Abstract
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.
Highlights
Effective conservation and management of cetaceans and other wide-ranging marine species depends on knowledge of when, where and how species use habitats, which can be challenging to assess across large temporal and spatial scales (e.g., Sequeira et al, 2019)
Though the precise spatial scale over which Environmental DNA (eDNA) signals are integrated in marine environments remains uncertain, most studies suggest that eDNA degrades quickly in seawater and is a reasonable indicator of recent presence (Thomsen et al, 2012; Port et al, 2016; Collins et al, 2018; Murakami et al, 2019). eDNA analyses have been applied to a variety of marine megafauna (Lafferty et al, 2018; Harper et al, 2020) including cetaceans such as harbor porpoise (Phocoena phocoena) (Foote et al, 2012; Parsons et al, 2018), killer whales (Orcinus orca) (Baker et al, 2018; Pinfield et al, 2019), and bowhead whales (Székely et al, 2021)
The results presented here indicate that eDNA has good potential as a complementary tool for cetacean surveys, especially for detecting large whales and assessing prey or co-distributed species of interest
Summary
Effective conservation and management of cetaceans and other wide-ranging marine species depends on knowledge of when, where and how species use habitats, which can be challenging to assess across large temporal and spatial scales (e.g., Sequeira et al, 2019). Standard methods for assessing cetacean distribution and movement include boat-based surveys, aerial surveys, satellite-tracked tags, and passive acoustic monitoring (PAM) (e.g., Van Parijs et al, 2009; Clark et al, 2010; Kaschner et al, 2012; Kanaji et al, 2017; Fiedler et al, 2018; Frasier et al, 2021; King et al, 2021) Combining these methods with novel techniques that permit detection of Cetacean eDNA in NY Bight non-vocalizing, non-visible individuals may offer the most effective means of surveying large areas for these highly mobile species. If eDNA can be optimized to detect baleen whales and odontocetes successfully, this approach could potentially be combined with other survey methods to better inform area-based management, detect prey and other species interactions, and to identify specific individuals
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