Environmental DNA (eDNA) for monitoring marine mammals: Challenges and opportunities

Abstract

Monitoring marine mammal populations is essential to permit assessment of population status as required by both national and international legislation. Traditional monitoring methods often rely on visual and/or acoustic detections from vessels and aircraft, but limitations including cost, errors in the detection of some species and dependence on taxonomic expertise, as well as good weather and visibility conditions often limit the temporal and spatial scale of effective, long-term monitoring programs. In recent years, environmental DNA (eDNA) has emerged as a revolutionary tool for cost-effective, sensitive, non-invasive species monitoring in both terrestrial and aquatic realms. eDNA is a rapidly developing field and a growing number of studies have successfully implemented this approach for the detection and identification of marine mammals. Here, we review 21 studies published between 2012 and 2021 that employed eDNA for marine mammal monitoring including single species detection, biodiversity assessment and genetic characterization. eDNA has successfully been used to infer species presence (especially useful for rare, elusive or threatened species) and to characterize the population genetic structure, although additional research is needed to support the interpretation of non-detections. Finally, we discuss the challenges and the opportunities that eDNA could bring to marine mammal monitoring as a complementary tool to support visual and acoustic methods.

Seas the DNA? Limited detection of cetaceans by low‐volume environmental DNA transect surveys

“…Additional factors which could have influenced the lack of detection in our study includes shedding rates of target species, depth of sample collection, and influence of environmental factors such as current direction and strength (Baker et al, 2018;Foote et al, 2012;Govindarajan et al, 2022;Mächler et al, 2016;Mathieu et al, 2020;Pinfield et al, 2019;Schabacker et al, 2020;Sepulveda et al, 2019;Suarez-Bregua et al, 2022). Based on a combination of physiological (i.e., body size) and behavioral (i.e., breaching, feeding, socializing, or diving) factors, it is expected that different cetacean species shed DNA into their environment at different rates (Alter et al, 2022;Barnes et al, 2014;Parsons et al, 2018).…”

“…More recently, there has been an increased uptake of utilizing eDNA as a tool for detecting and monitoring marine biodiversity (Dalongeville et al., 2022; Gilbey et al., 2021; Kopp et al., 2023; Miya, 2022). Despite this, there remains limited application of eDNA for marine mammal monitoring (Suarez‐Bregua et al., 2022). Though scarce, previous cetacean (whales, dolphins, and porpoise) studies have primarily focused on detecting single species through either targeted ‘flukeprint’ sampling (Alter et al., 2022; Baker et al., 2018; Parsons et al., 2018; Robinson et al., unpublished data; Székely et al., 2021), or indirect sampling via transects (or similar; Juhel et al., 2021; Ma et al., 2016; Székely et al., 2021; Zhang et al., 2023).…”

“…Similar to the scarcity of cetacean-based studies, reported detection rates of cetacean eDNA in situ are equally as limited (Suarez-Bregua et al, 2022). A combination of volume sampled, environmental conditions at the time of DNA deposition and collection, technology and approaches used for DNA detection (i.e., quantitative PCR (qPCR) vs. droplet digital PCR), and proximity to target species are factors that determine both DNA degradation rates and/ or likelihood of detecting target species (Barnes et al, 2014;Cao et al, 2012;Padilla et al, 2015;Pinfield et al, 2019;Schabacker et al, 2020;Sepulveda et al, 2019;Strickler et al, 2015;Suarez-Bregua et al, 2022;Xiong et al, 2016). Lack of knowledge surrounding the role of environmental factors on the temporal and spatial persistence of cetacean eDNA has been identified as a major limitation for the application of eDNA for cetacean monitoring (Suarez-Bregua et al, 2022).…”

“…Suarez-Bregua et al (2022), more research on the fate of eDNA in the dynamic marine environment is required, which can then be combined with species-specific approaches to improve confidence in eDNA outcomes and ultimately move eDNA tools into the next era of biodiversity monitoring.AUTH O R CO NTR I B UTI O N SCR and KD conceived the study, KD and AM collected samples with support from volunteers and other Ocean Wise staff, CVR and AM completed primer design, CVR and RG conducted eDNA analysis, CVR wrote the manuscript with support from all co-authors.ACK N OWLED G M ENTSWe wish to acknowledge that this research took place on the traditional territory of the Nine Allied Tribes of Metlakatla and Lax Kw'alaams who have been stewards of these lands and waters since time immemorial. This project was supported partially by a financial contribution from Fisheries and Oceans Canada/Ce projet fut partiellement appuyé par une contribution financière de Pêches et océans Canada.…”

Environmental DNA reveals spatial patterns of fish and plankton diversity at a floating offshore wind farm

“…As a non‐target species for the MiFish primers, presumably the actual abundance of harbor porpoise in the area could be higher than indicated in the MiFish data. Species‐specific primers for harbor porpoise are available (Foote et al, 2012), and a design that included such primers could provide additional environmental monitoring utility of eDNA studies of environmental impact at OWF sites with modest additional effort (Suarez‐Bregua et al, 2022).…”