Browsing by Author "Smith, Geoff M."
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- Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identificationPublication . Mylopotamitaki, Dorothea; Harking, Florian S.; Taurozzi, Alberto J.; Fagernäs, Zandra; Godinho, Ricardo Miguel; Smith, Geoff M.; Weiss, Marcel; Schüler, Tim; McPherron, Shannon P.; Meller, Harald; Cascalheira, João; Bicho, Nuno; Olsen, Jesper V.; Hublin, Jean-Jacques; Welker, FridoHigh-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.
- Identifying the unidentified fauna enhances insights into hominin subsistence strategies during the Middle to Upper Palaeolithic transitionPublication . Sinet-Mathiot, Virginie; Rendu, William; Steele, Teresa E.; Spasov, Rosen; Madelaine, Stéphane; Renou, Sylvain; Soulier, Marie-Cécile; Martisius, Naomi L.; aldeias, vera; Endarova, Elena; Goldberg, Paul; McPherron, Shannon J. P.; Rezek, Zeljko; Sandgathe, Dennis; Sirakov, Nikolay; Sirakova, Svoboda; Soressi, Marie; Tsanova, Tsenka; Turq, Alain; Hublin, Jean-Jacques; Welker, Frido; Smith, Geoff M.Understanding Palaeolithic hominin subsistence strategies requires the comprehensive taxonomic identification of faunal remains. The high fragmentation of Late Pleistocene faunal assemblages often prevents proper taxonomic identification based on bone morphology. It has been assumed that the morphologically unidentifiable component of the faunal assemblage would reflect the taxonomic abundances of the morphologically identified portion. In this study, we analyse three faunal datasets covering the Middle to Upper Palaeolithic transition (MUPT) at Bacho Kiro Cave (Bulgaria) and Les Cottes and La Ferrassie (France) with the application of collagen type I peptide mass fingerprinting (ZooMS). Our results emphasise that the fragmented component of Palaeolithic bone assemblages can differ significantly from the morphologically identifiable component. We obtain contrasting identification rates between taxa resulting in an overrepresentation of morphologically identified reindeer (Rangifer tarandus) and an underrepresentation of aurochs/bison (Bos/Bison) and horse/European ass (Equus) at Les Cottes and La Ferrassie. Together with an increase in the relative diversity of the faunal composition, these results have implications for the interpretation of subsistence strategies during a period of possible interaction between Neanderthals and Homo sapiens in Europe. Furthermore, shifts in faunal community composition and in carnivore activity suggest a change in the interaction between humans and carnivores across the MUPT and indicate a possible difference in site use between Neanderthals and Homo sapiens. The combined use of traditional and biomolecular methods allows (zoo)archaeologists to tackle some of the methodological limits commonly faced during the morphological assessment of Palaeolithic bone assemblages.
- Subarctic climate for the earliest Homo sapiens in EuropePublication . Pederzani, Sarah; Britton, Kate; Aldeias, Vera; Bourgon, Nicolas; Fewlass, Helen; Lauer, Tobias; McPherron, Shannon P.; Rezek, Zeljko; Sirakov, Nikolay; Smith, Geoff M.; Spasov, Rosen; Tran, N.-Han; Tsanova, Tsenka; Hublin, Jean-JacquesThe expansion of Homo sapiens across Eurasia marked a major milestone in human evolution that would eventually lead to our species being found across every continent. Current models propose that these expansions occurred only during episodes of warm climate, based on age correlations between archaeological and climatic records. Here, we obtain direct evidence for the temperatures faced by some of these humans through the oxygen isotope analysis of faunal remains from Bacho Kiro Cave, Bulgaria, the earliest clear record of H. sapiens in Europe. The results indicate that humans ∼45,000 years ago experienced subarctic climates with far colder climatic conditions than previously suggested. This demonstrates that the early presence of H. sapiens in Europe was not contingent on warm climates. Our results necessitate the revision of key models of human expansion and highlight the need for a less deterministic role of climate in the study of our evolutionary history.
- Subsistence behavior during the Initial Upper Paleolithic in Europe: site use, dietary practice, and carnivore exploitation at Bacho Kiro Cave (Bulgaria)Publication . Smith, Geoff M.; Spasov, Rosen; Martisius, Naomi L.; Sinet-Mathiot, Virginie; Aldeias, Vera; Rezek, Zeljko; Ruebens, Karen; Pederzani, Sarah; McPherron, Shannon P.; Sirakova, Svoboda; Sirakov, Nikolay; Tsanova, Tsenka; Hublin, Jean-JacquesThe behavioral dynamics underlying the expansion of Homo sapiens into Europe remains a crucial topic in human evolution. Owing to poor bone preservation, past studies have strongly focused on the Initial Upper Paleolithic (IUP) stone tool record. Recent excavations and extensive radiocarbon dating at Bacho Kiro Cave (Bulgaria) pushed back the arrival of IUP H. sapiens into Europe to ca. 45,000 years ago. This site has exceptional bone preservation, and we present the study of 7431 faunal remains from across two IUP layers (I and J) and one Middle Paleolithic layer (K). We identified a shift in site use and occupation intensity through time, marked by increased find density and human modifications in Layer I. Alongside a decrease in carnivore presence and seasonality data demonstrating human presence in all seasons, this indicates a more frequent or prolonged occupation of the site by IUP groups. Contrarily, the dietary focus across the IUP and Middle Paleolithic layers is similar, centered on the exploitation of species from a range of habitats including Bos/Bison, Cervidae, Equidae, and Caprinae. While body parts of large herbivores were selectively transported into the site, the bear remains suggest that these animals died in the cave itself. A distinct aspect of the IUP occupation is an increase in carnivore remains with human modifications, including these cave bears but also smaller taxa (e.g., Canis lupus, Vulpes vulpes). This can be correlated with their exploitation for pendants, and potentially for skins and furs. At a broader scale, we identified similarities in subsistence behavior across IUP sites in Europe and western Asia. It appears that the first IUP occupations were less intense with find densities and human modifications increasing in succeeding IUP layers. Moreover, the exploitation of small game appears to be limited across IUP sites, while carnivore exploitation seems a recurrent strategy.