Empirical Applications of Environmental DNA (eDNA) in Fish Systematics and Fisheries Resource Management

Environmental DNA (eDNA) has rapidly matured from an emerging molecular tool into a mainstream method for aquatic biodiversity assessment, transforming how we study, monitor, and manage fish populations across freshwater and marine ecosystems. By sequencing the genetic material that organisms shed into water — through mucous, scales, faeces, and gametes — eDNA offers a non-invasive, sensitive, and cost-effective alternative to conventional survey methods. In principle, it allows scientists to detect species presence, estimate biodiversity, and even infer relative abundance without deploying a single capture method, resolving questions in fish systematics, biodiversity monitoring, and fisheries resource management that were previously difficult or impossible to answer at scale.

However, the empirical record remains considerably more complex than this promise suggests. eDNA detection is highly sensitive to water flow, temperature, degradation rates, and sampling design, and presence/absence calls can vary substantially between protocols even within the same water body. Translating a DNA signal into a defensible abundance estimate — the metric fisheries managers require for quota-setting and stock assessment — remains an open methodological question, with correlation-to-biomass relationships frequently found to be site-specific and incompletely resolved. In systematics, eDNA's dependence on reference databases means its taxonomic resolution is bounded by the sequences already catalogued: cryptic species, hybrids, and poorly sequenced regional taxa can be missed or misassigned as a result. A further challenge lies in methodological fragmentation — a technique valued for reducing invasive sampling has, in practice, generated considerable variation in its own primer selection, extraction protocols, and bioinformatic pipelines, which can limit cross-study comparability as the field matures.

The result, to date, is a body of literature rich in proof-of-concept but comparatively thin on standardised, management-ready applications. Closing that gap is the central motivation for this collection. Questions of detection sensitivity, quantification accuracy, reference database completeness, and integration with conventional fisheries science are precisely what determine whether eDNA can be trusted as a decision-making tool rather than a purely exploratory one. We are particularly interested in work that moves the field from demonstration toward validated, reproducible, and policy-relevant practice.

This Research Topic invites empirical studies that advance the application of eDNA across fish systematics and fisheries resource management, including but not limited to:
- eDNA metabarcoding for aquatic biodiversity assessment and ecosystem monitoring
- Fish systematics, taxonomy, phylogeography, and conservation genomics using eDNA
- Detection and monitoring of cryptic, rare, endangered, invasive, and commercially important species
- eDNA-based estimation of fish biomass, abundance, stock structure, and fisheries resources
- Fish migration, habitat connectivity, and population dynamics
- Impacts of pollution, habitat degradation, invasive species, and climate change on aquatic ecosystems
- Advances in eDNA methodology — sampling, extraction, sequencing, bioinformatics, reference libraries, and data standardization
- Temporal and spatial dynamics of fish communities
- Long-term biodiversity monitoring, restoration ecology, and ecosystem health assessment
- Integration of eDNA with conventional surveys, remote sensing, ecological modelling, AI, and machine learning
- Applications in ecosystem-based fisheries management, conservation planning, and policy development

We welcome manuscripts that discuss eDNA's role in evidence-based fisheries science and conservation policy.