Determining how cetaceans and other threatened marine animals use coastal habitats is critical to the effective conservation of these species. Environmental DNA (eDNA) is an emerging tool that can potentially be used to detect cetaceans over broad spatial and temporal scales. In particular, eDNA may present a useful complementary method for monitoring their presence during visual surveys in nearshore areas, and for co-detecting prey. In conjunction with ongoing visual surveys, we tested the ability of eDNA metabarcoding to detect the presence and identity of cetaceans in the New York Bight (NYB), and to identify fish species (potential prey) present in the area. In almost all cases in which humpback whales and dolphins were visually observed, DNA from these species was also detected in water samples. To assess eDNA degradation over time, we took samples in the same location 15 and 30 min after a sighting in seven instances, and found that eDNA often, but not always, dropped to low levels after 30 min. Atlantic menhaden were detected in all samples and comprised the majority of fish sequences in most samples, in agreement with observations of large aggregations of this important prey species in the NYB. While additional data are needed to better understand how factors such as behavior and oceanographic conditions contribute to the longevity of eDNA signals, these results add to a growing body of work indicating that eDNA is a promising tool to complement visual and acoustic surveys of marine megafauna.

The American Eel Anguilla rostrata has experienced a marked population decline due to a multitude of threats, including pollution, overfishing, and damming. Government agencies responsible for American Eel management have identified gaps in survey coverage and understanding of habitat needs as critical obstacles to recovery. However, efforts to expand American Eel monitoring are hindered by this species’ resistance to capture, the wide variety of habitats in which they occur, and their extensive natural range, which would be cost prohibitive to survey using established techniques. Surveys based on analysis of environmental DNA (eDNA) may offer an affordable and efficient means of closing these gaps. While eDNA methods are increasingly used as a rapid, minimally invasive means of detecting species presence, attempts to use them to produce quantitative estimates of abundance have yielded mixed results. In order to evaluate the viability of eDNA as a quantitative American Eel monitoring tool, we compared the concentration of American Eel DNA in water samples to estimates of numerical and biomass density measured by electrofishing in the Bronx River, New York. Our results revealed a strong, positive association between DNA concentration and numerical density but no relationship with biomass density. Mass‐specific eDNA production rates were found to decline with mean American Eel weight. While further study will be required to determine whether the observed relationship between DNA concentration and numerical abundance is consistent across sites and whether it can be generalized to other systems, our findings suggest that eDNA will likely be a feasible and cost‐effective option for surveying American Eel abundance throughout their range.

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