Environmental DNA captures elasmobranch diversity in a temperate marine ecosystem

Abstract

Many sharks, skates, and rays (elasmobranchs) are highly threatened by the activities of commercial fisheries, and a clear understanding of their distributions, diversity, and abundance can guide protective measures. However, surveying and monitoring elasmobranch species can be highly invasive or resource-intensive, and utilization of non-invasive environmental DNA-based methods may overcome these problems.Here, we studied spatial and seasonal variation in the elasmobranch community of the Western English Channel using environmental DNA (eDNA) collected from surface and bottom waters periodically over an annual cycle (2017)(2018). In total we recovered 13 elasmobranch species within eDNA samples, and the number of transformed eDNA reads was positively associated with species (hourly) catch data resolved from 105-year time series trawl data . These results demonstrate the ability of eDNA to detect and semi-quantitatively reflect the prevalence of historically dominant and rare elasmobranch species in this region. Notably, eDNA recorded a greater number of species per sampling event than a conventional trawl survey in the same area over the same sampling years (2017)(2018). Several threatened species were recovered within the eDNA, including undulate ray, porbeagle shark, and thresher shark. Using eDNA, we found differences in elasmobranch communities among sampling stations and between seasons, but not between sampling depths. Collectively, our results suggest that non-invasive eDNA-based methods can be used to study the spatial and seasonal changes in the diversity and abundance of whole elasmobranch communities within temperate shelf habitats. Given the threatened status of many elasmobranchs in human-impacted marine environments, eDNA analysis is poised to provide key information on their diversity and distributions to inform conservationfocused monitoring and management.

Elasmobranchs’ metabarcoding requires a pragmatic approach to reach its promises

“…Elasmobranchs’ metabarcoding has been reaching great outcomes reporting the successful detection of studied species, in particular when compared to conventional biomonitoring methods (see Boussarie et al, 2018; Ip et al, 2021; Liu et al, 2022); nonetheless, the species undetected by eDNA remain poorly discussed. As metabarcoding is still a growing field, it is impossible to know if the absence of expected species is true or if it results from methodological limitations (Liu et al, 2022; Dunn et al, 2022). Here, we discuss the potential increase in the detection rate of elasmobranch species (Box 1).…”

“…Although the Elas02 marker has not been shown to be a good choice and certainly the alternatives mentioned above must be considered, other studies have reached expressive results using the same primer (Mariani et al 2021; Liu et al, 2022). Then other methodological changes should be investigated.…”

“…It is possible that this occurred due to the implementation of a realistic sampling strategy – similar to what MPA’s managers in tropical areas would use (i.e., lack of refrigeration, logistical constraints, and prolonged periods of time before the filtering procedure). To overcome this challenge when refrigerators are infeasible, it seems a plausible recommendation to substitute Whirl-Pak bags in a rigid and hermetic sampler (for example, Nalgene Sample Bottle, used by West et al, 2020; Liu et al, 2022) and protect eDNA samples cooled and stored on ice until filtering, similarly as described by Simpfendorfer et al, (2016) when rare species in a logistic-limited environment are detected.…”

“…For instance, the incidental amplification of prokaryotic DNA by the Elas02 primer represents an important waste of sequencing depth/effort (Collins et al, 2019). As also reported by Dunn et al (2022), the adjustment of some parameters may potentially increase the coverage of elasmobranch detection…”

“…The metabarcoding approach has been proven to be an efficient tool for marine monitoring and ecosystem health assessment (Thomsen et al, 2012; Leray and Knowlton, 2015). And, recent studies provided a proof-of-concept that sharks, rays, and their relatives can be monitored using eDNA metabarcoding (Fraija-Fernández et al, 2020; Ip et al, 2021; Mariani et al, 2021; Marwayana et al, 2021; Monuki et al, 2021; Liu et al, 2022; Dunn et al, 2022).…”