The efficacy of whole human genome capture on ancient dental calculus and dentin

ObjectivesDental calculusis among the richest known sources of ancient DNAin the archaeological record. Although most DNA within calculusis microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculusis also a viable substrate for whole human genomerecovery using targeted enrichment techniques. Materials and methodsTotal DNA extracted from 24 paired archaeological human dentin and calculussamples was subjected to whole human genomeenrichment using in‐solution hybridization capture and high‐throughput sequencing. ResultsTotal DNA from calculusexceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculusand dentin was not significantly different. Whole genome enrichment resulted in up to four‐fold enrichment of the human endogenous DNA content for both dentin and dental calculuslibraries, albeit with some loss in complexity. Recovering more on‐target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum‐level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off‐target sequences in human genome‐enriched calculuslibraries may still be useful for oral microbiome reconstruction. DiscussionWhile ancient human dental calculusdoes contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.