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

Marine protected areas (MPAs) have been increasingly developed to protect
fish communities and restore their ecological services. Shallow water
(above -30 m) 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 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 (eDNA)
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 harbouring the
lowest diversity. A reserve effect on species richness was observed for
shallow reefs but not for the mesophotic zone. 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.