Temporal seascape genomics identifies evolutionary significant units in a highly exploited marine resource, the wedge clam Donax trunculus.
Clam fisheries along the Spanish coast have declined unevenly, while stock management often follows political rather than biological boundaries. To inform conservation and fishery management, this study used temporal seascape genomics to assess population structure, genetic diversity and effective population size (Ne) in the wedge clam Donax trunculus across approximately 2,000 km of the Iberian coast. Using 7,830 putatively neutral and 649 candidate outlier SNPs from 331 individuals, the analyses confirmed broad Atlantic-Mediterranean differentiation, identified the Alboran Sea as a distinct genetic unit, and revealed finer-scale Atlantic substructure. Temporal genomic comparisons showed that population structure remained largely stable over the study period, although genetic diversity changed in a site-specific manner across fishing areas. Genotype-environment analyses indicated that spatial structure explained more genomic variation than environmental predictors, especially after accounting for spatial- environmental collinearity. Overall, the results show that temporal seascape genomics can distinguish persistent biogeographic structure from short-term, local genomic change in exploited marine invertebrates, providing a robust framework for biologically informed stock delineation. The genetically distinct groups identified here should therefore be considered separately in conservation, fishery management and any future reinforcement planning.