Combined methodologies for gaining much information from ancient dental calculus: testing experimental strategies for simultaneously analysing DNA and food residues

Abstract

Dental calculus from archaeological samples is a rich source of ancient biomolecules, such as DNA, proteins, and microremains, mainly related to food. Focusing on different contents, laboratory procedures require specific treatments that necessitate the same material and are generally mutually exclusive; therefore, the low quantity of the starting material is often the main limiting factor for gathering data. Here, we compare different combinations of laboratory procedures in order to identify the best strategy for simultaneously extracting DNA and isolating plant residue. Preliminary tests were performed on fresh plant materials to verify the effects of the DNA extraction protocols on starch grains and phytoliths. Different combined experimental procedures were successively applied to the dental calculus of three medieval individuals. Our results confirmed that authentic genetic data could be recovered from ancient dental calculus using protocols commonly used for extracting DNA from ancient bones and teeth, and the residual pellet could be successfully used for morphological characterization of plant residues. In addition, we confirmed that, although most DNA within calculus is microbial, the whole human mitochondrial genome could be reconstructed using target enrichment techniques.