Epi-eDNA: From Methylation Signal Detection to Functional Ecological Monitoring

Chengbin Liu, Fei Xia, Itsuki T. Hirayama, Genfu Yagi, Masayuki Ushio

Environmental DNA (eDNA) technology has revolutionized biomonitoring, primarily capturing the presence/absence of target taxa. Recent advances have revealed that eDNA also retains epigenetic signatures (epi-eDNA), particularly DNA methylation, which enable functional ecological insights. This review synthesizes three pivotal milestones: (1) Initial detection of methylation signals in eDNA, confirming the feasibility of the epi-eDNA concept, (2) verification of stability across environmental matrices, demonstrating fidelity to source-tissue profiles despite degradation, and (3) emerging applications as ecological indicators—using epigenetic clocks for age-structure assessment, sex-specific markers for population sex ratios, germ cells methylation for spawning detection, and stress-linked methylation for health monitoring. This review highlights the potential of epi-eDNA in non-invasive population-level trait inference, overcoming the limitations of traditional eDNA. Future integration with multi-omics and sequencing innovations will unlock unprecedented precision in conservation and ecosystem management.