Hybrid population of highly divergent groups of the intertidal goby Chaenogobius annularis

•A transition zone between two groups of Chaenogobius annularis was analyzed.•Hybridization was detected in a population at the center of the zone.•Most individuals appeared to be post-F2 hybrids with unique genetic features.•The hybrid population must be associated with ancient hybridization.

Hybrid zones, where two genetic groups come in contact, provide valuable opportunities for testing whether reproductive isolation is complete between the groups. The intertidal goby Chaenogobius annularis comprises a group in the Sea of Japan and another group in the Pacific Ocean that exhibit a substantial level of genetic divergence; however, it is unclear whether they are reproductively isolated. In this study, we analyzed six populations sampled around a transition zone (approximately 300 km) between the two major groups, i.e., along the Sanriku coast of the northeastern Pacific coastline of the Japanese Archipelago, using mitochondrial DNA sequences of the cytochrome b gene, the allozyme loci of malate dehydrogenase, and eight microsatellite DNA loci. We detected considerable genetic admixture in the Taro population located at the center of the transition zone, where most individuals (98%) appeared to be post-F2 hybrids. Bayesian clustering analysis, mitochondrial DNA phylogenetic tree, and private alleles in the allozyme and microsatellite DNA loci demonstrated that contemporary gene flow has been negligible between the hybrid population and either of the two groups. These findings demonstrate the long-term isolation and self-sustaining nature of this population after ancient hybridization.