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.

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).

Runs_a

Compressed file containing the compressed forward and reverse sequence files of runs 1 through 4.

corr_tag

File linking the sequence files to the sample information.
column 1: run code
column 2: run type
column 3: project name
column 4: sample name (lab identifier, starts with "SPY")
column 5: sample name with PCR replicate number
column 6: tag name = position on plate
column 7: tag sequence
column 8: forward primer sequence
column 9: reverse primer sequence

corr_field

File linking the sample laboratory ID to the sample (field) metadata. 
Assigning the field ID allows to run the analyses on https://github.com/eboulanger/MEDeDNA--reserves
column 1: sample lab code
column 2: sample field code
column 3: sampling date
column 4: longitude coordinate of the transect center
column 5: latitude coordinate of the transect center

MEDeDNA_refdb_teleo

New mediterranean fish reference sequences for the teleo barcode.
column 1: local reference database identifier
column 2: lab code
column 3: field code
column 4: species scientific name
column 5: teleo sequence