Exploring reserve and depth refuge effects on marine fish communities: Insights from environmental <scp>DNA</scp> metabarcoding

Abstract Marine protected areas (MPAs) have been increasingly developed to protect fish communities and restore their ecological services. Shallow water fish populations may also find a natural refuge in the depths of the mesophotic reefs to escape overfishing and climate change. While a lot of knowledge has been acquired in the last decades about the effect of MPAs and, more recently, about mesophotic ecosystems, thanks to advances in monitoring methods, little is known about the effect of the interaction between protection and depth. Using environmental DNA metabarcoding, we sampled rocky fish assemblages of the Cap Roux no‐take marine reserve and the surrounding fished areas, covering several depth strata ranging from the surface to mesophotic depths. We found that protection, depth, and their interaction had a significant effect on fish diversity and assemblage composition. The vast majority of the 66 fish taxa identified in this study were detected inside the MPA. On the other hand, depth had a negative impact, with mesophotic reefs harboring the lowest diversity. Shallow protected locations were composed of rich fish assemblages, including targeted and threatened species that were rarely detected or even undetected outside the MPA and/or at mesophotic depths. In this study, depth does not seem to act as an efficient refuge for shallow communities. We suggest that the only effective protection comes from the MPA, highlighting the importance of these management tools for the long‐term conservation of fish populations.