Ancient proteins from a 20-million-year-old rhino tooth are transforming our understanding of evolution.
Researchers have made a major breakthrough in understanding rhino evolution by analyzing proteins extracted from a fossilized tooth that is over 20 million years old.
By examining these ancient protein sequences, scientists discovered that this prehistoric rhino separated from other members of the rhino family during the Middle Eocene to Oligocene period, approximately 41 to 25 million years ago.
The findings also offered new insight into when the two main branches of the rhino family, Elasmotheriinae and Rhinocerotinae, split from one another. The evidence points to a more recent divergence during the Oligocene (about 34 to 22 million years ago) than previous fossil-based studies had indicated.
This successful recovery and analysis of enamel proteins marks a significant leap in molecular paleontology, extending the known limit for evolutionary protein preservation to a timeframe ten times older than the most ancient DNA ever recovered.
Confirming Authenticity With Chemistry
The team at York was involved in confirming that the proteins and amino acids were genuinely ancient. They analyzed the rhino tooth, which was unearthed in Canada’s High Arctic, using a technique known as chiral amino acid analysis to gain a clearer understanding of how the proteins within it had been preserved.
By measuring the extent of protein degradation and comparing it to previously analyzed rhino material, they were able to confirm that the amino acids were original to the tooth and not the result of later contamination.
Dr. Marc Dickinson, co-author and postdoctoral researcher at the University of York’s Department of Chemistry, said: “It is phenomenal that these tools are enabling us to explore further and further back in time. Building on our knowledge of ancient proteins, we can now start asking fascinating new questions about the evolution of ancient life on our planet.”
The rhino is of particular interest as it is now classified as an endangered species, and so understanding its deep-time evolutionary history, allows us to gain vital insights into how past environmental changes and extinctions shaped the diversity we see today.
To date, scientists have relied on the shape and structure of fossils or, more recently, ancient DNA (aDNA) to piece together the evolutionary history of long-extinct species. However, aDNA rarely survives beyond 1 million years, limiting its utility for understanding the deep evolutionary past.
Proteins Reveal More Than DNA Alone
While ancient proteins have been found in fossils from the Middle-Late Miocene, – roughly the last 10 million years – obtaining sequences detailed enough for robust reconstructions of evolutionary relationships was previously limited to samples no older than four million years.
The new study, published in the journal Nature, significantly expands that window, demonstrating the potential of proteins to persist over vast geological timescales under the right conditions.
Fazeelah Munir, who analyzed the tooth as part of her doctoral research at the University of York’s Department of Chemistry, said: “Successful analysis of ancient proteins from such an old sample gives a fresh perspective to scientists around the globe who already have incredible fossils in their collections. This important fossil helps us to understand our ancient past.”
The fossil was in a region of Canada currently characterized by permafrost, and researchers say that dental enamel and the relatively cold environment the fossil was found in, played an important part in the long preservation of the proteins.
Dental enamel provides a stable ‘scaffold’ that can protect ancient proteins from degradation over geological time. The hardness of enamel, which results from a complex structure of minerals, acts as a protective barrier, slowing down the breakdown of proteins that occurs after death.
Professor Enrico Cappellini, from Globe Institute, University of Copenhagen, said: “The Haughton Crater may be a truly special place for paleontology: a biomolecular vault protecting proteins from decay over vast geological timescales.
“Its unique environmental history has created a site with exceptional preservation of ancient biomolecules, akin to how certain sites preserve soft tissues. This finding should encourage more paleontological fieldwork in regions around the world.”
Ryan Sinclair Paterson, postdoctoral researcher at the Globe Institute, University of Copenhagen, added: “This discovery is a game-changer for how we can study ancient life.”
Reference: “Phylogenetically informative proteins from an Early Miocene rhinocerotid” by 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, 9 July 2025, Nature.
DOI: 10.1038/s41586-025-09231-4
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