Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.
Methods
30 L of seawater were collected along 2 km transects and filtered using 0.20-µM filtration capsules. Environmental DNA was extracted and amplified by PCR with the fish-specific primer pair teleo targeting a 70 bp fragment at the end of the mitochondrial DNA 12S rRNA gene. PCR reactions were carried out in 12 replicates per sample and unique tags were given to each sample. A paired-end sequencing (2x125 bp) was carried out on a MiSeq (Illumina, San Diego, CA, USA).