where an anterior process is offset from the 424 process formed by the capitulum and tuberculum [39,71]. We reiterate that the condition in C. 425 microlanius is identical to that in archosauromorphs (figure 2c, figure 3 in [18]); the comparisons 426 made by Whiteside et al. [19] are across non-homologous structures and result from a 427 misinterpretation of cervical rib anatomy. 428 429 Cervical and dorsal vertebral intercentra. Whiteside et al. [19] suggest that we inferred the 430 presence of cervical and dorsal intercentra in Cryptovaranoides microlanius; however, we did 431 not propose this in our paper. In fact, Whiteside et al. [13] state in their original paper that there 432 “are gaps between the vertebrae indicating that intercentra were present (but displaced in the 433 specimen) on CV3 and posteriorly. Some images of bones on the scans are identified as 434 intercentra” (p. 11, [13]). The statement in [19] consequently represents an incorrect attribution 435 and an incorrect characterization of our reexamination, as we determined that no cervical and 436 dorsal intercentra were preserved or present in the holotype. Whiteside et al. [19] justify their 437 position that cervical intercentra are present in C. microlanius based on the morphology of 438 another isolated bone that they refer to this taxon. In any case, the absence of dorsal intercentra is 439 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 16 not a distinguishing feature of squamates because several lineages of squamates, including 440 lacertids, xantusiids, gekkotans, and the stem-squamate Bellairsia gracilis all possess cervical 441 and dorsal intercentra [38,72,73]. 442 443 Anterior dorsal vertebrae, diapophysis fuses to parapophysis. Whiteside et al. [19] concur with 444 Brownstein et al. [18] that the diapophyses and parapophyses are unfused in the anterior dorsals 445 of the holotype of Cryptovaranoides microlanius, and restate that fusion of these structures is 446 based on the condition they observed in isolated vertebrae that they again refer to C. microlanius 447 without justification. As such, this feature should not be scored as present for C. microlanius. 448 449 Zygosphene–zygantrum in dorsal vertebrae. Whiteside et al. [19] again claim that the 450 zygosphene-zygantrum articulation is present in the dorsal series of Cryptovaranoides 451 microlanius based on the presence of ‘rudimentary zygosphenes and zygantra’ in isolated 452 vertebrae that they again refer to this species without justification. The structures that Whiteside 453 et al. [19] label as the zygosphenes and zygantra (figure 3 in [19]) are clearly not, however, 454 zygosphenes and zygantra, as the former is by definition a centrally located wedge-like process 455 that fits into the zygantrum, which is a fossa on the following vertebra. The structures labeled 456 zygosphenes and zygantra by Whiteside et al. [19] are the dorsal surfaces of the 457 prezygopophyses and the medial margins of the postzygapophyses. 458 459 Anterior and posterior coracoid foramina/fenestra. Whiteside et al. [19] use isolated coracoids 460 referred to Cryptovaranoides microlanius to support their claim that the upper ‘fenestra’ 461 (foramen) of the coracoid in the holotype specimen is indeed a foramen. Confusingly, Whiteside 462 et al. [19] label this feature as the ‘primary coracoid fenestra’ in their figure 3i-j, even though it is 463 clearly the coracoid foramen. Whiteside et al. [19] appear to have confused the coracoid 464 foramen, which is completely bounded by bone and placed inside the coracoid, with the coracoid 465 fenestra, which is bounded in part by the coracoid (the coracoid margin is curved to form part of 466 the bounding region in species with the coracoid fenestra) but also by the interclavicle (see 467 figures in [18,21]. The coracoid fenestra is not contained within the coracoid. This feature is also 468 not shown to be optimized as a pan-squamate synapomorphy in any phylogeny including 469 Cryptovaranoides microlanius [13,19], so its bearing on the identification of C. microlanius as a 470 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 17 pan-squamate is unclear to us. Finally, we note here that Whiteside et al. [19] appear to have 471 labeled a small piece of matrix attached to a coracoid that they refer to C. microlanius as the 472 supracoroacoid [sic] foramen in their figure 3, although this labeling is inferred because only 473 “suc, supracoroacoid [sic]” is present in their figure 3 caption. 