Refining the distribution and confirming the phylogenetic relationship of the endangered landlocked harbour seal Phoca vitulina mellonae using environmental DNA

The endangered landlocked subspecies of harbour seal Phoca vitulina mellonae, composed of 50–600 individuals, inhabits a wide subarctic lake ecosystem of 700 km 2 in Canada. Its critical habitat was identified and is protected under Canada’s Species at Risk Act. Since 2019, environmental DNA (eDNA) detections are used to increase the subspecies surveying capacity. A probe-based qPCR assay and a metabarcoding assay were developed to enable a sensitive occurrence survey and a mitochondrial DNA diversity survey, respectively. Repeated temporal or spatial eDNA detections with the qPCR assay suggested the subspecies occurrence in waterbodies inside but also outside the critical habitat. Our results also showed that eDNA copy numbers estimated with the qPCR assay are affected by the sampling month and the water volume, and that they correlate negatively with distances from seals. Haplotypes obtained from the metabarcoding assay confirmed the subspecies’ distinct clade in P. vitulina’s global diversity. The network of samplers and the eDNA detection results underscore the role of eDNA survey in improving endangered marine mammal distribution characterization in areas with limited accessibility.