Genetic diversity in mitochondrial DNA reveals the effect of a Fisheries Protection Zone on exploited marine species in the Menorca Channel (Western Mediterranean)

Overexploitation can drive evolutionary changes and erode genetic diversity, reducing species’ adaptive capacity to environmental and anthropogenic pressures. Spatial marine conservation measures, such as Marine Protected Areas and Fisheries Protection Zones (FPZs), aim to mitigate these impacts by preserving biodiversity and promoting sustainable fisheries. Recently, nucleotide diversity of the mitochondrial Cytochrome C Oxidase subunit I (COI) marker has emerged as a promising proxy for assessing species conservation status. To evaluate the effectiveness of an FPZ established in 2016 in the Menorca Channel, COI genetic diversity was assessed in four exploited marine species across three areas: the FPZ and two nearby non-protected zones. All species exhibited consistently higher genetic diversity within the FPZ, despite evidence of high gene flow among areas. Coalescent simulations were used to model expected genetic diversity under neutral scenarios of bottlenecks and expansions, with magnitudes estimated from differences in nucleotide diversities observed between fished and non-fished zones. Simulations supported a scenario of population expansion in the FPZ, contrasting with signs of genetic erosion in fished areas. These patterns align with Vessel Monitoring System (VMS) data, which show a post-protection-establishment shift in fishing effort toward non-protected zones, potentially contributing to population declines outside the FPZ. This study provides genetic evidence of the positive effects of fishing restrictions on fishery resources in the Menorca Channel, supporting the FPZ’s role in preserving genetic diversity and promoting population recovery. Furthermore, it highlights COI nucleotide diversity as a simple, cost-effective tool for monitoring marine species’ conservation status and guiding resource management strategies.