474 475 Atlas pleurocentrum fused to axis pleurocentrum. Whiteside et al. [19] reiterate their claim that 476 the atlas and axis pleurocentra are present in Cryptovaranoides microlanius based on their 477 identification of an isolated, globose bone fragment as the atlas intercentrum, but provide no 478 additional justification for this identification and refer the reader to their original paper for a 479 figure of this bone [13], which is only visible on CT scans due to its entombment within the 480 matrix that includes the holotype. To this end, Whiteside et al. [19] revise their initial 481 interpretation of the what they identify as the preserved atlas-axis region, but again without any 482 justification or figures detailing how they reidentified a bone fragment that they had initially 483 believed was a cervical intercentrum as the atlas centrum and intercentrum 2. Thus, Whiteside et 484 [19] do not provide any additional description of how they reidentified these bones or a figure 485 illustrating their revised interpretation, and so we cannot comment on the strength of their 486 revised interpretation. Again, we note that we were not able to identify the morphology of the 487 atlas and axis with any confidence in the holotype of C. microlanius, and so we again believe any 488 relevant characters should be scored as missing data for this taxon. 489 490 Midventral crest of presacral vertebrae. Whiteside et al. [19] appear to agree with our assertion 491 that a midventral crest is not present on the presacral vertebrae [18]. We never challenged their 492 scoring of keels on the caudal centra as missing data. Rather, we stated that keels are clearly 493 present on the cervical vertebrae [18]. 494 495 Angular does not extend posteriorly to reach articular condyle. Whiteside et al. [19] state that 496 the posterior portion of the angular is present medially on the right mandible in the holotype, and 497 provide an interpretation of the anatomy of this region. They cite figure 3a in Whiteside et al. 498 [19], but this shows the mandible in lateral view and only a small portion of the angular is 499 visible. As such, it is not clear to us what they interpret to be the posterior portion of the angular. 500 In any case, we could not identify anywhere on the CT scans or on the accessible portions of the 501 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 18 real specimen (e.g., figure 2b in [19]) the feature that Whiteside et al. [19] consider to be the 502 posterior angular extent. Whiteside et al. [19] describe the posterior extent of the angular as a 503 ‘contoured feature,’ but we are entirely unclear about what this actually describes. 504 505 Ulnar patella. The only disagreement between our interpretation [18] and that made by 506 Whiteside et al. [13,19] concerns whether the ulnar patella is absent due to the ontogenetic state 507 or preservation status of the holotype [13,19] or an ontogenetically invariable feature of the 508 anatomy of Cryptovaranoides microlanius [18]; we suggested the latter based on our observation 509 that the forelimb of the holotype is articulated and mostly complete. 510 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 19 Overarching Empirical Problems in Whiteside et al. [19]. 511 Unassignable specimens and “hypodigm inflation.” Whiteside et al. [13] and Whiteside et al. 512 [19] describe and defend their addition of isolated elements to fill in gaps in the holotype concept 513 of Cryptovaranoides to build, in our view, an unjustifiably inflated hypodigm. WEA24 (p. 15) 514 try to ameliorate this problem in their Section (5.5) where they state that: “We emphasize that we 515 always match isolated bones with their equivalents on the holotype…” and then state in 516 contradiction that: “We consider it remiss not to include isolated bones as they provide details 517 which no scan can. Furthermore, as the holotype is a juvenile, they give additional information 518 from larger, and presumably older individuals, on characters of the holotype otherwise 519 unavailable or uncertain.” (boldface added). In summary, Whiteside et al. [19] claimed to only 520 match isolated bones with equivalent ones in the holotype but also acknowledged use of 521 elements that are not comparable with the ones in the holotype. This lack of consistency is a 522 serious empirical issue. 