Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome

Abstract A compelling interest in marine biology is to elucidate how species boundaries between sympatric free‐spawning marine invertebrates such as bivalve molluscs are maintained in the face of potential hybridization. Hybrid zones provide the natural resources for us to study the underlying genetic mechanisms of reproductive isolation between hybridizing species. Against this backdrop, we examined the occurrence of introgressive hybridization (introgression) between two bivalves distributed in the western Pacific margin, Atrina japonica and Atrina lischkeana, based on single‐nucleotide polymorphisms (SNPs) derived from restriction site‐associated DNA sequencing. Using 1066 ancestry‐informative SNP sites, we also investigated the extent of introgression within the genome to search for SNP sites with reduced interspecies gene flow. A series of our individual‐level clustering analyses including the principal component analysis, Bayesian model‐based clustering, and triangle plotting based on ancestry–heterozygosity relationships for an admixed population sample from the Seto Inland Sea (Japan) consistently suggested the presence of specimens with varying degrees of genomic admixture, thereby implying that the two species are not completely isolated. The Bayesian genomic cline analysis identified 10 SNP sites with reduced introgression, each of which was located within a genic region or an intergenic region physically close to a functional gene. No, or very few, heterozygotes were observed at these sites in the hybrid zone, suggesting that selection acts against heterozygotes. Accordingly, we raised the possibility that the SNP sites are within genomic regions that are incompatible between the two species. Our finding of restricted interspecies gene flow at certain genomic regions gives new insight into the maintenance of species boundaries in hybridizing broadcast‐spawning molluscs.