Updated cranial and mandibular description of the Late Cretaceous (Maastrichtian) baenid turtle Saxochelys gilberti based on micro-computed tomography scans and new information on the holotype-shell association

Saxochelys gilberti is a baenid turtle from the Late Cretaceous Hell Creek Formation of the United States of America known from cranial, shell, and other postcranial material. Baenid turtles are taxonomically diverse and common fossil elements within Late Cretaceous through Eocene faunas. Detailed anatomical knowledge is critical to understanding the systematics and morphological evolution of the group. This is particularly important as baenids represent an important group of continental vertebrates that survived the mass extinction event associated with the Cretaceous/Paleogene boundary. High-resolution micro-computed tomography scanning of the holotype skull reveals additional anatomical details for the already well-known Saxochelys gilberti. This includes the revision of some anatomical statements from the original description, but also detailed knowledge on internal anatomical features of the braincase and the description of a well-preserved axis (cervical vertebra 2). Our new detailed description and previous work on the shell and postcrania make Saxochelys one of the best-described, nearly complete baenid turtles, which are often only known from either isolated shell or cranial material. A revised phylogenetic analysis confirms the position of Saxochelys gilberti as a derived baenid (Eubaeninae) more closely related to Baena arenosa than to Eubaena cephalica.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-023-00301-6.

Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)

The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for which there appear to be unstated working assumptions to scoring that are incompatible with the character definitions (e.g., scoring of taxa with incomplete skulls for characters based on skull length). Correction of these scores and other pervasive errors recovered a distinctly less resolved topology than previous studies, more in agreement with my own matrix. This suggests that previous analyses may have been compromised, and that the only real consensus of dissorophid phylogeny is the lack of one.

The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters

The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as "Ocadia" kehreri and "Ocadia" messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.

A review of the carotid artery and facial nerve canal systems in extant turtles

The cranial circulation and innervation systems of turtles have been studied for more than two centuries and extensively used to understand turtle systematics. Although a significant number of studies related to these structures exists, a broader comprehension of variation across the tree has been hindered by poor sampling and a lack of synthetic studies that addressed both systems together. We here provide new insights regarding the carotid circulation and facial nerve innervation systems in a broad set of extant turtles using CT (computed tomography) scans, which allow us to trace the canals these structures form in bone and understand the interaction between both systems. We document that the palatine artery, including the lateral carotid canal, is absent in all pleurodires and carettochelyids and was likely reduced or lost several times independently within Testudinoidea. We also highlight osteological correlates for the location of the mandibular artery. We finally summarize variation regarding the placement of the mandibular artery, location of the geniculate ganglion, placement of the hyomandibular and vidian nerves, and situations where we recommend caution when assessing canals in fossils. A morphometric study confirms that the relative sizes of the carotid canals are correlated with one another. Our results have the potential for building new phylogenetic characters and investigating the circulation systems of fossil taxa, which are expected to shed light on the evolution of the circulation system of turtles and clarify some unresolved relationships between fossil turtle clades.

Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods

BACKGROUND

In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods.

METHODS

We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure.

RESULTS

Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony.

A new testudinoid turtle from the middle to late Eocene of Vietnam

BACKGROUND

Testudinoidea is a major clade of turtles that has colonized different ecological environments across the globe throughout the Tertiary. Aquatic testudinoids have a particularly rich fossil record in the Tertiary of the northern hemisphere, but little is known about the evolutionary history of the group, as the phylogenetic relationships of most fossils have not been established with confidence, in part due to high levels of homoplasy and polymorphism.

METHODS

We here focus on describing a sample of 30 testudinoid shells, belonging to a single population that was collected from lake sediments from the middle to late Eocene (35-39 Ma) Na Duong Formation in Vietnam. The phylogenetic placement of this new material is investigated by integrating it and 11 other species of putative geoemydids from the Eocene and Oligocene to a recently published matrix of geoemydid turtles, that embraces the use of polymorphic characters, and then running a total-evidence analysis.

RESULTS

The new material is highly polymorphic, but can be inferred with confidence to be a new taxon, Banhxeochelys trani gen. et sp. nov. It shares morphological similarities with other southeastern Asian testudinoids, Isometremys lacuna and Guangdongemys pingi, but is placed phylogenetically at the base of Pan-Testuguria when fossils are included in the analysis, or as a stem geoemydid when other fossils are deactivated from the matrix. The vast majority of other putative fossil geoemydids are placed at the base of Pan-Testuguria as well.

DISCUSSION

The phylogenetic placement of fossil testudinoids used in the analysis is discussed individually and each species compared to Banhxeochelys trani gen. et sp. nov. The high levels of polymorphism observed in the new taxon is discussed in terms of ontogenetic and random variability. This is the first time that a large sample of fossil testudinoids has its morphological variation described in detail.