Genomic signatures of divergent selection and gene flow are well studied in young species pairs but it is not clear how these processes shape genomic divergence following secondary contact after long-term isolation. Japan Sea and Pacific Ocean sticklebacks are an excellent system to investigate this. Unlike most stickleback species pairs, they are fully marine and are thought to have diverged during the early Pleistocene when sea level change geographically isolated the Sea of Japan. Strong reproductive isolation, including hybrid sterility, has evolved but introgression occasionally occurs where the two species overlap in the northern parts of the Japanese archipelago. A long period of geographical isolation between these species has likely led to the evolution of genome-wide barrier loci, introgression should therefore occur predominately in regions of high recombination and should be lowest at sex chromosomes, previously shown to play a role in speciation in this system.
Using 26 resequenced genomes we first identified the evolutionary history of this system; using Approximate Bayesian Computation we identified a period of geographical isolation and secondary contact as the most likely divergence scenario. We then used a comparative genome sea approach to characterise genomic differentiation and identify introgression between the two species. Small-scale introgression was widespread throughout the autosome but was lowest in regions of low recombination, specifically on sex chromosomes. Our results suggest that lower recombination between divergent sex chromosomes in this species pair has played a major role in maintaining these species in the face of gene flow following secondary contact.