Phylogenetically informative proteins from an Early Miocene rhinocerotid
Paterson, Ryan S Mackie, Meaghan Capobianco, Alessio Heckeberg, Nicola S Fraser, Danielle Demarchi, Beatrice Munir, Fazeelah Patramanis, Ioannis Ramos-Madrigal, Jazmín Liu, Shanlin
Paterson, Ryan S
Mackie, Meaghan
Capobianco, Alessio
Heckeberg, Nicola S
Fraser, Danielle
Demarchi, Beatrice
Munir, Fazeelah
Patramanis, Ioannis
Ramos-Madrigal, Jazmín
Liu, Shanlin
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2025-07-09
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2024-06-07
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palaeontology
phylogenetics
proteomics
phylogenetics
proteomics
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Abstract
In the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference<sup>1-4</sup>. Still, even though ancient proteins have been reported from the Middle-Late Miocene<sup>5,6</sup>, the recovery of protein sequences providing subordinal-level phylogenetic insights does not exceed 3.7 million years ago (Pliocene)<sup>1</sup>. Here, we push this boundary back to 21-24 million years ago (Early Miocene) by retrieving enamel protein sequences of a rhinocerotid (Epiaceratherium sp.; CMNFV59632) from Canada's High Arctic. We recover partial sequences of seven enamel proteins and more than 1,000 peptide-spectrum matches, spanning at least 251 amino acids. Endogeneity is in line with thermal age estimates and is supported by indicators of protein damage, including several spontaneous and irreversible chemical modifications accumulated during prolonged diagenesis. Bayesian tip-dating places the divergence time of CMNFV59632 in the Middle Eocene-Oligocene, coinciding with a phase of high rhinocerotid diversification<sup>7</sup>. This analysis identifies a later Oligocene divergence for Elasmotheriinae, weakening alternative models suggesting a deep basal split between Elasmotheriinae and Rhinocerotinae<sup>8,9</sup>. The findings are consistent with hypotheses on the origin of the enigmatic fauna of the Haughton Crater, which, in spite of considerable endemism, has similarity to distant Eurasian faunas<sup>10,11</sup>. Our findings demonstrate the potential of palaeoproteomics in obtaining phylogenetic information from a specimen that is approximately ten times older than any sample from which endogenous DNA has been obtained so far.
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Paterson, R.S., Mackie, M., Capobianco, A. et al. Phylogenetically informative proteins from an Early Miocene rhinocerotid. Nature 643, 719–724 (2025). https://doi.org/10.1038/s41586-025-09231-4
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Copyright © The Author(s) 2025. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. The linked file is the published version of the article.
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0028-0836
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1476-4687
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openAccess