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 (Engraulis encrasicolus), defining management units has been complicated by a complex evolutionary history and the coexistence of distinct ecotypes. Despite recent advances using high-resolution genomic markers, key uncertainties persist regarding population structure and connectivity, particularly between the Bay of Biscay and Atlantic Iberian Waters stocks and their links to neighboring northern and southern regions. Here, we analyze thousands of genetic markers from individuals spanning both assessed stocks and adjacent areas, including representatives of the two recognized ecotypes (marine and coastal). Our comprehensive population genomic analyses identify three major lineages, northern marine, southern marine, and coastal, shaped by historical processes and ecological differentiation. Notably, genetic divergence between ecotypes exceeds that observed among geographically distant populations within the same ecotype, highlighting the need to incorporate ecological as well as spatial drivers when delineating stocks. Our findings demonstrate that current management units do not capture the underlying biological structure of European anchovy, which could lead to local overexploitation due to inadequate Total Allowable Catch (TAC) settings. This study emphasizes the need to incorporate genetic data when defining biologically relevant management units, with the goal of improving stock assessments, safeguarding adaptive potential, and ensuring the long-term sustainability of the species.