Development of an eDNA‐based survey method for urban fish markets

Abstract

1. Fish and fishery products are among the most highly traded commodities in the world, and over-exploitation continues to threaten the biodiversity and sustain-ability of global stocks. The state of knowledge for many fish species is limited by current monitoring techniques, which rely on labour-intensive visual or ge-netic surveys of individual specimens (often at inconsistent or coarse taxonomic resolution).2. To address the need for more efficient methods that effectively monitor trade, we developed a novel application of eDNA-based metabarcoding that can iden-tify a broad range of fish taxa from effluent water draining from urban fish markets. Using samples collected at three Hong Kong fish markets over a 5- day period, we tested two DNA capture protocols (filtration vs. precipitation) with the goal of ensuring that methods were relatively easy to implement with-out sacrificing species coverage relative to each other and to a standard visual sur vey.3. eDNA- based survey methods were able to overcome many of the challenges associated with visual identification, such as resolving morphologically simi-lar species and accounting for butchered fish products. However, rare and/or quickly transiting species occasionally went undetected. The two variations of eDNA isolation methods performed almost identically, emphasizing the relative robustness of eDNA metabarcoding, and allowing for user flexibility depending on the turbidity of collected waters. Our results demonstrate the ability of a few spatial and temporal replicates to generate an efficient and accurate market- wide species inventory that can complement visual inspections and guide tar-geted investigations of illegal trade.4. This research provides important baseline information on the capabilities of eDNA metabarcoding as a non-invasive survey tool, with the potential to complement conventional surveys. To our knowledge, this study is the first proof of concept using eDNA metabarcoding to monitor wildlife trade and also highlights the poten-tial for eDNA metabarcoding to be applied to investigations of urban ecology.