The Pragmatic Sceptic: A Practical Approach for Integrating Environmental DNA Into Marine Stock Assessment and Fisheries Management Fish and Fisheries

The ‘omics revolution’ has advanced scientific understanding of marine ecosystems and led to a rapid increase in data that can inform species' population structure, distribution, and abundance. Of the 'omics data types, environmental DNA (eDNA) may present the most cost‐effective opportunity for developing quantitative estimates of abundance trends, a key input for stock assessment models. However, eDNA has yet to be widely adopted for stock status determinations within regional fisheries management organisations. We review progress towards addressing key challenges that limited the application of eDNA in marine fisheries management, including advances in (1) the quantitative relationship between eDNA observations and species biomass, (2) reducing false‐negative and false‐positive detections, (3) defining the spatial scale of eDNA, (4) collecting biological data from eDNA surveys, (5) quantifying uncertainty in eDNA surveys, and (6) responding to scepticism of new survey methods. We use a case study with Pacific hake (<styled-content style="fixed-case">Merluccius productus</styled-content>) to demonstrate the development of an eDNA index and its direct integration into an age‐structured stock assessment model. Given the many ways in which the field of eDNA has matured, we propose that eDNA can meaningfully inform a range of fisheries management needs, and outline a roadmap for using eDNA in stock assessment models in data‐limited to data‐rich species. A primary impediment to operationalising eDNA as stock assessment model inputs is the lack of interdisciplinary research teams, including geneticists, ecological modellers, and stock assessment scientists, which are necessary to interpret methods and results across scientific disciplines and ensure data are used appropriately.