Unraveling the evolutionary mechanisms and consequences of hybridization is a major concern in biology. Many studies have documented the interplay between recombination and selection in modulating the genomic landscape of introgression, but few have considered how associations with phenotype may affect this landscape. Here, we use the European seabass (Dicentrarchus labrax), a key species in marine aquaculture that undergoes natural hybridization, to determine how selection on phenotype modulates the introgression landscape between Atlantic and Mediterranean lineages. We use a high-density SNP array to assess individual local ancestry along the genome and improve the mapping of muscle fat content, a polygenic trait that is divergent between lineages. Taking into account variation in recombination rates, we reveal a purging of Atlantic ancestry in the admixed Mediterranean populations. While Atlantic individuals had higher muscle fat content, we observed that genomic regions associated with this trait also displayed reduced introgression of Atlantic ancestry. These results emphasize how selection against maladapted alleles shape the genomic landscape of introgression.

Unveiling the implications of hybridization on fitness stands as a primary focus in the realms of ecology and evolution. Numerous investigations elucidate how evolutionary mechanisms regulate the intricate pattern of introgression across genomes, yet few have examined the consequential impact of genetic admixture on fitness attributes. Leveraging the Western Mediterranean population of the European seabass (Dicentrarchus labrax), a population formed through hybridization of the Atlantic and Mediterranean lineages in the Alboran Sea, we utilized the Axiom Sea Bass 57k SNP DlabChip array to genotype 1850 hybrid individuals. This enabled us to evaluate the correlation between individual admixture levels and fitness traits under varying thermal conditions (19°C, 21°C, 23°C, and 25°C). Our initial findings unveil a male-biased sex ratio and high temperature sensitivity among admixed individuals with a greater proportion of Atlantic ancestry. Subsequently, our analysis demonstrates that individuals with a higher Atlantic genetic background also exhibit reduced body weight (a parameter linked to fecundity in fish) compared to those with lower Atlantic ancestry. These outcomes underscore the disadvantageous nature of Atlantic ancestry introgression in the Mediterranean region, aligning with previous observations of the elimination of Atlantic ancestry segments subsequent to hybridization.