In situ microRaman spectroscopy as a screening tool for assessing human DNA preservation in ancient dental remains

Ancient DNA (aDNA) and protein analysis of human remains enables reconstructions of population history, kinship, diet, health and social structure of ancient communities. Ancient DNA yields important genetic information, nonetheless its extraction requires sampling, which is an important concern especially for rare and valuable samples. Furthermore, poor preservation of aDNA results to low endogenous DNA yield, and considering that analyses are costly and time-consuming, efficient pre-screening methods are needed to identify samples with higher probability of aDNA survival. Here, we present an in situ, non-invasive micro-Raman spectroscopy approach as a screening tool capable of predicting DNA preservation in ancient teeth. Because aDNA tends to persist in teeth preserving part of their proteinaceous (primarily collagen) component, the relative abundance of protein to mineral provides an indirect indication for DNA preservation. A set of 49 ancient teeth, dated from 8800 BCE to 1941 CE, were analyzed using for sample classification the amide-to-phosphate AmI/P index, defined as the intensity ratio of the amide I band (1666 cm − 1 ) over the phosphate band (PO₄ 3− , 957 cm − 1 ). Measurements on the cementum area of the teeth, known to be protein-rich, revealed a weak but clear correlation between AmI/P and endogenous DNA amounts, independently determined via standard aDNA analysis. Among 25 aDNA-rich teeth, 23 were correctly identified (92% acceptance), and 13 of 20 aDNA-poor teeth were indicated to be so (65% rejection). Overall, Raman spectroscopy provides a valid, in situ, non-invasive pre-screening strategy for prioritizing ancient teeth with higher collagen content and greater likelihood of yielding endogenous human DNA. • Raman spectroscopy provides a fully non-invasive, in-situ method to pre-screen ancient teeth for DNA preservation. • The amide-to-phosphate Raman index Am/P reflects the proteinaceous content relative to the hydroxyapatite matrix. • The approach correctly identified 92% of aDNA-rich and 65% of aDNA-poor samples. • Raman spectroscopy can guide sample selection, reducing destruction of archaeological remains and prioritize samples with greater likelihood of yielding endogenous human DNA