Dataset Information

Decontamination enhances palaeoproteomic analysis of a Pleistocene hominin tooth from Khudji, Tajikistan

ABSTRACT: Contamination is a potential issue in palaeoproteomic studies of human evolution, as it may mask low-abundance endogenous proteins and introduce modern variation into the reconstructed ancient proteome. This contamination may stem from many sources, such as the burial environment, storage facilities, and subsequent handling. Here, we apply a bleach decontamination protocol to a Pleistocene hominin tooth from the archaeological site of Khudji, Tajikistan, which was found to be heavily contaminated with skin-derived proteins during initial analysis. Bleach treatment removed nearly all contaminating proteins from the dentine proteome, without damaging endogenous proteins. Finally, phylogenetic analysis of the reconstructed proteome showed that the tooth likely stems from a Neanderthal.

INSTRUMENT(S):

ORGANISM(S): Homo

TISSUE(S): Dentin

SUBMITTER: Zandra Fagernäs

LAB HEAD: Frido Welker

PROVIDER: PXD050370 | Pride | 2025-04-24

REPOSITORIES: Pride

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			Action	DRS
	20230614_EXPL8_nLC11_GT_collab_77min_DDA_Blank_P0442.raw	Raw
	20230614_EXPL8_nLC11_GT_collab_77min_DDA_P0441.raw	Raw
	20230614_EXPL8_nLC11_GT_collab_77min_DDA_P0441.spider.mzidentml_1_2_0.xml	Mzid
	20231005_EXPL5_nLC11_GT_collab_77min_DDA_Blank_P0581.raw	Raw
	20231005_EXPL5_nLC11_GT_collab_77min_DDA_Blank_P0581.spider.mzidentml_1_2_0.xml	Mzid

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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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Decontamination enhances palaeoproteomic analysis of a Pleistocene hominin tooth from Khudji, Tajikistan

Dataset's files

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