Efficacy of whole human genome capture and high-throughput sequencing on ancient dental calculus and dentine.

Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for mitogenome reconstruction using targeted enrichment. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome in-solution targeted enrichment and high-throughput sequencing. Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the human DNA content of calculus and dentin was not significantly different when normalized for sample input. Whole genome capture resulted in modest enrichments of the human endogenous DNA content of up to 4.4-fold for calculus and 3.8-fold for dentin, albeit with some loss in complexity. Recovering more data for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. Comparison of microbial phylum-level community structure revealed no major differences between pre- and post-capture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. The low relative proportion of human DNA in calculus poses challenges for population genetics analyses. Whole genome enrichment can help increase the proportion of recovered human reads while still allowing for oral microbiome reconstruction, but further optimization is necessary.