Differential sampling for genetic analyses of Treponema pallidum and for radiocarbon dating in archaeological bone

Molecular recovery of T. pallidum DNA in dry bone poses methodological challenges. Here we evaluate recovery success from a molecularly confirmed co-infection with yaws (T. pallidum pertenue) and plague (Y. pestis).

Pulverised bone from three pathological anatomical elements from individual AGU007 excavated from Aguonų street, Vilnius, Lithuania was used for DNA analysis. Three additional anatomical elements from individual AGU007 were used to obtain radiocarbon dates.

High-throughput sequencing of bulk DNA content followed by computational analysis. DNA sequencing and genomic analysis following molecular enrichment for T. pallidum. Radiocarbon dating combined with computational molecular dating.

T. pallidum and Y. pestis DNA were identified in a cranial fragment from individual AGU007. Radiocarbon dates from this individual combined with another narrowed the temporal range to the latter part of the 15th century at the 2-sigma level.

Detection of T. pallidum DNA in multiple skeletal elements from an individual confirmed to have an active yaws infection at time of death gave further insight into preferred sampling locations for molecular detection of treponemal infections. While the highest molecular recovery came from teeth, the parietal bone provided adequate recovery.

This research indicates that sampling for molecular analysis of T. pallidum infections should include (if available) one tooth and one lesion indicative of active infection at the time of death. Accommodating radiocarbon date probability distributions and Bayesian inference has the potential to increase molecular dating precision.

T. pallidum DNA preservation is not predictable across the skeleton.

We encourage ethical and minimalist sampling strategies for further research.