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Peer Community JournalPaleontologyPeer-reviewed journal article

EVOLUTIONARY ASSEMBLY OF CROWN REPTILE ANATOMY CLARIFIED BY LATE PALEOZOIC RELATIVES OF NEODIAPSIDA

Xavier A. JenkinsiD, Roger BensoniD, David P. FordiD, Claire BrowningiD, Vincent FernándeziD, Kathleen DollmaniD, Timothy Gomes, Elizabeth Griffiths, Jonah N. ChoiniereiD, Brandon R. PeecookiD

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Abstract

Living reptiles include more than 20,000 species with disparate ecologies. Direct anatomical evidence from Neodiapsida, which includes the reptile crown-group and its closest extinct relatives, shows that this diversity originates from a single common ancestor that lived some over 255 million years ago in the Paleozoic. However, the evolutionary assembly of crown reptile traits is poorly understood due to the lack of anatomically close relatives of Neodiapsida1-7. We present a substantially revised phylogenetic hypothesis, informed by new anatomical data from high-resolution synchrotron tomography of Paleozoic stem reptiles8-9. We find strong evidence placing the clade Millerettidae as the sister group to Neodiapsida, which uniquely share a suite of derived features. This grouping, for which we name the new clade Parapleurota, replaces previous phylogenetic paradigms by rendering the group Parareptilia as a polyphyletic assemblage of stem-reptiles, of which millerettids are the most crownward. Our findings address long-standing issues in Paleozoic reptile evolution10-17, such as firm support for the placement of captorhinids outside of crown Amniota and most varanopids as synapsids. These results greatly improve the fit of early amniote phylogeny to the observed stratigraphic record and reveal stepwise origin of crown reptile anatomy, including a middle Permian origin of tympanic hearing and loss of the lower temporal bar. This evolutionary framework provides a platform for investigating the diversification of the reptile crown group in the Early Triassic that was foundational to the origins of important living and extinct groups including dinosaurs (including birds), marine reptiles, crocodilians, and lepidosaurs.

In-depth summary

Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 9 (18 Aug 2025)

Synchrotron microtomography and a 167-taxon phylogenetic matrix place Millerettidae as sister to Neodiapsida (forming Parapleurota), dismantling Parareptilia and Eureptilia while dating tympanic hearing to the middle Permian.

Prevailing hypotheses divide Paleozoic reptiles into Parareptilia and Eureptilia, leaving long Permian ghost lineages and obscuring how crown reptile traits like tympanic hearing and temporal fenestration arose. High-resolution synchrotron tomography of previously inaccessible cranial and postcranial anatomy resolves former parareptiles as a polyphyletic assemblage of stem-reptiles leading to Neodiapsida.

Key results

  1. ShownMillerettidae is recovered as the immediate sister group to Neodiapsida, forming a clade named Parapleurota and rendering Parareptilia and Eureptilia polyphyletic.

    Parapleurota is supported by 21 unambiguous autapomorphies, Bremer support of 5, and Bayesian posterior probability of 1; forcing monophyly requires 81 extra parsimony steps for Parareptilia, 105 for Eureptilia excluding Millerettidae, and 64 for Diapsida excluding Millerettidae. · Phylogenetic analyses; Millerettids as crownward stem-reptiles; Figure legends

  2. ShownVaranopids are placed within Synapsida as earliest-diverging eupelycosaurs, while captorhinids, protorothyridids, Hylonomus, and recumbirostrans fall outside crown Amniota.

    Heleosaurus braincase and palatal characters support varanopids as eupelycosaurs (posterior probability 0.98, 14 unambiguous synapomorphies), while Captorhinidae (posterior probability 1), Hylonomus (posterior probability 0.85), and Recumbirostra (30 extra steps required to place in reptiles) fall on the amniote stem. · Phylogenetic analyses; Improving the stratigraphic fit of the early…

  3. ShownBreaking apart Parareptilia and placing millerettids sister to Neodiapsida substantially improves congruence with the Permian-Triassic stratigraphic record.

