Assessment of Endogenous DNA in Dog Petrosal Bones
All ancient DNA (aDNA) studies are limited by the degraded and fragmented nature of aDNA, and the low endogenous DNA content of the majority of archaeological samples. In recent years, the targeted sampling of specific skeletal elements in humans – particularly the petrous portion of the temporal bone (pars petrosa) – has been utilised to mitigate some of these issues. In contrast, the potential of similar approaches in the sampling of faunal populations is yet to be fully explored. Here, to empirically characterise the utility of petrous for aDNA analysis relative to other skeletal elements in non-human species, we present the first comparative aDNA study utilising paired dog (Canis lupus familiaris) skeletal elements (petrous vs. bone/tooth) (n=56). This allowed for the exploration of aDNA preservation across skeletal elements, considering both endogenous and exogenous fractions. Our results suggest that endogenous DNA yields from petrous may be up to 200x higher than other skeletal elements from the same individual. However, petrous appear to have lower microbial species richness when compared to other skeletal elements, including pathogens. We leverage the findings of our research to identify the most suitable substrate(s) for the genetic analysis of archaeological dog specimens and other mammalian fauna.
All ancient DNA (aDNA) studies are limited by the degraded and fragmented nature of aDNA, and the low endogenous DNA content of the majority of archaeological samples. In recent years, the targeted sampling of specific skeletal elements in humans – particularly the petrous portion of the temporal bone (pars petrosa) – has been utilised to mitigate some of these issues. In contrast, the potential of similar approaches in the sampling of faunal populations is yet to be fully explored. Here, to empirically characterise the utility of petrous for aDNA analysis relative to other skeletal elements in non-human species, we present the first comparative aDNA study utilising paired dog (Canis lupus familiaris) skeletal elements (petrous vs. bone/tooth) (n=56). This allowed for the exploration of aDNA preservation across skeletal elements, considering both endogenous and exogenous fractions. Our results suggest that endogenous DNA yields from petrous may be up to 200x higher than other skeletal elements from the same individual. However, petrous appear to have lower microbial species richness when compared to other skeletal elements, including pathogens. We leverage the findings of our research to identify the most suitable substrate(s) for the genetic analysis of archaeological dog specimens and other mammalian fauna.
Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich