A high phylogenetic differentiation rate of long-distant migratory passerines characterizes the Japanese archipelago. Since birds are assumed to easily fly over the sea, colonization route to the archipelago and the geographic barrier for Japanese populations remained ambiguous from a traditional phylogeographic perspective deduced by non-volant animals.
 Here, we conducted integrative phylogeographic approaches in the Brown Shrike Lanius cristatus. Species distribution modeling (SDM) can predict relative distribution ranges of populations, possibly inferring a geographic barrier. Migratory routes revealed by light-level geolocators may infer an immigration route to the archipelago since a migratory route is known to retrace a past colonization route.
 Divergence of the Japanese population was inferred around the time periodical submergence of the continental shelf became frequent, using mitochondrial DNA. The predicted LGM distribution by SDM inferred that the subsequent submergence of the continental shelf isolated the archipelagic population. Light-level geolocators revealed a migratory route across the East China Sea between the archipelago and the continent, which traced over the LGM range of the Japanese population. This supported that the emerged continental shelf served as an immigration route to Japan. Our scenario inferred that divergence in Japanese migratory birds may have rather be facilitated by their high dispersal abilities.