Towards an Archaeological Workflow for SedaDNA Sample Collection: Methods and Best Practices for Minimising Surface Contamination

Abstract

Sedimentary ancient DNA (sedaDNA) has been successfully recovered from diverse contexts, enabling researchers to address paleoenvironmental questions such as ecosystem changes and climatic shifts, along with archaeological questions related to past human activities, diet, health, and interactions with their environment. Despite its potential, the reliability of sedaDNA data depends on proper sampling and handling practices. Contamination remains a significant challenge in ancient DNA research. Nonetheless, a challenge arises in implementing this in practice, as a specialised DNA expert is not always available in a timely manner to perform sampling procedures. This study presents tailored workflows for two widely used sedaDNA sampling methods by archaeologists without sedaDNA expertise. To benchmark these protocols, we introduced controlled, artificial DNA contaminants onto sediment surfaces prior to sampling. Then, we evaluate their effectiveness in reducing surface contamination by quantifying the level of artificial DNA detected. Subsequently, we compare results between samples taken by archaeologists with and without sedaDNA expertise. Our results demonstrate that existing sampling protocols, when slightly adapted, significantly minimise surface contamination while also being executable by ordinary archaeologists with no sampling experience. Additionally, our findings suggest that subsampling sediments with minimal surface contamination from previously collected materials is viable, emphasising the potential of archived sediment collections for sedaDNA analysis.