Metabarcoding detection frequency tracks ddPCR copy number for ancient fish eDNA in marine sediments

Environmental DNA (eDNA) analysis — detecting genetic material shed by organisms into their surroundings — has become an important tool in ecology, conservation genomics, and the study of past biodiversity. Sedimentary ancient DNA (sedaDNA) extends this approach into deep time, but the highly degraded, low-concentration nature of ancient material makes reliable detection and quantification challenging, particularly when target taxa are numerically rare relative to background DNA.

A preprint posted to bioRxiv investigates whether replicate detection frequency in high-throughput metabarcoding assays — a compositional approach that surveys community-level diversity — can serve as a proxy for absolute eDNA abundance as measured by droplet digital PCR (ddPCR). Using cod and herring eDNA extracted from ancient marine sediments, the authors report a correlation between the two metrics, suggesting that metabarcoding, while inherently compositional, can yield semi-quantitative signal when replicate structure is analysed appropriately.

The findings are relevant to researchers using sedaDNA to reconstruct historical fish population dynamics, assess the impact of past environmental change on marine communities, and inform conservation baselines. The work is not directly relevant to human genetics but has methodological implications for any eDNA or ancient DNA application where low-abundance targets must be distinguished from noise. As a preprint, the findings have not yet been peer-reviewed.