The potential of methylation signal detection in eDNA toward functional ecological monitoring

Environmental DNA technology has revolutionized biomonitoring, primarily capturing the presence/absence of target taxa. Recent advances have revealed that eDNA also retains epigenetic signatures. In this perspective, we focus on DNA methylation signals in eDNA, which we define as meth-eDNA, and analyze three pivotal topics: (1) Detection of methylation signals in eDNA, (2) stability in aquatic environment, and (3) applications as ecological indicators. This perspective highlights the potential of meth-eDNA in non-invasive population-level trait inference. Future integration with multi-omics and sequencing innovations will achieve more precision in ecosystem conservation and management.