    The revised topology improves gap excess ratio (GER*) by at least 27% and modified Manhattan stratigraphic measure (MSM*) by 28% over 1,000 resampling iterations (positive MSM*Diff in 100% of comparisons against 62 constrained trees), shortening the Millerettidae ghost lineage by ~35 Ma and the Diapsida ghost lineage by ~15 Ma. · Stratigraphic Fit; Stratigraphic Fit; Improving the stratigraphic fit of the early…

  4. ShownTympanic hearing and loss of the lower temporal bar originated in the middle Permian ancestor of Parapleurota, whereas upper temporal fenestrae evolved convergently.

    Equal-rates Markov models show a tympanic fossa on the quadrate, squamosal, and quadratojugal in early parapleurotans (tympanic-to-stapedial footplate area ratio of 4:1 in Milleropsis and 7:1 in SAM-PK-K7710) that migrated onto the quadrate in Neodiapsida, alongside independent upper temporal fenestrae in Araeoscelidia and Neodiapsida. · Ancestral-State Reconstruction; Evolution of Temporal Fenestration in Amniota; Tympanic hearing was initiated before the origin…

Methods, data and reproducibility

High-resolution propagation phase-contrast synchrotron X-ray microtomography and museum micro-CT scans of Paleozoic and Triassic amniotes were segmented in 3D to score 647 cranial and postcranial characters across 167 operational taxonomic units. Phylogenetic relationships, stratigraphic congruence (MSM* and GER*), and ancestral states were inferred using maximum parsimony, Bayesian inference, and Markov models.

  • Synchrotron and laboratory X-ray microtomography scans of Paleozoic and Triassic amniote fossils including Milleropsis, Milleretta, Youngina, Araeoscelis, Heleosaurus, and SAM-PK-K7710 · extinct Paleozoic and Triassic amniotes · n = 3 Milleropsis skulls in nodule BP/1/720 plus additional specimens · BP/1/720, BP/1/3822, BP/1/4203, SAM-PK-K7710, AMNH FARB 5561, AMNH FARB 4686
  • Morphological character-taxon matrix of Paleozoic and Triassic tetrapods and amniotes (including 68 newly added taxa and 259 new characters) · extinct and extant tetrapods and amniotes · n = 167 operational taxonomic units, 647 characters · https://osf.io/9jac3/
Methods & tools
Dragonfly 2022.268, TNT v1.6, PAUP* 4.0a169, MrBayes 3.2.7a, R, phytools (fitMk), MorphoSource
Code & protocols
https://osf.io/9jac3/
Data & accessions
https://osf.io/9jac3/
Software & environment
Dragonfly 2022.268, TNT v1.6, PAUP* 4.0a169, MrBayes 3.2.7a, R with phytools package
Reproducibility gaps
CT scan data and 3D models are deposited on MorphoSource and listed in Table 1 (table contents not included in text); candidate stem turtles (e.g., Eunotosaurus africanus) were omitted from the matrix.
Limitations (4)
  • Candidate stem turtles such as Eunotosaurus africanus were excluded from the phylogenetic dataset, and crown group definition instead relied on molecular hypotheses placing turtles sister to archosaurs. · stated by the authors
  • A middle-early to middle Permian ghost lineage (Artinskian to Roadian) remains along the parapleurotan stem between Orovenator and Lanthanolania due to paleolatitudinal sampling biases in the rock record. · stated by the authors
  • Incomplete preservation of the temporal region in Orovenator and Lanthanolania leaves uncertainty in scoring several characters near the base of Parapleurota. · stated by the authors
  • Exact placement of Lanthanosuchus among early tetrapods and the relationships of Carboniferous stem-amniotes like Hylonomus and microsaurs require additional 3D imaging and taxon sampling. · stated by the authors

Read this if you study early amniote and reptile evolution, vertebrate paleontology, or morphological phylogenetics of the Permian-Triassic transition.

Citations
32
FWCI
18.87
Field percentile
top 1%

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