Addressing data-deficiency of threatened sharks and rays in a highly dynamic coastal ecosystem using environmental DNA

Abstract

Marine biodiversity loss is accelerating, leading to the elevated extinction risks of many species, including sharks and rays. To mitigate these losses, information on their distribution and community composition is needed. Monitoring these (often) mobile species is challenging, especially in remote, highly dynamic and turbid coastal areas. Here, we use an environmental DNA (eDNA) approach to: (1) establish the presence and distribution of elasmobranch species, (2) compare this to a conventional fisheries-dependent approach, and (3) determine the influence of season, area-based protection and habitat on elasmobranch community composition in the highly dynamic Bijagós Archipelago in Guinea-Bissau (West Africa). We collected 127 seawater samples and detected elasmobranch DNA in 58 (45.7%) of these samples, confirming the presence of 13 different elasmobranch species (2 sharks, 11 rays), including seven threatened species. Eight of the species detected by the eDNA-approach were also recorded in a fisheries observer program, which recorded another eight species not detected by the eDNA approach. The most commonly occurring species, based on the number of eDNA sampling locations were the pearl whipray (Fontitrygon margaritella), smalltooth stingray (Hypanus rudis), scalloped hammerhead shark (Sphyrna lewini), and the blackchin guitarfish (Glaucostegus cemiculus). Species composition and richness differed significantly before (January-March) and after the rainy season (November-December). Furthermore, we showed that community composition and species richness did not differ between protected (MPA) and non-protected areas of the archipelago. Thus, we confirm that eDNA approaches are a valuable and non-invasive tool to study threatened shark and ray species in data-deficient and dynamic coastal areas, especially when combined with conventional monitoring methods such as fisheries-dependent information.