Genomic Insights into the Population Structure and Adaptive Variation of Mullus barbatus in the Mediterranean Sea

Background Red mullet ( Mullus barbatus ) is a key species in Mediterranean fisheries, yet its stock structure and population dynamics remain poorly understood due to a lack of comprehensive genomic resources. This study provides the first high-quality reference genome for M. barbatus and a comprehensive set of SNP markers to investigate its population structure and adaptive potential across the Mediterranean. Results Using the newly generated chromosome-level reference genome, we re-analyzed a Mediterranean-wide reduced-representation genomic dataset. Our analysis reveals a panmictic population structure with strong genetic connectivity across the species’ range, likely driven by extensive larval dispersal and multigenerational gene flow. Despite minimal genome-wide differentiation, outlier analysis identified candidate loci under directional selection, linked to key biological processes such as ontogeny and environmental adaptation. Conclusions This study presents the first genomic resource for M. barbatus , providing valuable insights into its genetic structure and adaptive mechanisms. The identification of loci under selection paves the way for future genomic studies to explore how M. barbatus adapts to environmental and anthropogenic pressures. These findings hold significant implications for the sustainable management of Mediterranean fisheries, especially in the context of climate change and conservation.