Evolutionary assembly of crown reptile anatomy clarified by late Paleozoic relatives of Neodiapsida

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1. Version published to 10.24072/pcjournal.620

   Aug 28, 2025
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   Peer Community in Paleontology

   Aug 19, 2025

   Despite more than a century of studies on the origin and early evolution of amniotes, many controversies still surround this topic, as shown by the abundant flow of recent studies in this field (e.g., Fröbisch et al., 2025). Our ideas on this topic have changed substantially over the last century, even though a deep divergence between mammals and reptiles (now often conceptualized as crown-groups) and even the composition of their total groups (traditionally called Synapsida Osborn, 1903 and Sauropsida Huxley, 1864) has been fairly stable (except for the discovery of new taxa) for more than a century (Broom, 1924). However, many other points have been contentious recently, even the identity of the long-extinct taxa that belong on either side of this basal dichotomy. For instance, varanopids, which were thought to be synapsids at least …

   Despite more than a century of studies on the origin and early evolution of amniotes, many controversies still surround this topic, as shown by the abundant flow of recent studies in this field (e.g., Fröbisch et al., 2025). Our ideas on this topic have changed substantially over the last century, even though a deep divergence between mammals and reptiles (now often conceptualized as crown-groups) and even the composition of their total groups (traditionally called Synapsida Osborn, 1903 and Sauropsida Huxley, 1864) has been fairly stable (except for the discovery of new taxa) for more than a century (Broom, 1924). However, many other points have been contentious recently, even the identity of the long-extinct taxa that belong on either side of this basal dichotomy. For instance, varanopids, which were thought to be synapsids at least since the 1920s, have been suggested to be sauropsids instead (e.g., Ford and Benson, 2020). Within sauropsids, several early cladistic studies (e.g., Gauthier et al., 1988; Laurin and Reisz, 1995; deBraga and Rieppel, 1997) suggested a fairly basal dichotomy between parareptiles, which include bolosaurids, millerettids, pareiasaurs and procolophonids, among others, and eureptiles, which include “protorothyridids” (a possibly paraphyletic group), captorhinids and diapsids. The position of turtles has long been problematic; early parsimony-based studies placed them as sister-group of Captorhinidae (Gauthier et al., 1988), among parareptiles (Laurin and Reisz, 1995; Lee, 1995) and among diapsids, close to lepidosaurs (deBraga and Rieppel, 1997). 

   Our ideas on the evolution of several morphological characters have also changed rather drastically over the last century or so. For instance, the temporal fenestration, which was once emphasized and had been used to divide amniotes into anapsids, synapsids and diapsids, is now known to display much more homoplasy than previously realized (Cisneros et al., 2004; Werneburg 2019). Similarly, our ideas on the evolution of the tympanic ear have been revised several times. 

   The latest phylogenetic analysis of early sauropsids by Jenkins et al. (2025a) focuses on all these topics. This is a major piece of work, based on a new data matrix of 167 taxa scored for 647 characters, which all scientists interested in the origin of and early evolution of reptiles and of some of their key characters should read carefully. Despite the impressive size of the data matrix, the paper does not address the origin of turtles, a problem so prickly that it was also avoided by several other recent morphology-based phylogenetic analyses (e.g. Ezcurra, 2016; Ford and Benson, 2020; Buffa et al., 2024). Thus, Jenkins et al. (2025a) assume that the reptilian crown corresponds to the diapsid crown, as suggested by a fairly widespread consensus among molecular systematists that turtles form a clade with archosaurs (e.g., Brown and Thomson, 2017), for which the name Archelosauria has been proposed (Crawford et al., 2015). At least two morphological analyses also support this topology, although with low support (Simões et al., 2022; Wolniewicz et al., 2023). 

