Phylogenetically informative proteins from an Early Miocene rhinocerotid

Ryan S. Paterson (), Meaghan Mackie, Alessio Capobianco, Nicola S. Heckeberg, Danielle Fraser (), Beatrice Demarchi, Fazeelah Munir, Ioannis Patramanis, Jazmín Ramos-Madrigal, Shanlin Liu, Abigail D. Ramsøe, Marc R. Dickinson, Chloë Baldreki, Marisa Gilbert, Raffaele Sardella, Luca Bellucci, Gabriele Scorrano, Michela Leonardi, Andrea Manica, Fernando Racimo, Eske Willerslev, Kirsty E. H. Penkman, Jesper V. Olsen, Ross D. E. MacPhee, Natalia Rybczynski (), Sebastian Höhna and Enrico Cappellini ()
Additional contact information
Ryan S. Paterson: University of Copenhagen
Meaghan Mackie: University of Copenhagen
Alessio Capobianco: Ludwig-Maximilians-Universität München
Nicola S. Heckeberg: Ludwig-Maximilians-Universität München
Danielle Fraser: Canadian Museum of Nature
Beatrice Demarchi: University of Turin
Fazeelah Munir: University of York
Ioannis Patramanis: University of Copenhagen
Jazmín Ramos-Madrigal: University of Copenhagen
Shanlin Liu: Chinese Academy of Sciences
Abigail D. Ramsøe: University of Copenhagen
Marc R. Dickinson: University of York
Chloë Baldreki: University of York
Marisa Gilbert: Canadian Museum of Nature
Raffaele Sardella: Sapienza University of Rome
Luca Bellucci: Università di Firenze
Gabriele Scorrano: University of Copenhagen
Michela Leonardi: University of Cambridge
Andrea Manica: University of Cambridge
Fernando Racimo: University of Copenhagen
Eske Willerslev: University of Copenhagen
Kirsty E. H. Penkman: University of York
Jesper V. Olsen: University of Copenhagen
Ross D. E. MacPhee: American Museum of Natural History
Natalia Rybczynski: Canadian Museum of Nature
Sebastian Höhna: Ludwig-Maximilians-Universität München
Enrico Cappellini: University of Copenhagen

Nature, 2025, vol. 643, issue 8072, 719-724

Abstract: Abstract In the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference1–4. Still, even though ancient proteins have been reported from the Middle–Late Miocene5,6, the recovery of protein sequences providing subordinal-level phylogenetic insights does not exceed 3.7 million years ago (Pliocene)1. 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 diversification7. This analysis identifies a later Oligocene divergence for Elasmotheriinae, weakening alternative models suggesting a deep basal split between Elasmotheriinae and Rhinocerotinae8,9. 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 faunas10,11. 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.

Date: 2025
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DOI: 10.1038/s41586-025-09231-4

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