Ancient Dental Calculus as a Reservoir of Whole Human Mitogenomes

Until recently, one challenge of ancient DNA research has been the necessary destruction of skeletal material in order to extract human genetic information. Calcified dental plaque (dental calculus) can be removed from dentition without damaging the underlying teeth or surrounding bone and it has been shown to be an excellent reservoir of microbial and dietary biomolecules and microfossils. Here, we examine the preservation of human mitochondrial DNA in dental calculus by performing high-throughput mitogenome sequencing of material from six individuals from Norris Farms #36, a Mississippian period Oneota cemetery in Illinois dating back to 700BP. DNA was extracted in a dedicated ancient DNA facility at the University of Oklahoma and built into shotgun libraries. Following library amplification, each sample underwent a mitochondrial DNA capture and enrichment protocol at Arizona State University and was sequenced on an Illumina MiSeq platform. Medium coverage (7-34x) whole mitogenomes were successfully recovered from all six samples from Norris Farms #36 including three which were previously unsuccessful for HVRI sequencing using traditional PCR-based methods. In one calculus sample, the proportion of endogenous mtDNA increased from \u3c0.0001% in unenriched shotgun to 0.34% using mitochondrial capture and enrichment. This research demonstrates that calculus, an abundant and ubiquitous archaeological substrate, contains sufficient host information for whole mitogenome reconstruction. These findings have important implications for the use of dental calculus as an alternative material in archaeological studies of maternal ancestry