Biology subjects

Troche, G.

Publications and source records attributed to Troche, G..

5 recordsLinked to original sources

bioRxiv2025

Composition variations in archaeological human bone proteomes

Sampling strategies within the field of skeletal palaeoproteomics are often based on specimen availability. Knowledge of bone biology might assist in improving sample selection strategies and minimise unnecessary sampling of precious (hominin) material. We study ten bone sample locations across four bone elements, for a total of 10 adult, archaeological human skeletons. We compare bone proteome composition and modification for skeletal elements formed through endochondral and intramembranous ossification, as well as cortical-trabecular bone pairs of three skeletal locations. We observe minimal differences in bones formed through the two ossification processes, outside of the exclusive presence of cartilage-related proteins in endochondral bone samples. We observe higher protein concentrations, a larger number of protein groups and peptides, and lower rates of deamidation in cortical bone compared to trabecular bone proteomes, this indicates that cortical bone provides a better preservation environment compared to trabecular bone. Throughout our analysis, the petrous bone stands out, with the largest and most complex proteomes recovered for all studied individuals. Formed through endochondral ossification, the petrous bone undergoes minimal turnover during life. Our observations indicate that the petrous bone is the ideal source of ancient protein sequence information.

evolutionary biology↗

bioRxiv2025

Identification and removal of contamination in palaeoproteomic analysis of dental enamel

Analysis of archaeological and palaeontological dental enamel allows for the study of taxonomy, phylogenetic relationships, and genetic sex of Pleistocene fauna and hominin remains. However, high-quality data is required for the study of degraded, chemically modified ancient proteomes. Protein contamination may hinder acquisition of such data, due to the abundance and better preservation of modern contaminating proteins. Here, we artificially contaminate a Pleistocene woolly rhinoceros tooth in order to investigate decontamination of archaeological dental enamel. We find that although the contaminating proteins are not identified, likely due to a lack of denaturation and digestion steps in archaeological dental enamel protein extraction protocols, contamination leads to significant loss of endogenous proteomic information. We thereafter compare five published decontamination methods, and find that a simple water or bleach wash prior to demineralization is most efficient at removing protein contamination. The water wash does not affect the endogenous proteome, while a bleach wash may lead to a loss of shorter intercrystalline peptides. We therefore conclude that decontamination is necessary in the study of ancient dental enamel, to ensure maximal retrieval of endogenous proteomic information, and can easily be achieved by incorporating a water or bleach wash step into the protein extraction protocol.

evolutionary biology↗

bioRxiv2025

New methods on the block: Taxonomic identification of archaeological bones in resin-embedded sediments through palaeoproteomics

The integration of biomolecular studies of past organisms with geoarchaeological studies can significantly improve our understanding of the relative chronology and context of archaeologically (in)visible behaviours. However, the complexity and sedimentological heterogeneity of archaeological deposits at a microscopic scale is often not taken into consideration in biomolecular studies. Here, we investigate the preservation and retrieval of palaeoproteomic data from bone fragments embedded in Pleistocene resin-impregnated sediment blocks. We show that resin impregnation has minimal effect on skeletal protein taxonomic identifications in modern skeletal material, but observe an increase in oxidation-related post-translational modifications. We then successfully retrieve proteins from resin-impregnated blocks from the Palaeolithic sites of Bacho Kiro Cave, La Ferrassie and Quincay. The taxonomic identifications of minute bones encased in resin are in line with previous analyses of the faunal communities of these sites, with a diversity of taxa (Bos sp./Bison sp., Equus sp., Ursus sp., and Caprinae) observed at a microscale in Bacho Kiro. This differs from results from La Ferrassie where most of the samples are identified as a single taxon (Bos sp./Bison sp.) across different areas of the site. The block from Quincay only provided taxonomic identification of two out of eleven bone-derived samples, likely due to diagenesis. Our work indicates that palaeoproteomes can be retrieved from bone fragments at a microstratigraphic resolution, enabling the detailed study of faunal community composition at a scale that more closely matches that of past human occupations. Significance StatementResin-embedded sediment blocks are widely used in archaeology and soil sciences to reconstruct past environments and human behavior, but their potential for biomolecular analysis is underexplored. Here, we demonstrate that ancient proteins can be successfully retrieved from bone fragments embedded in resin-impregnated sediment blocks from Pleistocene archaeological sites. Our findings show that resin impregnation has a minimal impact on protein recovery and that palaeoproteomics enables taxonomic identification of Pleistocene bone fragments at a microstratigraphic scale. This approach allows for reconstructing past faunal communities with unprecedented detail, improving our understanding of ancient ecosystems and the environmental contexts of early hominin occupations.

evolutionary biology↗

bioRxiv2024

Ancient biomolecular analysis of 39 mammoth individuals from Kostenki 11-Ia elucidates Upper Palaeolithic human resource use

Circular structures made from woolly mammoth bones are found across Ukraine and west Russia, yet the origin of the bones remains uncertain. We present ten new mammoth radiocarbon dates from the largest circular structure at Kostenki 11-Ia, identifying two mammoth mandibles [~]200-1,200 years older than the other dated materials from the site, suggesting skeletal material from long-dead individuals was scavenged and used in the site construction. Biomolecular sexing of 30 individuals showed a predominance of females, suggesting the Kostenki mammoths are primarily from herds. We identify six mitochondrial lineages across 16 samples, showing they are not all from the same matriline. Integrating biomolecular sexing with stable{delta} 13C and{delta} 15N isotope analysis, we find no isotopically-differentiated resource use by females and males, providing the first analysis of foraging differences between sexes in any Late Pleistocene megafauna. Our study highlights the significance of integrating ancient biomolecular approaches in archaeological inference. TeaserIntegrating 14C dating, ancient DNA, palaeoproteomics, and stable isotopes improves our understanding of Kostenki 11-Ia

evolutionary biology↗

bioRxiv2024

Cleaning the Dead: Optimized decontamination enhances palaeoproteomic analyses of a Pleistocene hominin tooth from Khudji, Tajikistan

The study of ancient proteins preserved in a range of archaeological, cultural heritage, and palaeontological materials is increasingly contributing to our understanding of human evolution and archaeological research questions. Many of the specimens studied have been excavated and stored for a significant duration prior to their proteomic analysis. Human handling and storage environments therefore provide ample opportunities for protein contamination onto and into specimens of interest to palaeoproteomic studies. As such, modern protein contamination limits access to endogenous proteomes. Here, we compare five approaches of bone protein decontamination applied to a Pleistocene Equus sp. bone fragment contaminated with a modern dog salivary proteome. We find that all tested methods reduce the protein contamination, but with different efficiencies. We find that a brief bleach wash is the most effective approach in removing modern protein contamination, and that no additional damage is caused to the endogenous proteome by this treatment. Next, we apply this approach to a hominin tooth found at Khudji, a Late Pleistocene archaeological site in Tajikistan. We demonstrate that a brief bleach wash removes almost all human skin protein contamination while retaining the endogenous hominin dentine proteome. Subsequent phylogenetic analysis of the Khudji dentine proteome allowed determination that the specimen is likely not a Denisovan, but still leaves ambiguity between an assignment to either modern humans or Neanderthals.

evolutionary biology↗