Phylogenetically informative proteins from an Early Miocene rhinocerotid

• 成果类型: Article
• 署名作者: Paterson, Ryan S.; Mackie, Meaghan; Capobianco, Alessio; Heckeberg, Nicola S.; Fraser, Danielle; Demarchi, Beatrice; Munir, Fazeelah; Patramanis, Ioannis; Ramos-Madrigal, Jazmin; Liu, Shanlin; Ramsoe, Abigail D.; Dickinson, Marc R.; Baldreki, Chloe; Gilbert, Marisa; Sardella, Raffaele; Bellucci, Luca; Scorrano, Gabriele; Leonardi, Michela; Manica, Andrea; Racimo, Fernando; Willerslev, Eske; Penkman, Kirsty E. H.; Olsen, Jesper V.; MacPhee, Ross D. E.; Rybczynski, Natalia; Hoehna, Sebastian; Cappellini, Enrico
• 署名单位: University of Copenhagen; University of Copenhagen; University of Munich; University of Munich; Carleton University; Carleton University; Smithsonian Institution; Smithsonian National Museum of Natural History; University of Turin; University of York - UK; Chinese Academy of Sciences; Institute of Zoology, CAS; Sapienza University Rome; University of Florence; University of Rome Tor Vergata; University of Cambridge; University of Cambridge; University of Bremen; American Museum of Natural History (AMNH)
• 刊物名称: Nature
• ISSN/ISSBN: 0028-1047
• DOI: 10.1038/s41586-025-09231-4
• 发表日期: 2025-07-17
• 关键词: haughton impact structure; devon-island; amino-acid; evolutionary history; genome sequence; perissodactyla; mammalia; AGE; fossils; ancient

摘要

In the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference1, 2, 3-4. 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.