Dataset Information

Tryps-IN: A streamlined palaeoproteomics workflow enables ZooMS analysis of 10,000-year-old petrous bones from Jordan rift-valley

ABSTRACT: Poor preservation of collagen in dry and/or arid environments has hindered the application of Zooarchaeology by mass spectrometry (ZooMS) analysis in many regions of the world. As a result many zooarchaeological investigations have relied exclusively on morphological assessment of fragmentary remains due to the inadequate preservation of biomolecules. The climatic conditions of Southwest Asia include extreme temperature fluctuations unconducive to preservation of proteins and DNA. We performed zooarchaeological analysis of remains from the 10,000-year-old site of Shkārat Msaied in Jordan and sub-sampled twenty-eight petrous bones, the hardest bone in the mammalian skeleton, for species identification by ZooMS. Using an unconventional and simplified extraction protocol we call Tryps-IN, in which digestion was performed without removal of the demineralising EDTA, we taxonomically identified several fragments, outperforming an established ZooMS work-flow. A subset of identifications was subsequently confirmed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) protein sequencing. The new methodology presented here opens the possibility of further bioarchaeological investigation of other fragmentary faunal assemblages within this region of archaeological significance.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Capra Sp.

TISSUE(S): Bone

SUBMITTER: Louise Le Meillour

LAB HEAD: Alberto Taurozzi

PROVIDER: PXD045412 | Pride | 2023-10-19

REPOSITORIES: Pride

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			Action	DRS
	20190203_QE7_nLC7_MEM_COLLAB_TJ_UofY_JORD12.raw	Raw
	20190203_QE7_nLC7_MEM_COLLAB_TJ_UofY_JORD23.raw	Raw
	20211027_EXPL2_nLC3_MEM_collab_77min_DDA_Ancient_bone_SM10.raw	Raw
	20211027_EXPL2_nLC3_MEM_collab_77min_DDA_Ancient_bone_SM18.raw	Raw
	20211027_EXPL2_nLC3_MEM_collab_77min_DDA_Ancient_bone_SM26.raw	Raw

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Project description:Groupers (Epinephelidae) are ecologically, commercially, and culturally important predatory fishes throughout their global distribution range in tropical, subtropical and occasionally temperate regions. They are key species for modern and ancient fisheries in the Mediterranean which have been heavily overfished in the past century leading to smaller catch sizes, lower CPUE, and decreased biomass. There are four species of grouper native to the Mediterranean within the Epinephelus genus.The abundance and distribution of grouper species prior to the 20th century in the Mediterranean remains poorly known. Using peptide mass fingerprinting, also known as Zooarchaeology by Mass Spectrometry (ZooMS), we investigated if ZooMS is a viable method for identifying intra-genus grouper bones to species level. Due to the lack of publicly available genomic sequences and for validation of ZooMS markers, we reconstructed collagen type I amino acid sequences using LC-MS/MS for four Epinephelus spp. Adequate variation between collagen sequences enabled the production of the best supported phylogenetic tree for Mediterranean Epinephelus spp. to date. We identified 23 previously undescribed ZooMS biomarkers capable of distinguishing groupers to the species level. Our novel biomarkers were applied to a case study of 23 grouper/comber fish bones from the Middle to Late Holocene archaeological site of Kinet Höyük, located along the coast of Iskenderun Bay, Turkey. ZooMS markers enabled species level identification of 19 bones with 18 identified as Epinephelus aeneus and 1 identified as Epinephelus marginatus. Combining ZooMS identifications with catch size reconstructions has revealed that E. aeneus is capable of growing ca. 30 cm larger than previously reported. This abundance and dominance of E. aeneus locally at Kinet Höyük is consistent with E. aeneus being the most prevalent grouper species in Iskenderun Bay today, testifying to several millennia of this species local population persistence despite fishing pressure, habitat degradation, and climatic changes.

Dataset Information

Tryps-IN: A streamlined palaeoproteomics workflow enables ZooMS analysis of 10,000-year-old petrous bones from Jordan rift-valley

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