ZooMS in southern Africa: Creating a comparative reference library for taxonomic identification

• Applicant: Professor Dr. Nicholas J. Conard
• Subject Area: Prehistory and World Archaeology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 545923777

The contribution of osseous assemblages to archaeological and palaeontological research is frequently hampered by high rates of fragmentation. This fragmentation adversely affects taxonomic and anatomical attribution and it is estimated that only a third of bones found in Pleistocene archaeological contexts can be identified on the basis of bone morphology, i.e. through visual inspection. Without a reliable means of identifying the taxon of fragmented bones these are often recorded as “indeterminate” fauna, excluding their integration into detailed zooarchaeological studies. High rates of fragmentation are common to regions like southern Africa where the University of Tübingen carries out several excavations on Middle Stone Age sites, including Sibhudu, Holley Shelter, and Geelbek Dunes. An emerging strategy for identifying the taxon of indeterminate bones is the use of a biomolecular technique called Zooarchaeology by Mass Spectrometry or ZooMS. ZooMS specifically targets type-I collagen, the dominant protein in bone, and uses the evolutionarily determined differences in the amino acid composition of collagen to taxonomically identify it. In mammals, taxonomic resolution using ZooMS usually reaches genus and family levels, however tribe and species-specific determinations are possible. Taxonomic identification using ZooMS is entirely reliant on a comparative reference library, whereby the peptide mass fingerprints of unknown samples are compared with previously studied fauna. To create this reference library, collagen needs to be sequenced using a tandem mass spectrometer. This allows for collagen peptide markers which can be used for taxonomic identification to be confirmed and then reliably utilized for standard ZooMS analysis. Through this project, we aim to significantly expand the ZooMS reference library for a region which would specifically benefit from novel methods for taxonomic identification. We will create a ZooMS reference library for 79 species native to southern Africa, including small, medium, and large mammals. We will then test this new comparative reference library on archaeological specimens obtained as part of excavations at Holley Shelter, Sibhudu, and Geelbek Dunes in South Africa. Funding is not required for the excavation or analysis of archaeological remains as part of this project, rather funds are sought specifically to sample from collections, recruit staff and for resources sufficient to create the comparative ZooMS reference library for southern Africa. Additionally, funds are sought to create scholarship opportunities for South African students to gain palaeoproteomic training at the University of Tübingen. While the Department of Early Prehistory and Quaternary Ecology typically studies Stone Age assemblages, this reference library would have broad applicability to all archaeological research carried out in the region.The contribution of osseous assemblages to archaeological and palaeontological research is frequently hampered by high rates of fragmentation. This fragmentation adversely affects taxonomic and anatomical attribution and it is estimated that only a third of bones found in Pleistocene archaeological contexts can be identified on the basis of bone morphology, i.e. through visual inspection. Without a reliable means of identifying the taxon of fragmented bones these are often recorded as "indeterminate" fauna, excluding their integration into detailed zooarchaeological studies. High rates of fragmentation are common to regions like southern Africa where the University of Tübingen carries out several excavations on Middle Stone Age sites, including Sibhudu, Holley Shelter, and Geelbek Dunes. An emerging strategy for identifying the taxon of indeterminate bones is the use of a biomolecular technique called Zooarchaeology by Mass Spectrometry or ZooMS. ZooMS specifically targets type-I collagen, the dominant protein in bone, and uses the evolutionarily determined differences in the amino acid composition of collagen to taxonomically identify it. In mammals, taxonomic resolution using ZooMS usually reaches genus and family levels, however tribe and species-specific determinations are possible. Taxonomic identification using ZooMS is entirely reliant on a comparative reference library, whereby the peptide mass fingerprints of unknown samples are compared with previously studied fauna. To create this reference library, collagen needs to be sequenced using a tandem mass spectrometer. This allows for collagen peptide markers which can be used for taxonomic identification to be confirmed and then reliably utilized for standard ZooMS analysis. Through this project, we aim to significantly expand the ZooMS reference library for a region which would specifically benefit from novel methods for taxonomic identification. We will create a ZooMS reference library for 79 species native to southern Africa, including small, medium, and large mammals. We will then test this new comparative reference library on archaeological specimens obtained as part of excavations at Holley Shelter, Sibhudu, and Geelbek Dunes in South Africa. Funding is not required for the excavation or analysis of archaeological remains as part of this project, rather funds are sought specifically to sample from collections, recruit staff and for resources sufficient to create the comparative ZooMS reference library for southern Africa. Additionally, funds are sought to create scholarship opportunities for South African students to gain palaeoproteomic training at the University of Tübingen. While the Department of Early Prehistory and Quaternary Ecology typically studies Stone Age assemblages, this reference library would have broad applicability to all archaeological research carried out in the region.

• DFG Programme: Research Grants
• International Connection: Spain
• Cooperation Partner: Dr. Samantha Brown