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The phylogeny of early amniotes and the affinities of Parareptilia and Varanopidae


Amniotes include mammals, reptiles and birds, representing 75% of extant vertebrate species on land. They originated around 318 million years ago in the early Late Carboniferous and their early fossil record is central to understanding the expansion of vertebrates in terrestrial ecosystems. We present a phylogenetic hypothesis that challenges the widely accepted consensus about early amniote evolution, based on parsimony analysis and Bayesian inference of a new morphological dataset. We find a reduced membership of the mammalian stem lineage, which excludes varanopids. This implies that evolutionary turnover of the mammalian stem lineage during the Early–Middle Permian transition (273 million years ago) was more abrupt than has previously been recognized. We also find that Parareptilia are nested within Diapsida. This suggests that temporal fenestration, a key structural innovation with important functional implications, evolved fewer times than generally thought, but showed highly variable morphology among early reptiles after its initial origin. Our phylogeny also addresses controversies over the affinities of mesosaurids, the earliest known aquatic amniotes, which we recover as early diverging parareptiles.

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Fig. 1: Maximum clade credibility tree recovered from Bayesian analysis using the time-calibrated FBD model.
Fig. 2: Phylogeny of major clades of early amniotes, showing two origins of temporal fenestration in synapsids (green) and reptiles (magenta).
Fig. 3: Phylogeny of early reptiles, showing changes in temporal fenestration.
Fig. 4: Phylogeny of major clades of early amniotes showing wholesale turnover of the mammalian total group (Synapsida) during the Early–Middle Permian transition.

Data availability

The data used in this study, including the character list, character/taxon matrix, full taxon list with sources and missing data metrics, age range notes for the FBD analysis and the NEXUS and Bayesian scripts have been archived and are available via Dryad online data storage89. All other data supporting the findings of this study are available in the Supplementary Information.


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We are grateful to R. Cifelli and J. Larson (Sam Noble Oklahoma Museum of Natural History, Norman), S. Pierce and J. Cundiff (Museum of Comparative Zoology, Harvard), B. Simpson and K. Angielczyk (Field Museum of Natural History, Chicago), J. Choiniere and S. Jirah (Evolutionary Studies Institute, Johannesburg), C. Beard and D. Miao (Kansas University Natural History Museum, Lawrence) and D. Evans and K. Seymour (Royal Ontario Museum, Toronto) for access to curated museum specimens. We also thank R. Warnock (ETH Zurich) for advice on Bayesian analysis. This research was supported by a NERC studentship for D.P.F. from the DTP Environmental Research Council, UK (no. NE/L0021612/1).

Author information




D.P.F. and R.B.J.B. conceived the project. D.P.F. collected the data and conducted the phylogenetic analysis and hypothesis testing. Both authors designed and produced the figures and wrote the manuscript.

Corresponding author

Correspondence to David P. Ford.

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The authors declare no competing interests.

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Extended data

Extended Data Fig. 1 Maximum parsimony strict consensus tree.

Strict consensus of 16 MPT’s recovered from maximum parsimony analysis, each with 1558 steps (consistency index 0.2356, retention index 0.5934, rescaled consistency index 0.1398). Figures above the nodes are Bremer support indices; figures below the nodes are bootstrap support indices. Bremer support below 2 or bootstrap support below 50 is omitted.

Extended Data Fig. 2 Bayesian maximum clade credibility tree (Mkv).

Maximum clade credibility tree recovered from Bayesian analysis using the non-time calibrated Mkv model. Figures adjacent to the nodes are the posterior probability value of the node.

Extended Data Fig. 3 Bayesian MCC tree (FDB) with node ages (median and 95% HPD).

Maximum clade credibility tree recovered from Bayesian analysis using the time calibrated fossilized-birth-death model with median node ages. Yellow horizontal bars represent 95% highest posterior density (HPD) interval at node age. Red figures adjacent to nodes are the median node ages. Abbreviations: Lopin. = Lopingian, Mid. = Middle, Miss. = Mississippian.

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Ford, D.P., Benson, R.B.J. The phylogeny of early amniotes and the affinities of Parareptilia and Varanopidae. Nat Ecol Evol 4, 57–65 (2020).

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