Related Experiment Video
Updated: Sep 16, 2025
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
3.5K
Phylogenetically informative proteins from an Early Miocene rhinocerotid
Ryan S Paterson1, Meaghan Mackie2,3, Alessio Capobianco4,5
1Globe Institute, University of Copenhagen, Copenhagen, Denmark. ryan.paterson@sund.ku.dk.
Nature
|July 9, 2025
Summary
Ancient proteins from Early Miocene rhinocerotid fossils push phylogenetic insights back 21-24 million years. Palaeoproteomics reveals new details on rhinocerotid diversification and ancient fauna origins.
Area of Science:
- Paleontology
- Molecular Biology
- Evolutionary Biology
Background:
- Ancient protein sequences are increasingly used for deep-time phylogenetic inference.
- Previous studies were limited to younger samples (Pliocene, ~3.7 million years ago).
Purpose of the Study:
- To extend the phylogenetic insights from ancient proteins further back in time.
- To analyze enamel proteins from an Early Miocene rhinocerotid fossil.
Main Methods:
- Retrieval of enamel protein sequences from a rhinocerotid fossil (Epiaceratherium sp.; CMNFV59632) from the Early Miocene.
- Analysis of over 1,000 peptide-spectrum matches and partial sequences of seven enamel proteins.
- Application of Bayesian tip-dating and assessment of protein damage indicators for endogeneity.
Main Results:
- Successfully recovered ancient protein sequences from a 21-24 million-year-old fossil, significantly pushing back the age limit for phylogenetic insights.
- Protein damage indicators confirmed the endogeneity of the retrieved sequences.
- Bayesian tip-dating suggested a Middle Eocene-Oligocene divergence for the specimen, aligning with rhinocerotid diversification.
Conclusions:
- Palaeoproteomics can yield valuable phylogenetic information from exceptionally old specimens, far older than those yielding endogenous DNA.
- The findings refine understanding of rhinocerotid evolutionary history, particularly the divergence of Elasmotheriinae.
- The results support hypotheses regarding the origins of the Haughton Crater fauna.
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