DOI: 10.5061/dryad.280gb5mwd
title: Data from: A new sphenodontian (Diapsida: Lepidosauria) from the Upper Triassic of Germany and its implications for the mode of sphenodontian evolution

description: The Arnstadt Formation of Saxony-Anhalt, Germany has yielded some of
 Germany’s most substantial finds of Late Triassic tetrapods, including the
 sauropodomorph Plateosaurus and the stem-turtle Proganochelys. Here, we
 describe an almost complete skull of a new sphenodontian taxon from this
 formation (Norian, 227-208 Ma), making it the oldest known articulated
 sphenodontian skull from Europe and one of the oldest in the world. The
 material is represented by the dermal skull roof and by the complete
 maxilla and temporal region, as well as parts of the palate, braincase,
 and lower jaw. A phylogenetic assessment recovers it as a basal
 sphenodontian closely related to Planocephalosaurus and to Eusphenodontia,
 making it the earliest-diverging sphenodontian known with an articulated
 skull. Its cranial anatomy is generally similar to the well-known
 Diphydontosaurus avonis from the Rhaetian of England, showing that this
 successful phenotype was already established in the clade around 10 myr
 earlier than long assumed. An analysis of evolutionary change rates
 recovers high rates of evolution in basal sphenodontians, with decreasing
 rates throughout the evolution of the group. However, contrary to previous
 studies, reversals in this trend were identified, indicating additional
 peaks of evolutionary change. These results improve our understanding of
 the early sphenodontian diversity in Europe, providing critical
 information on evolutionary trends throughout the history of the clade and
 sparking renewed interest in its evolution.
description: (a)   Computed Tomography The holotype
 MB.R.4520.2 is housed in the fossil reptile collection of the Museum für
 Naturkunde in Berlin (Germany). µCT scans were performed in house using a
 Phoenix|x-ray Nanotom S tomography machine (GE Sensing and Inspection
 Technologies GmbH, Wunstorf, Germany) with a voltage of 110 kV and a
 current of 150 µA, capturing 2,000 images with an exposure time of 750 ms
 and a resolution of 10.23 µm. Slices were reconstructed using the datos|x
 v.2.3.0.844 - RTM reconstruction software (GE Sensing and Inspection
 Technologies GmbH, Phoenix—x-ray) and the resulting volume was manually
 segmented and analysed in VG Studio Max 3.3 (Volume Graphics GmbH,
 Heidelberg, Germany) at the 3D-Visualisation Laboratory at the Museum of
 Natural History Berlin using the region grower and pen tools.
 (b)   Time-calibrated phylogenetic analysis A
 sphenodontian phylogeny was constructed to explore the relationship of
 <em>Parvosaurus harudensis</em> within Rhynchocephalia using
 the morphological matrix by [23]. In the analysis performed by [24],
 incompletely resolved phylogenies are prepared for the change rates
 analyses by breaking all polytomies at random, inevitably losing
 phylogenetic information. We solved this problem by running preliminary
 analyses and identifying rogue taxa to be excluded <em>a
 priori</em>, thus resolving all polytomies based on highest
 likelihood. <em>Sophineta cracoviensis</em> and the
 <em>Clevosaurus</em> complex (except for <em>C.
