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29 million years of diverse mammalian proteomes recovered from the East African Rift System

ABSTRACT: Here, we sample small proteomes from the interior enamel of 10 fossils deposited at seven paleontological sites between 1.5 and 29 Ma in the Turkana Basin, a region of northern Kenya in the East African Rift System. We find enamel protein fragments in all fossil specimens including a 29 Ma Arsinoitherium from Topernawi, belonging to a now extinct mammalian order. Identified proteins include the classical structural enamel proteins amelogenin, enamelin, and ameloblastin, but also uncommon enamel proteins including collagens and proteases. Protein fragment abundance and average length decline in progressively older fossils, but we observe significant variability in Early Miocene preservation from site to site, with proboscidean fossils from 16 Ma Buluk preserving substantially more proteins than Rhinocerotidae and Anthracotheriidae fossils from the marginally older Locherangan (18 Ma) and Hippopotamidae from the younger site of Napudet (c. 5-11 Ma). Most specimens yield known clade-specific diagenetiforms that support field taxonomic identifications, with the notable exception of the Arsinoitherium that is without living relatives. Consensus phylogenetic trees suggest the potential for paleoproteomics in supporting taxonomic identifications and resolving evolutionary relationships of extinct taxa but should be approached with caution due to sometimes sparse fragment identification and the potential for sequence diagenesis. We identify numerous likely modifications that support the ancient age of these proteins, and the oldest examples of advanced glycation end-products and carbamylation yet known. The persistence of protein sequences within dense enamel tissues in one of the persistently warmest places on Earth promises the discovery of far older proteomes that will aid in the study of the biology and evolutionary relationships of extinct taxa.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Hippopotamidae Indet. Arsinoitheriidae Indet. Archaeopotamus Palaeoloxodon Recki Prodeinotherium Hobleyi Chilotheridium Gomphotheriidae Indet. Rhinocerotidae Indet. Brachyodus Aequatorialis Zygolophodon Sp.

SUBMITTER: Timothy Cleland

PROVIDER: MSV000091838 | MassIVE | Tue May 02 08:38:00 BST 2023

SECONDARY ACCESSION(S): PXD041930

REPOSITORIES: MassIVE

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29 million years of diverse mammalian proteomes recovered from the East African Rift System

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