Comparison of aDNA Yields from Calculus and Tooth Roots in Pre-Columbian Skeletal Remains

Abstract

In recent years, dental calculus has emerged as an important source of ancient genetic material. However, calculus has not been extensively utilized as a source of endogenous host DNA when working with human skeletal remains. In this study we compare endogenous DNA yields obtained from extractions performed from both dental calculus and dental tooth roots for three pre-Columbian individuals, originating from three different archaeological sites of the island of Puerto Rico. Furthermore, in order to assess the effects of physical decontamination procedures on recovery of endogenous DNA, tooth root samples were further subdivided into two groups: one group was treated by removal of the cementum and the second group was left untreated. Extractions were then performed in three replicates for each individual, one from calculus, one from treated tooth roots and one from untreated tooth roots. DNA extracts were quantified, transformed into sequencing libraries, and enriched for the complete mitochondrial genome through in-solution hybridization capture. Preliminary results indicate that out of nine extracts obtained (three replicates for each individual) only seven were successfully built into libraries. Sequence data suggest that libraries made from treated tooth root extracts contain, on average, more sequence reads mapping to the reference and higher coverage than libraries built from untreated tooth root or calculus extracts. These results suggest that although calculus is a viable source of endogenous DNA, treated tooth root extractions result in higher overall endogenous DNA yields and a reduced presence of contaminant DNA molecules in these samples