Genomic Evidence for Revising Management Units of European Anchovy: Integrating Evolutionary Lineages into Fisheries Assessment

Effective fisheries management requires stock boundaries that accurately reflect underlying biological populations. In European anchovy, defining management units has been complicated by a complex evolutionary history and coexistence of distinct ecotypes. Despite recent advances using high-resolution genomic markers, key uncertainties persist regarding connectivity, particularly between the Bay of Biscay and Atlantic Iberian Waters stocks and their links to neighboring regions. Here, we analyze thousands of genetic markers from individuals spanning both assessed stocks and adjacent areas, including representatives of the two marine and coastal ecotypes. Our comprehensive population genomic analyses identify a northern marine, a southern marine, and a coastal linage, and reveal that divergence between ecotypes exceeds that observed among geographically distant populations within the same ecotype. Our findings demonstrate that current management units do not capture the underlying biological structure, which could lead to local overexploitation due to inadequate Total Allowable Catch settings. This study emphasizes the need to incorporate genetic data when defining management units, with the goal of improving stock assessment, safeguarding adaptive potential, and ensuring sustainability of the species.