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An early Miocene enamel proteome from an early diverging rhinocerotid

ABSTRACT: The evolutionary history of Rhinocerotidae has been the subject of significant debate among palaeontologists, with several paradigm shifts within the last quarter century, typically centered around a speculated deep-basal split between Rhinocerotinae and Elasmotheriinae. Here, we recover an endogenous ancient enamel proteome from an Early Miocene (20+Ma) old rhinocerotid from the Haughton Formation of Canada’s High Arctic. Ancient proteomes sufficient for phylogenetic analysis have not previously been recovered from beyond the Pliocene, making it difficult to reconstruct the evolutionary relationships and divergence times of fossil taxa that are beyond the reach of ancient DNA. Here, phylogenetic analysis of our proteomic data suggests the split between Elasmotheriinae and Rhinocerotinae occurred much later than previously speculated, in the late Eocene or Oligocene. The authenticity of ancient the ancient proteome is supported by a suite of post-translational modifications associated with advanced degradation, including a significant degree of arginine->ornithine conversion and high rates of advanced forms of tryptophan and histidine oxidation.

INSTRUMENT(S):

ORGANISM(S): Rhinocerotidae

TISSUE(S): Tooth Enamel

SUBMITTER: Ryan Sinclair Paterson

LAB HEAD: Enrico Cappellini

PROVIDER: PXD052635 | Pride | 2025-07-06

REPOSITORIES: Pride

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			Action	DRS
	20180328_QE5_nLC5_MEM_COLLAB_GeoG_1313.raw	Raw
	20180328_QE5_nLC5_MEM_COLLAB_GeoG_1314.raw	Raw
	20180328_QE5_nLC5_MEM_COLLAB_GeoG_1315.raw	Raw
	20180328_QE5_nLC5_MEM_COLLAB_GeoG_1316.raw	Raw
	20190302_QE7_nLC7_MEM_COLLAB_EvoG_1606.raw	Raw

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Project description:Pleistocene Pongo teeth show substantial variation in size and morphology, fueling taxonomic debates about the paleodiversity of the genus. We investigated prominent features of the enamel-dentine-junction junction (EDJ) – phylogenetically informative internal structures – of 71 fossil Pongo lower molars from various sites by applying geometric morphometrics and conducted paleoproteomic analyses from enamel proteins to attempt to identify extinct orangutan species. Forty-three orangutan lower molars representing Pongo pygmaeus and Pongo abelii were included for comparison. The shape of the EDJ was analyzed by placing five landmarks on the tip of the main dentine horns, and 142 semilandmarks along the marginal ridges connecting the dentine horns. Paleoproteomic analyses were conducted on 15 teeth of Late Pleistocene Pongo using high-resolution tandem mass spectrometry. The geometric morphometric results show variations in EDJ shape regarding aspects of the height and position of the dentine horns and connecting ridges. Despite the issue of molar position and sample size, modern molars are distinguished from fossil counterparts by their elongated tooth outline and narrowly positioned dentine horns. Proteomic results show that neither a distinction of P. pygmaeus and P. abelii, nor a consistent allocation of fossil specimens to extant species is feasible. Based on the EDJ shape, the (late) Middle to Late Pleistocene Pongo samples from Vietnam share the same morphospace, supporting the previous allocation to P. devosi, although substantial overlap with Chinese fossils could also indicate close affinities with P. weidenreichi. The hypothesis that both species represent one chronospecies cannot be ruled out. Two fossil specimens, one from Tam Hay Marklot (Laos, Late Pleistocene), and another from Sangiran (Java, Early to Middle Pleistocene), along with some specimens within the Punung sample (Java), exhibit affinities with Pongo abelii. The Punung fossils might represent a mix of early Late Pleistocene and later specimens (terminal Pleistocene to Holocene) related to modern Pongo. The taxonomy and phylogeny of the complete Punung sample needs to be further investigated.

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An early Miocene enamel proteome from an early diverging rhinocerotid

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