Temporal seascape genomics identifies evolutionary significant units in a highly exploited marine resource, the wedge clam Donax trunculus

Abstract Clam fishery stocks have experienced a significant, albeit uneven, decline along the Spanish coast, with stock delineation frequently mirroring political boundaries rather than biological ones. Nevertheless, it is crucial to align management units with the biological realities of the species to ensure sustainable exploitation. In this context, understanding the spatio-temporal population structure, genetic diversity, and effective population size (Ne) of the wedge clam Donax trunculus populations along the Iberian Peninsula coast is vital for making informed management decisions. Thus far, high-resolution genomic data on these key parameters remain limited for this species. Our analysis utilised a substantial dataset of 8,479 single-nucleotide polymorphisms (SNPs) derived from 331 individuals collected over approximately 2,000 kilometres along the Iberian coast, confirming a genetic structure that classified the individuals into three distinct groups: the Atlantic Ocean, the Balearic Sea, and the Alboran Sea. For the first time, we revealed contrasting temporal changes in neutral and adaptive genetic diversity across different fishing areas, reflecting the varying effectiveness of certain management strategies implemented to date. Furthermore, to safeguard genetic diversity and preserve potential local adaptations, we recommend that these genetically distinct groups be managed separately in future conservation, potential translocation and fishing plans. Competing Interest Statement The authors have declared no competing interest. Footnotes Funding sources This work was supported by Programa de Ayudas a Proyectos de I+D+I del Plan Complementario de Ciencias Marinas y del Plan de Recuperacion, Transformacion y Resiliencia de la Comunidad Autonoma de Andalucia, Project PCM_00122 to CR and MH. This study forms part of the ThinkInAzul programme supported by MCIN with funding from European Union Next Generation EU (PCM_00122 and PRTR-C17.I1). Declaration of Interest statement The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this manuscript.