DOI: 10.5061/dryad.ffbg79cv4
title: A reassessment of the enigmatic diapsid Paliguana whitei and the early history of Lepidosauromorpha

description: Lepidosaurs include lizards, snakes, amphisbaenians and the tuatara,
 comprising a highly speciose evolutionary radiation with widely varying
 anatomical traits. Their stem-lineage originated by the late middle
 Permian 259 million years ago, but its early fossil record is poorly
 documented, obscuring the origins of key anatomical and functional traits
 of the group. Paliguana whitei, from the Early Triassic of South
 Africa, is an enigmatic fossil species with potential to provide
 information on this. However, its anatomy and phylogenetic affinities
 remain highly uncertain, and have been debated since its discovery more
 than 100 years ago. We present microtomographic 3D imaging of the cranial
 anatomy of Paliguana whitei that clarifies these
 uncertainties, providing strong evidence for lepidosauromorph affinities
 based on the structure of the temporal region and the implantation of
 marginal dentition. Phylogenetic analysis including these new data
 recovers Paliguana as the earliest
 known stem-lepidosaur, within a long-lived group of
 early-diverging lepidosauromorphs that persisted to at least the Middle
 Jurassic. Our results provide insights into cranial evolution on the
 lepidosaur stem-lineage, confirming that characteristics of pleurodont
 dental implantation evolved early on the lepidosaur stem-lineage. In
 contrast, key functional traits related to hearing (quadrate conch) and
 feeding (streptostyly) evolved later in the lepidosaur crown-group.
description: We included new data on the anatomy of
 <i>Paliguana</i> to the phylogenetic matrix of Griffiths
 <i>et al. </i>2021, which was extensively modified from Simões
 <i>et al</i>. 2018. In addition to re-scoring the anatomy of
 <i>Paliguana</i>, we also revised the characters concerning
 the implantation of marginal dentition. Multistate characters 212 and 213
 of the original character–taxon matrix were removed and replaced by six
 new binary characters (ca 376–381), which recognise independent variation
 in the morphology of tooth implantation among reptiles. We also added a
 recently reported species to the data-set (<i>Vellbergia
 bartholomaei</i>) (refer to electronic supplementary material, data
 S5 for details on these changes, together with a revised character
 list). The modified character-taxon matrix was analysed
 using a non-time calibrated Bayesian Mkv model in MrBayes v.3.2.5
 (Ronquist <i>et al. </i>2012). The ‘standard’ datatype was
 used for morphological data, and the coding was set at ‘variable’ (that
 is, only variable characters being sampled) with rates set to a gamma
 distribution. The Mkv model analysis was performed with two runs of four
 chains each for 50 million generations, with tree sampling every 500th
 generation and a 25% burn-in. The average effective sample size for the
 two parameters (tree length and shape of gamma distribution) were in
 excess of 50,000, and the average potential scale reduction factor was
 1.000, with both chains demonstrating good convergence (average standard
 deviation of split frequencies 0.0028). Our results were expressed in a
 50% majority rule tree (halfcompat command in MrBayes) and in a maximum
 clade credibility tree (MCC). The MCC tree is a single tree in the
 posterior sample with the maximum sum of posterior clade probabilities
 across all the constituent bifurcations (Heled and Bouckarert 2013). We
 used TreeAnnotator (v1.10.4 Rambaut and Drummond 2002-2018) to recover the
 MCC from a combination of the posterior tree files of the two runs from
 MrBayes output (.t files), less the 25% burn-off, producing a total of
 150,000 trees. The script for the Bayesian analysis is provided in Part 6
 of Supplementary Data. Optimisation of the 50% majority rule tree and the
 MCC tree were performed for both ACCTRAN and DELTRAN in PAUP v.4.0a, build
 169 (Swofford, D.L. 2002)(refer to electronic supplementary material, data
 S2 and S3 for extended details).