From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era

Abstract

High-Throughput DNA Sequencing (HTS) technologies have changed the way in which we detect and assess DNA contamination in ancient DNA studies. Researchers use computational methods to mine the large quantity of sequencing data to detect characteristic patterns of DNA damage, and to evaluate the authenticity of the results. We argue that unless computational methods can confidently separate authentic ancient DNA sequences from contaminating DNA that displays damage patterns under independent decay processes, prevention and control of DNA contamination should remain a central and critical aspect of ancient human DNA studies. Ideally, DNA contamination can be prevented early on by following minimal guidelines during excavation, sample collection and/or subsequent handling. Contaminating DNA should also be monitored or minimised in the ancient DNA laboratory using specialised facilities and strict experimental procedures. In this paper, we update recommendations to control for DNA contamination from the field to the laboratory, in an attempt to facilitate communication between field archaeologists, anthropologists and ancient DNA researchers. We also provide updated criteria of ancient DNA authenticity for HTS-based studies. We are confident that the procedures outlined here will increase the retrieval of higher proportions of authentic genetic information from valuable archaeological human remains in the future.