Towards an archaeological workflow for sedaDNA sample collection: methods and best practices for minimizing surface contamination

Abstract

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 heavily depends on proper sampling and handling practices. Contamination remains a significant challenge in ancient DNA research, profoundly impacting data integrity and interpretation. Consequently, numerous studies have underscored the importance of minimizing contamination levels. Nonetheless, a challenge arises in implementing this in daily archaeological practice, as a specialized DNA expert is not always available. This study suggests two customised workflows of commonly used sedaDNA sampling techniques, redesigned for archaeologists without sedaDNA expertise. We test their effectiveness in the field. To benchmark these protocols, we applied artificial DNA contaminants onto sediment surfaces before sampling. Subsequently, we evaluate archaeologists effectiveness in reducing surface contamination by quantifying the level of artificial DNA detected. Finally, we compare results between samples taken by archaeologists with and without sedaDNA expertise. Our results demonstrate that existing sampling protocols, when slightly adapted to the needs of archaeologists, significantly minimize surface contamination to the point that they provide high-quality extraction. Additionally, our findings suggest that subsampling sediments with minimal surface contamination from previously collected materials is viable, emphasizing the potential of archived sediment collections for sedaDNA analysis.