Supplementary_Data_for_Inner_Ear_of_SquamatesSupplementary material S1 - Table S1 Specimen numbers, taxonomic authorities, and institutional abbreviations. Supplementary material S2 Landmark coordinates of all taxa included in the study (.nts format). Supplementary material S3 - Figures S1-S4 Figure S1, two phylogenies inclusive of fossil taxa that were used in this study; Figure S2, accuracy test of landmarking procedure; Figure S3, distribution of variance of the principal components; Figure S4, distribution of variance for the first 10 phylogenetic principal components derived from both phylogenies adopted (i.e. with Dinilysia as a stem alethinophidian and as a stem ophidian). Supplementary material S4 - Table S2 Ecology of all the taxa included in the study and literature sources. Supplementary material S5 Scripts used to run the analyses in R. Supplementary material S6 - Table S3 First 10 ordinary principal components for all taxa included in the study. Supplementary material S7 Three-dimensional ordinary PCA plot of PC1 vs PC2 vs PC3. Colour coding is the same as in Figure 2. Supplementary material S8 – Table S4 First 10 phylogenetic principal components (PPCs) for all taxa included in the study and for both phylogenentic PCA analyses (i.e. with Dinilysia as a stem alethinophidian and as a stem ophidian). Supplementary material S9 Three-dimensional phylogenetic PCA plot of PC1 vs PC2 vs PC3 (based on phylogeny where Dinilysia is a stem alethinophidian). Colour coding is the same as in Figure 2.Supplementary Data.zip

The inner ear morphology of 80 snake and lizard species, representative of a range of ecologies, is here analysed and compared to that of the fossil stem snake Dinilysia patagonica, using three-dimensional geometric morphometrics. Inner ear morphology is linked to phylogeny (we find here a strong phylogenetic signal in the data that can complicate ecological correlations), but also correlated with ecology, with Dinilysia resembling certain semi-fossorial forms (Xenopeltis and Cylindrophis), consistent with previous reports. We here also find striking resemblances between Dinilysia and some semi-aquatic snakes, such as Myron (Caenophidia, Homalopsidae). Therefore, the inner ear morphology of Dinilysia is consistent with semi-aquatic as well as semi-fossorial habits: the most similar forms are either semi-fossorial burrowers with a strong affinity to water (Xenopeltis and Cylindrophis) or amphibious, intertidal forms which shelter in burrows (Myron). Notably, Dinilysia does not cluster as closely with snakes with exclusively terrestrial or obligate burrowing habits (e.g. scolecophidians and uropeltids). Moreover, despite the above similarities, Dinilysia also occupies a totally unique morphospace, raising issues with linking it with any particular ecological category.