523 524 Apomorphic characters not empirically obtained. Whiteside et al. [19] discussed nearly 30 525 anatomical characters (Sections 2-6), most of which are used to support their core hypothesis that 526 Cryptovaranoides is a squamate. Yet, none of these 30 characters or conditions are actually 527 found by Whiteside et al. [19] to be synapomorphies of Squamata in their various phylogenetic 528 analyses. In other words, they did not present the results of their Tests of Congruence, but rather 529 simply elected to argue that untested interpretations of anatomy were apomorphies, 530 synapomorphies, or shared characters.This is a non-trivial substantive methodological flaw in 531 Whiteside et al. [13], that was perpetuated in Whiteside et al. [19], and that nullifies the bulk of 532 the arguments presented repeatedly in both studies. 533 In Section 6, Whiteside et al. [19] (p. 16) indicate they modified the datasets of 534 Brownstein et al. [18] and [38], but preferred the results of [11] and performed two different 535 analyses based on [38]: one using only morphological data, and one using morphological data 536 with several constraints from a molecular backbone. The former was tested using maximum 537 parsimony and the latter using Bayesian inference. What is not clear from either Section 6 or 7, 538 is which phylogenetic analysis was used by WEA24 to “review the apomorphy distribution”. But 539 this uncertainty is inconsequential as the apomorphy distributions discussed in Section 7 of 540 Whiteside et al. [19] were not derived from their phylogenetic analyses. Instead, Whiteside et al. 541 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 20 [19] (p. 19) exclusively extracted characters from the literature to support their identification of 542 Cryptovaranoides as a squamate, rather than basing this inference primarily on their own 543 phylogenetic analyses. These literature sourced characters include “two diagnostic characters of 544 Squamata (=crown-clade Squamata)” and “…further eight squamate synapomorphies” listed by 545 WEA24 (Section 7, p. 19). As stated by the authors, “we give the citation for the squamate 546 synapomorphy at the end of each character”— indicating that these diagnostic characters or 547 synapomorphies were picked from the literature and not derived from ancestral state 548 reconstructions based on their phylogenetic results. 549 In order to check the characters listed by Whiteside et al. [19] (p.19) as “two diagnostic 550 characters” and “eight synapomorphies” in support of a squamate identity for Cryptovaranoides, 551 we conducted parsimony analysis of the revised version of the dataset [38] provided by WEA24 552 in TNT v 1.5 [74]. We used Whiteside et al.’s [19] own data version—e.g., with (0) scored for 553 character 1 and not including character 383. We recovered eight apomorphies at the squamate 554 node of which only three were recovered as unambiguous synapomorphies (boldface indicates 555 the state as scored by Whiteside et al. [19]for Cryptovaranoides): 556 Ch. 138. Basisphenoid (or fused parabasisphenoid), ventral aspect, shape, concavity: 557 single (0)/divided (1)/ absent (2). 0 -> 2 558 Ch. 142. Prootics, alar crest: absent (0)/ present (1). 0->1 559 Ch. 347. Prefrontal/palatine antorbital contact: absent (0) / narrow forming less than 1/3 560 the transverse distance between the orbits (1) / contact broad, forming at least 1/2 the distance 561 between the orbits (2). 01->2 562 The eight features described by Whiteside et al. [19] (p.19) as synapomorphies for 563 Cryptovaranoides + Squamata were also not inferred at their recovered crown squamate node 564 from their own results. Rather, they were copied nearly verbatim from principally two sources 565 [21,75] and presented as if they were recovered as synapmorphies by Whiteside et al. [19] (p. 566 19). In Table 1, the italicized text is from Whiteside et al. [19] (p.19), including their literature 567 source for the supposed synapomorphy. The non-italicized text is the character number and state 568 from [11] as recovered by us from the TNT analysis conducted for this reassessment of 569 Whiteside et al. [19]. We also include where in our phylogeny the character state is recovered as 570 synapomorphic (Table 1). 571 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 21 Our reanalysis shows that Whiteside et al. [19] did not diagnose Cryptovaranoides + 572 crown Squamata based on synapomorphies found by their own analyses as there were only three 573 (see our results above). Instead, Whiteside et al. [19] provided ad hoc mischaracterizations of 574 diagnostic features of crown Squamata from studies that did not include Cryptovaranoides and 575 then discussed and reviewed synapomorphies of Squamata from these sources [21,75]. Because 576 each additional taxon has the possibility of inducing character reoptimization, an empirical 577 analysis of character optimization that includes a given new taxon is necessary to support 578 referring said taxon to any particular clade. If Cryptovaranoides was indeed a Triassic crown 579 squamate, it could plausibly show character distributions not previously sampled among known 580 members of the crown or stem group. 581 582

