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.

Fish larvae were collected by the continuous plankton recorder (CPR, operated by SAHFOS) all year long between 1951 and 2005 along transects in the Celtic Sea and English Channel. The CPR is towed by ships of opportunity at speeds of 15 to 20 knots, at an approximate depth of 10 m. Water enters the recorder through an aperture of 1.27 cm2, and is filtered through a continuously moving band of silk with an average mesh size of 270 μm.

Fish larvae were collected by the continuous plankton recorder (CPR, operated by SAHFOS) all year long between 1951 and 2005 along transects in the Celtic Sea and English Channel. The CPR is towed by ships of opportunity at speeds of 15 to 20 knots, at an approximate depth of 10 m. Water enters the recorder through an aperture of 1.27 cm2, and is filtered through a continuously moving band of silk with an average mesh size of 270 μm.

Wave hindcast based on WAVEWATCH III ® with parameterization from Romero (2019) adapted by Alday and Ardhuin (2023) as “TEST702”.