Population structure of endangered spinetail devil ray (Mobula mobular) in the Lesser Sunda Seascape, Indonesia, revealed using microsatellite and mitochondrial DNA

The Lesser Sunda Seascape (LSS) is a critical habitat for various megafauna, including the spinetail devil ray (Mobula mobular). For decades, bycatch from drift gillnet fisheries has increased in the LSS, posing a greater threat to their populations. Migratory species require population-based management to effectively address their conservation needs and ensure their long-term survival. Fifty-five samples were collected from three locations within the LSS, i.e., East Flores (19), West Manggarai (15), and East Java (21). This study aims to understand the population genetic structure of M. mobular within the three different locations around the LSS using eight microsatellite markers and mitochondrial DNA (mtDNA) NADH-dehydrogenase subunit 5. The analysis of molecular variances result indicated the significant result between the three locations based on microsatellite data (0.0876, p < 0.05 for eight loci and 0.1360, p < 0.05 for four loci) and mtDNA (0.04820, p < 0.05). The pairwise genetic differentiation index (Fst) revealed that East Flores versus West Manggarai has a nonsignificant value (p > 0.05). Meanwhile, East Flores or West Manggarai versus East Java showed a significant Fst value (p < 0.05). In conclusion, microsatellite and mtDNA results revealed that in the LSS, spinetail devil rays are divided into two distinct subpopulations: the Savu Sea (East Flores and West Manggarai) subpopulation and the East Java subpopulation. Even though there are two potential subpopulations in the LSS, co-management of this species should be prioritized in the LSS due to the indication of shared haplotypes between those locations.