and Conclusions. 583 As we noted above and in Brownstein et al. [18], the anatomy of Cryptovaranoides is 584 similar to many Late Triassic neodiapsid reptiles. For example, the quadrates of 585 Cryptovaranoides are closely comparable to those of archosauromorphs such as Prolacerta [76], 586 Macronemus [77] and Malerisaurus [78], with which Cryptovaranoides shares the presence of a 587 notch on the quadrate for an immobile articulation with the squamosal. Furthermore, WEA24’s 588 inference that the quadrate, the notch, and the articulation with the squamosal was mobile, i.e., 589 streptostylic as in squamates, is unfounded. 590 Similarly, the vertebrae and cervical ribs of the holotype of Cryptovaranoides do not 591 resemble those of squamates, but in fact share important features with non-squamate 592 neodiapsids, especially archosauromorphs (a point left unaddressed by Whiteside et al. [19]). For 593 example, whereas fusion of the neural arches to the centra occurs during embryonic ossification 594 in squamates [79], in Cryptovaranoides unfused bony neural arches and centra are present, as 595 commonly observed in archosaurs and other non-lepidosauromorph neodiapsids [80,81]—we 596 provide a long-form review of these and other features in Cryptovaranoides that compare 597 favorably with non-squamate reptiles in Supplementary Material. 598 Several errors in Whiteside et al. [13] identified in Brownstein et al. [18], and subsequent 599 errors in Whiteside et al. [19] that were discussed above result in the incorrectly interpreted 600 neodiapsid and lepidosaur anatomy of Cryptovaranoides and consequently provide erroneous 601 scorings for Cryptovaranoides for morphological character matrices. Whiteside et al. [19] also 602 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 22 make additional errors on an alpha taxonomic level, such as the unjustified inflation of the 603 Cryptovaranoides hypodigm based on contradictory arguments pertaining to the assignment of 604 fragmentary and isolated elements to the holotype. Finally, we highlight here that where 605 Whiteside et al. [13] and Whiteside et al. [19] should have reported their own recovered 606 synapomorphies, that is, the actual results of their phylogenetic analyses, rather than listing a 607 substantive number of supposed apomorphies that the authors argue support the squamate 608 affinities of Cryptovaranoides broadly, and anguimorph affinities more specifically. On a 609 methodological and analytical level, we do not consider that manually selecting apomorphic 610 characters supporting their preferred placement of Cryptovaranoides instead of using characters 611 empirically obtained from phylogenetic ancestral state reconstruction of their phylogenetic 612 results, stands as valid support of a phylogenetic hypothesis. 613 We end with a perspective on the fossil record of neodiapsid evolution. The anatomies 614 and morphologies that diagnose crown group squamates are many and varied, and except for a 615 few features, hardly universally distributed amongst the living and fossil members of the crown. 616 They are themselves the product of some 250 million years of evolutionary time and would not 617 have evolved in a linear fashion. Rather, phylogenetic analyses of diverse extinct and living 618 reptile clades have shown that the squamate bauplan originated in the context of extensive 619 mosaic and homoplastic osteological character evolution [8,30,34,47,58]. We do not doubt that 620 members of Pan-Squamata were present during the Triassic; this is supported by the fossil record 621 [8] as well as numerous time-calibrated phylogenies based on genomic [48,49] morphological 622 [34,38,47] and total-evidence [8,30] data. However, Whiteside et al. [13] and Whiteside et al. 623 [19] have provided no direct osteological evidence that supports the presence of crown Squamata 624 or any of its inclusive clades in the Triassic. 625 626

