Sedimentary ancient DNA expands bioarchaeological evidence and interpretation at Roman Harelbeke

Sedimentary ancient DNA (sedaDNA) can expand archaeological research by recovering broad biological signals from small amounts of sediment. Here, we apply shotgun sedaDNA metagenomics and target capture (also known as hybridization capture) to disused Roman wells from the vicus of Harelbeke, Belgium, dated to ca. 160-300 CE, and integrate the results with existing bioarchaeological datasets. Moving beyond individual introduced taxa as proxies for Roman influence, we reconstruct community-level profiles spanning consumption-related, synanthropic, and environmental organisms. SedaDNA reproduced most established bioarchaeological signals, including cultivated plants and domestic animals, while also recovering additional environmental taxa that established methods underrepresented. Mitochondrial target capture strengthened selected faunal detections and enabled phylogenetic placement of a pig (Sus scrofa) within the European mitochondrial lineage. The predominance of previously established consumption-related taxa is consistent with subsistence continuity and selective adoption of Roman-introduced resources, although taxon counts alone cannot establish their relative importance. Analytical-effort modeling further indicates that batch-based sedaDNA workflows can provide broad biological profiles at lower cost and time investment than established archaeological methods. Overall, sedaDNA complements conventional bioarchaeology by broadening taxonomic recovery, supporting scalable sampling, and providing a broad-spectrum approach to reconstructing settlement ecology, subsistence, and human-environment interaction.