   Jenkins et al. (2025a) analyzed their matrix through parsimony and Bayesian phylogenetic inference. They confirm the systematic position of some taxa whose affinities have been questioned recently. Thus, the synapsid status of most varanopids is confirmed, although two recently-described, poorly known taxa (Cabarzia and Ascendonanus) previously attributed to Varanopidae appear to be sauropsids closely related to Orovenator. Jenkins et al.’s (2025a) analysis also provides a new perspective on controversial issues that are outside the main scope of their paper. For instance, Recumbirostra is placed well outside the amniote crown, contrary to some recent suggestions (e.g., Pardo et al., 2017) that have proven controversial (Modesto, 2024). Recumbirostra is composed of taxa that used to be considered “microsaurs” and had previously been suggested to be stem-amphibians (Marjanović and Laurin, 2019) or stem-amniotes (Ruta and Coates, 2007; Pardo et al., 2017). Jenkins et al. (2025a) cannot discriminate between these two alternative positions of Recumbirostra because no lissamphibian was included in the matrix, although the authors assume that Lissamphibia originated from temnospondyls. In any case, the results of Jenkins et al. (2025a) agree with those of Marjanović and Laurin (2019), Reisz et al. (2024), and Jenkins et al. (2025c – using a quite different dataset from 2025a) among others, in excluding “Recumbirostra” from the amniote crown. 

   On the contrary, many other features of the phylogeny presented by Jenkins et al. (2025a) break with tradition, which does not imply that these findings are wrong! Most obviously, Jenkins et al. (2025a) split what was once called Parareptilia into three clades located on the reptilian stem, which include, from the root crownwards: first, Bolosauridae; second, a large clade composed of Acleistorhinidae, Pareiasauromorpha and Procolophonoidea; and third, a more crownward clade composed of Millerettidae. Also intriguing is the position of Hylonomus and Captorhinidae, previously considered eureptiles, which Jenkins et al. (2025a) place on the amniote stem, rootward from Diadectomorpha. Even more surprising are the inferred taxonomic affinities of Lanthanosuchus shown in their Figure S3. Lanthanosuchus is usually considered to be a parareptile, but Jenkins et al. (2025a) place it as the sister-group of Chroniosaurus, which is typically considered to be a stem-amniote (Witzmann and Schoch, 2018), but may be a stem-tetrapod (Marjanović and Laurin, 2019). 

   Jenkins et al. (2025a) also use their phylogeny to reassess the evolution of a few key morphological characters. One of them is the temporal fenestration; they infer that the appearance of the lower temporal fenestra is a synapomorphy of Amniota, an unorthodox hypothesis that is strongly supported by the new phylogeny. This hypothesis was previously mentioned, but only as a plausible alternative to the established consensus, by Piñeiro et al. (2012), but it is also supported by the discovery of a lower temporal fenestra in several parareptile taxa (Cisneros et al., 2004). 

   Jenkins et al. (2025a) also suggest that the tympanic ear appeared by the Middle Permian, before the reptilian (or saurian) crown-group, because they identify an incipient tympanum in younginiforms and even millerettids, which they recover as successively more remote sister-groups of the reptilian (or saurian) crown. This interpretation, as well as the scores of several cells in their data matrix, is supported by new anatomical observations based on recent CT-scans (Jenkins et al., 2025b), which adds weight to this new evolutionary scenario on tympanum evolution and to the phylogeny. Under that scenario, a tympanic middle ear convergently appeared in Procolophonia and therapsids, a synapsid clade that includes mammals. 

   How will this new set of proposals stand up to scrutiny, and how will it be accepted by the community? It is too early to tell, and this is surely not the final point in the controversies surrounding the origin of the reptilian crown group. But this new analysis will have to be taken seriously by the community, given the amount of work that the authors have put into this, and the fact that it has already been thoroughly evaluated by three rounds of careful, detailed peer reviews (plus two additional rounds of comments of my own), as documented on the PCI Paleo web site. This new study will surely foster discussion on the origin and early evolution of reptiles, which can only lead to scientific progress.

   I thank both reviewers (David Marjanović and Valentin Buffa) for comments on a draft of this recommendation. However, this does not imply that they endorsed the final version; the views expressed herein are solely mine.

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   Version published to 10.1101/2024.11.25.625221 on bioRxiv

   Nov 26, 2024