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It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 30 Figures 867 868 869 870 Figure 1. Comparison of jugal morphologies among living lepidosaurs. Note the variability in 871 the presence and development of the posterior process, as well as the presence of an ossified 872 jugal itself. CT scan images are from digimorph.org. 873 874 875 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 31 876 Figure 2. Comparison of palatine morphologies. Blue shading indicates choanal fossa. Top 877 image of Cryptovaranoides referred palatine is from Whiteside et al. [19]. 878 879 880 881 882 883 884 885 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 32 886 Figure 3. Choanal fossa character scoring. 887 888 889 Prominent choanal fossa on anterior margin of ventral surface of palatine Sphenodon punctatus after Gauthier et al. (2012) †Eoscincus ornatus after Brownstein et al. (2022) 0: absent 2: present and extending over halfway along palatine considered “prominent” by WEA24 1: present, limited to anterior third of palatine †Helioscopos dickersonae after Meyer et al. (2023) †Cryptovaranoides Holotype .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 33 890 Figure 4. Comparison of vomer morphologies. Top image is Eoscincus ornatus from Brownstein 891 et al. (2022). Note that the rows of vomerine teeth are posteriorly placed, and the vomerine 892 ridges are large and laterally placed. Bottom image of Cryptovaranoides holotype is from 893 Whiteside et al. [19]. 894 895 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 34 896 897 Figure 5. Quadrate-squamosal articulation character scoring. 898 899 900 901 Figure 6. Anterior articulation of vomer and maxilla character scoring. 902 903 904 Cephalic head of (mobile) quadrate with notch for the squamosal, peg-in-notch articulation 0: absent 1: present Sphenodon punctatus after Gauthier et al. (2012) Amphiglossus splendidus after Gauthier et al. (2012) †Cryptovaranoides Holotype considered “present” by WEA24 feature WEA24 identify as notch notchsquamosal quadrate Vomer and maxilla meet at anterior margin of fenestra exochoanalis 0: absent 1: present considered “present” by WEA24 Sphenodon punctatus after Gauthier et al. (2012) premaxilla vomer maxilla Pogona vitticeps after Gauthier et al. (2012) †Cryptovaranoides Holotype damaged .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 35 905 Figure 7. Presence of a medially positioned posterior mylohyoidal foramen on the mandible. As 906 shown, there is no identifiable foramen on the mandible of Cryptovaranoides. Bottom image of 907 Cryptovaranoides holotype skull is from Whiteside et al. [19]. 908 909 910 911 Celestus enneagrammus after Gauthier et al. (2012) †Cryptovaranoides Holotype position of foramen according to WEA24 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 36 912 913 914 915 916 Figure 8. Comparison of the humerus of Cryptovaranoides microlanius to Puercosuchus 917 traverorum [26]. Left image of Cryptovaranoides holotype humerus is from Whiteside et al. 918 [19]. 919 920 921 922 923 †Cryptovaranoides Holotype †Peurcosuchus traverorum after Marsh et al. (2022) .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint 37 Table 1. 924 925 Character Number in Tałanda et al. (2022) Study Cited in WEA24 Synapomorphy of Unambiguous Optimization Cephalic head of (mobile) quadrate with notch for the squamosal, peg-in-notch articulation with rod- shaped squamosal 123 de Queiroz and Gauthier (2020) Pan-Squamata 1→0 V omer and maxilla meet at anterior margin of fenestra exochoanalis 371 Gauthier et al. (2012) N/A N/A Prominent choanal fossa on anterior margin of ventral surface of palatine 100 Gauthier et al. (2012) Lepidosauria N/A Subdivision of embryonic metotic fissure by the crista tuberalis into vagus (jugular) foramen and recessus scala tympani 382 Simões et al. (2018); de Queiroz and Gauthier (2020) N/A N/A No quadrate foramen 118 Gauthier et al. (2012) Lepidosauria 1→0 Medially positioned posterior mylohyoidal foramen on mandible 163 Gauthier et al. (2012) N/A N/A Fusion of exoccipitals and opisthotics forming an otoccipital 151 Gauthier et al. (2012); de Queiroz and Gauthier (2020) N/A N/A Trunk vertebrae lack intercentra 237 de Queiroz and Gauthier (2020) Pan-Unidentata 1→0 926 927 928 929 930 .CC-BY 4.0 International licenseavailable under a was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (whichthis version posted April 23, 2025. ; https://doi.org/10.1101/2025.04.18.649532doi: bioRxiv preprint