Fourier-transform infrared (FTIR) spectroscopy on archaeological sediments as a tool for selecting samples for ancient DNA

Abstract

The retrieval of ancient DNA (aDNA) from archaeological sediments represents a promising alternative approach to sampling frequently scarce skeletal remains for palaeogenetic investigations (e.g., Slon et al 2017; Gelabert et al., 2021; Vernot et al., 2021). Yet, the source of the DNA fragments within substrates, and the factors that lead to their long-term preservation, remain poorly understood. As a result, the current practice of sample selection in the field tends to be mostly haphazard, leading to a wide variability in the success of aDNA recovery from archaeological sediments. We set out to develop an innovative strategy to field sampling of sediments, aimed to improve the speed and efficiency of screening samples for aDNA analysis, while concurrently ensuring affordability and an easy interpretation of the results. Employing a semi-portable Fourier-transform infrared (FTIR) spectroscopic instrument, we conducted a comprehensive characterization of archaeological sediments. This facilitated the examination of bioapatite spectral features, that we used as a proxy for bone particles, from which we could test predictions regarding the presence or absence of aDNA fragments. The efficacy of this methodology was validated using sediment samples from different archaeological sites within the southern Levant, characterized by distinct contextual attributes (e.g., environmental conditions, type of site, age, etc.) and varying degrees of aDNA preservation. Preliminary results suggest that our approach could facilitate the selection of samples more likely to preserve aDNA in fieldwork settings, while hinting at the possible source of these aDNA fragments in the sediments. Acknowledgements: This study is funded by the John Templeton Foundation (grant #62571 to V.S.) Bibliography Gelabert, et al. 2021, Current biology: vol. 31,16:3564-3574.e9. doi:10.1016/j.cub.2021.06.023 Vernot, B. et al. 2021, Science vol. 372,6542:eabf1667. doi:10.1126/science.abf1667 Slon, V. et al., (2017), Science 356(6338): 605-608