Genomic insights into population structure and somatic condition in the European sardine

The European sardine is experiencing a decline in somatic condition and body size, raising concerns about the long-term viability of its populations. Despite its ecological and economic importance, population structure and adaptive variability in this species remain insufficiently understood. We used a genomic approach to investigate population structure and examine associations between genetic markers and somatic condition across six locations in the Atlantic Ocean and Mediterranean Sea. Based on 5,506 SNPs, we identified strong genetic differentiation between the Atlantic–Alboran group and the remaining Mediterranean populations. We also detected weaker but significant structure within the Mediterranean. The Almeria–Oran Front was confirmed as a major biogeographical barrier, while the Adriatic population showed evidence of genetic admixture, consistent with a transitional role between the western and eastern Mediterranean. Although population differentiation was detected using both neutral and selected loci, outlier SNPs (2.3% of all loci) contributed disproportionately to divergence (FST = 0.242), highlighting the role of local adaptation. Estimates of effective population size (Ne) are affected by chromosomal inversions, as linked loci within these regions bias Ne downward, with a pronounced reduction in Ne in Mediterranean populations. Using two complementary approaches, we identified four SNPs (potentially up to 30) significantly associated with somatic condition (Kn). Together, these results provide new insights into the genetic structure and adaptive potential of European sardines and represent the first genomic evidence linking specific loci to somatic condition. Our findings highlight the value of integrating genomic and phenotypic data to inform conservation and management strategies.