中新世早期犀类动物的系统发育信息蛋白，这一成果由哥本哈根大学Enrico Cappellini研究组经过不懈努力而取得。该项研究成果发表在2025年7月9日出版的《自然》上。

小组把界限推回21-24 百万年前（中新世早期），通过从加拿大高北极地区检索犀牛（Epiaceratherium sp.；CMNFV59632）的釉质蛋白序列。该课题组人员恢复了七个珐琅蛋白的部分序列和超过1000个肽谱匹配，跨越至少251个氨基酸。内生性与热年龄估计一致，并得到蛋白质损伤指标的支持，包括在长期成岩作用中积累的几种自发和不可逆的化学修饰。贝叶斯尖端定年将CMNFV59632的分化时间定在中始新世-渐新世，与鼻甾体高度分化相吻合。这一分析确定了Elasmotheriinae在渐新世后期的分化，削弱了另一种模式，即Elasmotheriinae和犀牛科之间存在深层的基础分裂。

这些发现与关于Haughton陨石坑神秘动物群起源的假设一致，尽管有相当多的地方性，但它们与遥远的欧亚动物群有相似之处。他们的发现证明了古蛋白质组学在从一个样本中获取系统发育信息方面的潜力，这个样本比迄今为止获得内源性DNA的任何样本都要古老大约10倍。

据悉，在过去的十年中，古代蛋白质序列已成为深时间系统发育推断的宝贵数据来源。然而，尽管已经报道了来自中新世中晚期的古代蛋白质，但提供次级系统发育见解的蛋白质序列的恢复不超过3.7百万年前（上新世）。

附：英文原文

Title: Phylogenetically informative proteins from an Early Miocene rhinocerotid

Author: Paterson, Ryan S., Mackie, Meaghan, Capobianco, Alessio, Heckeberg, Nicola S., Fraser, Danielle, Demarchi, Beatrice, Munir, Fazeelah, Patramanis, Ioannis, Ramos-Madrigal, Jazmn, Liu, Shanlin, Ramse, Abigail D., Dickinson, Marc R., Baldreki, Chlo, 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, Hhna, Sebastian, Cappellini, Enrico

Issue&Volume: 2025-07-09

Abstract: 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 3.7million years ago (Pliocene)1. Here, we push this boundary back to 21–24million 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.

DOI: 10.1038/s41586-025-09231-4

Source: https://www.nature.com/articles/s41586-025-09231-4