Geochemical ENhancEment of Ancient DNA from SedImentS

Ancient DNA (aDNA) provides an archive of human evolution of unprecedented fidelity. The field has unveiled the intricate web of interactions among ancient human populations, revealing interbreeding events with Neanderthals and Denisovans that have shaped the genetic landscape of modern humans. This revelation recalibrates our understanding of human evolution and illuminates migration patterns across ancient landscapes. Recent advances in sample preparation and DNA retrieval have enabled the recovery and analysis of ancient human and faunal DNA directly from sediments. Sediment aDNA (sedaDNA) holds enormous potential to significantly expand our ability to detect ancient humans and animals across a broader range of archaeological sites, breaking free from the constraints imposed by the scarcity of well-preserved and valuable bone fragments for aDNA recovery. Ancient DNA-specific wet lab protocols have improved the quantity of DNA isolated and extracted. However, these methods were developed for boneeeth, and not sedaDNA. The project aims to address and overcome these challenges. Our interdisciplinary team will harness our previous successful methodological development for improving DNA yield from bones to sediments in a novel approach that also aims to determine the inhibition patterns of sediments from various locations and identify the sources of aDNA in these sediments. The approach would also increase aDNA yields from samples that previously did not pass quality and quantity thresholds, improving success rates and greatly expanding the potential pool of sediments from which aDNA can be recovered. A key innovation is the development of bespoke density separation techniques designed to enhance aDNA yields by overcoming challenges posed by traditional extraction methods. More specifically, we will assess the degree of inhibition caused by various substances in sediment samples and quantify the amount of modern DNA contamination. We will optimise the disaggregation of sediment particles to improve density separation efficiency and better separate aDNA sources from inhibitory substances. We will also identify the sources of aDNA and modern DNA contamination within the sediment by analysing the geochemical host phases and identifying biomarkers, and then test different extraction conditions based on the geochemical host phases of the different density fractions to improve aDNA recovery. Focusing on the complex relationships between aDNA and its mineralogical hosts, we aim to unlock new dimensions of paleogenomic research, addressing gaps left by conventional methodologies. Techniques informed by our geochemical and aDNA analyses (MINERVA project) could significantly improve aDNA recovery efficiency, serving as a model for future archaeological and paleogenomic studies.