Phylogenetically informative proteins from an Early Miocene rhinocerotid.

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dc.creatorPaterson, Ryan S
dc.creatorMackie, Meaghan
dc.creatorCapobianco, Alessio
dc.creatorHeckeberg, Nicola S
dc.creatorFraser, Danielle
dc.creatorDemarchi, Beatrice
dc.creatorMunir, Fazeelah
dc.creatorPatramanis, Ioannis
dc.creatorRamos-Madrigal, Jazmín
dc.creatorLiu, Shanlin
dc.creatorRamsøe, Abigail D
dc.creatorDickinson, Marc R
dc.creatorBaldreki, Chloë
dc.creatorGilbert, Marisa
dc.creatorSardella, Raffaele
dc.creatorBellucci, Luca
dc.creatorScorrano, Gabriele
dc.creatorLeonardi, Michela
dc.creatorManica, Andrea
dc.creatorRacimo, Fernando
dc.creatorWillerslev, Eske
dc.creatorPenkman, Kirsty EH
dc.creatorOlsen, Jesper V
dc.creatorMacPhee, Ross DE
dc.creatorRybczynski, Natalia
dc.creatorHöhna, Sebastian
dc.creatorCappellini, Enrico
dc.date2025-07-16T15:35:09Z
dc.date2025-07
dc.date2024-06-07
dc.date2025-07-16T15:34:57Z
dc.date.accessioned2026-08-03T04:38:53Z
dc.descriptionAcknowledgements: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement (no. 861389 - PUSHH). E.C., I.P., K.E.H.P., F.R., J.V.O., M.M. and R.S.P. are supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 101021361 - BACKWARD). M.M. was also supported by the Danish National Research Foundation grant PROTEIOS (DNRF128), and M.D., K.E.H.P. and C.B. by the UK NERC (NE/S010211/1 & NE/S00713X/1). D.F. was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC RGPIN-2018-05305) and a Research Activity Grant through the Canadian Museum of Nature. This work was supported by the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether-Programme (Award HO 6201/1-1 to SH) and by the European Union (ERC, MacDrive, GA 101043187). B.D. was supported by the European Union (ERC-2023-COG HORIZON AviArch GA 101125532). M.L. received funding from the Leverhulme Research Grant RPG-2020-317. E.W. is supported by the Lundbeck Foundation (grant nos. R302-2018-2155, R155-2013-16338), the Novo Nordisk Foundation (grant no. NNF18SA0035006), the Wellcome Trust (grant no. UNS69906), Carlsberg Foundation (grant no. CF18-0024), the Danish National Research Foundation (grant nos. DNRF94, DNRF174), the University of Copenhagen (KU2016 programme), Ferring Pharmaceuticals A/S, and Germany’s Excellence Strategy (EXC-2077), project no. 390741603. L.B. and R.S. thank M. Rubini of the Soprintendenza Archeologia Belle Arti e Paesaggio per le province di Frosinone e Latina for the permission to study Stephanorhinus samples from Fontana Ranuccio. L.B. and R.S. also acknowledge S. Grimaldi and F. Parenti (Istituto Italiano di Paleontologia Umana) for allowing us access to the Fontana Ranuccio collections and F. Strani for her valuable support in the selection of Stephanorhinus samples from Fontana Ranuccio. The authors thank L. Pandolfi for valuable constructive criticism on aspects of the manuscript. Field work in Canada’s High Arctic was supported by a palaeontology permit to N.R. from the Government of Nunavut, Department of Culture, Language, Elders and Youth (D.R. Stenton, J. Ross), with the permission of the Qikiqtani Inuit Association, particularly Grise Fiord. M. Dawson’s field work, which resulted in the collection of most of the rhinocerotid, in 1986, was supported by National Geographic. Associated fieldwork led by N.R. was also supported by the Canadian Museum of Nature and the Polar Continental Shelf Program.
dc.descriptionIn 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.
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dc.identifier0028-0836
dc.identifiers41586-025-09231-4
dc.identifier9231
dc.identifierhttps://www.repository.cam.ac.uk/handle/1810/387119
dc.identifier1476-4687
dc.identifier.urihttps://repo.dare.co.zw/handle/123456789/192048
dc.languageen
dc.languageeng
dc.publisherSpringer Nature
dc.publisherhttps://doi.org/10.1038/s41586-025-09231-4
dc.subjectAnimals
dc.subjectArctic Regions
dc.subjectBayes Theorem
dc.subjectCanada
dc.subjectDental Enamel
dc.subjectFossils
dc.subjectPerissodactyla
dc.subjectPhylogeny
dc.subjectProteins
dc.titlePhylogenetically informative proteins from an Early Miocene rhinocerotid.
dc.typeArticle

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