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

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.