Abstract
Coastal areas experience among the highest cumulated human pressures across the world's oceans with severe consequences on some fish populations which become scarce and at risk of local extirpation. Marine protected areas (MPAs) are essential for conserving these threatened populations, but they often cover only the most superficial waters and are not three-dimensionally extensive enough, leaving most mobile species with a large home range like elasmobranchs vulnerable to human pressures. Here we explored the role of mesophotic and deep-water habitats as refuges for elasmobranchs and the most at-risk species in the Parc Naturel Marin du Cap Corse et de l'Agriate, a large MPA in the Mediterranean Sea. Using the metabarcoding of 200 environmental DNA samples of seawater filtered between 1 and 835 m depth we revealed that fish species diversity was the highest in the mesophotic habitat (30-149 m). We also found the highest number of endangered species, including Evolutionary Distinct and Globally Endangered (EDGE) species such as Rostroraja alba and Squatina squatina, in this key habitat. Species composition varied significantly with depth, revealing a stratification linked to human pressure and environmental conditions. Protecting both mesophotic and deeper habitats (below 150 m) thus appears crucial to preserving biodiversity, species with unique functional roles but also those with unique phylogenetic diversity, in order to ensure ecosystem resilience in the face of climate change and overexploitation. The full protection of deep-water refuges within the western Mediterranean basin is essential to ensure the preservation of the most at-risk species, with the possibility of rewilding by connectivity other depleted adjacents habitats.