Eighteen million years of diverse enamel proteomes from the East African Rift

Daniel R. Green (), Kevin T. Uno (), Ellen R. Miller, Craig S. Feibel, Eipa Emmanuel Aoron, Catherine C. Beck, Aryeh Grossman, Francis M. Kirera, Martin M. Kirinya, Louise N. Leakey, Cynthia Liutkus-Pierce, Fredrick K. Manthi, Emmanuel K. Ndiema, Isaiah O. Nengo, Cyprian Nyete, John Rowan, Gabrielle A. Russo, William J. Sanders, Tara M. Smiley, Patricia Princehouse, Natasha S. Vitek and Timothy P. Cleland ()
Additional contact information
Daniel R. Green: Harvard University
Kevin T. Uno: Harvard University
Ellen R. Miller: Wake Forest University
Craig S. Feibel: Rutgers University
Eipa Emmanuel Aoron: Harvard University
Catherine C. Beck: Hamilton College
Aryeh Grossman: Midwestern University
Francis M. Kirera: Mercer University
Martin M. Kirinya: Turkana Basin Institute
Louise N. Leakey: Turkana Basin Institute
Cynthia Liutkus-Pierce: Appalachian State University
Fredrick K. Manthi: National Museums of Kenya
Emmanuel K. Ndiema: National Museums of Kenya
Isaiah O. Nengo: Turkana Basin Institute
Cyprian Nyete: Turkana Basin Institute
John Rowan: University of Cambridge
Gabrielle A. Russo: Stony Brook University
William J. Sanders: University of Michigan
Tara M. Smiley: Stony Brook University
Patricia Princehouse: Turkana University College
Natasha S. Vitek: Stony Brook University
Timothy P. Cleland: Smithsonian Institute

Nature, 2025, vol. 643, issue 8072, 712-718

Abstract: Abstract Research into the palaeobiology of extinct taxa through ancient DNA and proteomics has been mostly limited to Plio-Pleistocene fossils1–9, due to molecular breakdown over time, which is exacerbated in tropical settings1–3. Here we sample small proteomes from the interior enamel of fossils at palaeontological sites from the Pleistocene to the Oligocene in the Turkana Basin, Kenya, which has produced a rich record of Cenozoic mammalian evolution10. Through a mass-spectrometry-based proteomic workflow, and using criteria to locate diagenetiforms derived from enamel, we recover fragments of enamelin, ameloblastin, matrix metalloprotease-20 and dentin matrix acidic phosphoprotein 1 from an Early Miocene rhinocerotid and several proboscideans collected from the sites of Buluk (16 million years ago; Ma) and Loperot (18 Ma). Diagenetiform counts decline in progressively older fossils, and we observe variability in Early Miocene preservation across sites. Phylogenetic analyses reveal the contribution of these sequences to the systematic placement of extinct taxa, although we caution that this approach must account for sparse fragments, uncertainty in fragment identification and possible sequence diagenesis. We identify likely modifications that support the ancient age of these proteins, and some of the oldest examples of advanced glycation end-products yet known. The discovery of protein sequences within dense enamel tissues in one of the persistently warmest regions on Earth promises the discovery of much older proteomes that will aid in the study of the palaeobiology and evolutionary relationships of extinct taxa.

Date: 2025
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DOI: 10.1038/s41586-025-09040-9

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