 hudsoni</em>) were pruned from the parsimony phylogenetic and
 evolutionary rates analyses. This, with the addition of
 <em>Parvosaurus harudensis</em>, resulted in a matrix
 comprising of 30 taxa and 131 characters. To provide a
 timescale for the phylogeny, first and last appearance dates (FAD and LAD,
 respectively) were compiled for each taxon from the Paleobiology Database
 (see Supplementary Data). The age of <em>Parvosaurus
 harudensis</em> is based on the Arnstadt Formation in which it
 occurs, and so the upper and lower boundaries of the Norian were used as
 LAD and FAD, respectively. Two different dating approaches were performed
 to facilitate assessment of the stability of the time-scaling and
 evolutionary rates methods. Following the methods and settings recommended
 by [72] and [73], branch lengths were computed in R v.4.1.0 (R Core Team,
 2021) using the ‘equal’ and ‘minimum branch length’ [mbl] methods. For the
 ‘equal’ method, the root-length was fixed to a 2 myr duration. For the
 ‘mbl’ method, it was set to a minimum duration of 1 myr. This way of
 time-calibration was chosen over a Fossilised Birth Death model through
 Bayesian Inference to allow for more direct comparison to the evolutionary
 change rates analysis performed by [24]. In order to track the influence
 of <em>Parvosaurus harudensis </em>on the phylogeny and
 evolutionary change rates, all analyses were performed twice, once
 including, and once excluding <em>Parvosaurus
 harudensis</em><em>.</em> (1)  
 Bayesian analysis The phylogenetic analysis was
 performed with the settings from [23] under the Mk model [74], applying a
 gamma distribution for variable rates. No outgroup was set. The analysis
 was run for 10<sup>7</sup> generations with 2 runs for 4
 chains each. Parameters were sampled for every 1,000 generations and
 relative burn-in was set to 50%. Posterior node probabilities for all
 Bayesian phylogenies were exported from FigTree v.1.4.4. All recovered
 phylogenies can be viewed in the Supplementary Data.
 (2)   Maximum parsimony analysis A
 phylogenetic maximum parsimony analysis was performed in TNT v.1.5 [75]
 under implied weights, with a concavity index (K) = 3 (all analyses
 performed with higher k -values resulted in the same singular tree). As
 for the Maximum Likelihood rates analyses, a single, fully resolved tree
 was beneficial, Parsimony was preferred as input for the evolutionary
 rates analyses over Bayesian Inference methods as seen in [23]. All
 branches were collapsed to zero length prior to the analysis. Trees were
 searched using 1,000 replications of Wagner trees with a single random
 seed and Tree Bisection Reconnection (TBR), saving 10 trees per each of
 the 1,000 replications. This resulted in the output of a single, fully
 resolved tree with a fit of 21.80595. Character state changes were counted
 for each branch using TNT v.1.5 and mapped on the phylogeny using the
 “Branch length” function (see Supplementary Fig. S10).
 [c] Evolutionary rates analysis Evolutionary
 rates were assessed using Maximum Likelihood methods following the
 protocols of [24, 73, 74, 76, 77]. The time-calibration and evolutionary
 rates analyses were performed in R v.4.1.0 (R Core Team, 2021) with the
 Claddis [77], paleotree [78] and tidyverse [79] packages with a modified
 version of the script by [24] and [73]. All analyses were repeated and
 averaged over 100 repetitions. To address uncertainty arising from
 sampling each terminal taxon’s age, node ages were randomised for each of
 the 100 replicates within the range of estimated ages. LRT significance
 testing was chosen over AIC for better comparability to the script by [24]
 with an alpha threshold of 0.01 used to evaluate significance, and with
 Benjamini-Hochberg false discovery rate correction. Partitions were used
 for time-bins, character partitions, clade partitions and branch
 partitions (see Supplementary Data). Time-bins were partitioned into
 geochronologic ages ranging from the Wuchiapingian (Upper Permian) to the
 Maastrichtian (Late Cretaceous). Characters were partitioned into cranial
 and postcranial characters. Evolutionary rates of the time-calibrated
 phylogeny were assessed over 100 runs with randomised dates and the
 resulting rates were illustrated by averaging over the 100 runs.
description: # A new sphenodontian (Diapsida: Lepidosauria) from the Upper Triassic of
 Germany and its implications for the mode of sphenodontian evolution
 [https://doi.org/10.5061/dryad.280gb5mwd](https://doi.org/10.5061/dryad.280gb5mwd) ## Description of the data and file structure Supplementary material includes: 1\) Bayesian phylogenetic analysis; 2\) Maximum Parsimony phylogenetic analysis; 3\) R script for the evolutionary rates analysis; 4\) input and output data and calculations made for the phylogenetic and rates analyses; 5\) a PDF file containing additional figures showing anatomical features, phylogenetic results and evolutionary rates results; 6\) the original μCT dataset; 7\) the reconstructed 3D surface models.