Hybridization patterns between Rhynchocypris lagowskii and R. oxycephala in a naturally sympatric river

Abstract Hybridization between closely related species provides insights into reproductive isolation and speciation. Here, we investigated hybridization between two minnow species, Rhynchocypris lagowskii and Rhynchocypris oxycephala , in the Seri River, Shiga Prefecture, central Japan, within their natural sympatric range. Mitochondrial DNA phylogeny confirmed that both species in this river represent native populations. Genome-wide SNP analyses using MIG-seq revealed clear genetic differentiation between the two species, with R. lagowskii predominating downstream and R. oxycephala upstream. Triangle plot analysis identified F 1 hybrids (1.1%) and backcrosses to R. lagowskii (4.8%) and R. oxycephala (12%), all of which were restricted to the middle reaches. Under our sampling design and analytical conditions, no F 2 or later-generation individuals and mitochondrial introgression was detected, suggesting potential postzygotic isolation, while spatial segregation may contribute to prezygotic isolation. These findings confirm that hybridization occurs in natural sympatry yet species boundaries are maintained, making this system a valuable model for studying speciation.