Genomic and geographic footprints of differential introgression between two highly divergent fish species

Investigating variation in gene flow across the genome between closely related species is important to understand how reproductive isolation builds up during the speciation process. An efficient way to characterize differential gene flow is to study how the genetic interactions that take place in hybrid zones selectively filter gene exchange between species, leading to heterogeneous genome divergence. In the present study, genome-wide divergence and introgression patterns were investigated between two sole species, Solea senegalensis and Solea aegyptiaca, using a restriction-associated DNA sequencing (RAD-Seq) approach to analyze samples taken from a transect spanning the hybrid zone. An integrative approach combining geographic and genomic clines methods with an analysis of individual locus introgression taking into account the demographic history of divergence inferred from the joint allele frequency spectrum was conducted. Our results showed that only a minor fraction of the genome can still substantially introgress between the two species due to genome-wide congealing. We found multiple evidence for a preferential direction of introgression in the S. aegyptiaca genetic background, indicating a possible recent or ongoing movement of the hybrid zone. Deviant introgression signals found in the opposite direction supported that the Mediterranean populations of S. senegalensis could have benefited from adaptive introgression. Our study thus illustrates the varied outcomes of genetic interactions between divergent gene pools that recently met after a long history of divergence.