Complex geohistory of continental islands advanced allopatric evolution even for the highly dispersive generalist red fox (Vulpes vulpes): multiple phylogenetic groups in the Japanese Archipelago

The red fox (Vulpes vulpes) plays a key role as an apex-generalist predator in terrestrial ecosystems. We estimated the phylogeographic structure, time to most recent common ancestor (tMRCA), and demographic dynamics based on the mitochondrial DNA cytochrome b gene and partial D-loop region sequences of 182 red foxes in the Japanese Archipelago, and discussed the geohistory and biotic interactions that influenced them. The Hondo red fox (Vulpes vulpes japonica), distributed on Honshu, Shikoku, and Kyushu islands, was supported as a monophyletic group. The tMRCA of the Hondo clade was ~0.148 (95% highest posterior density: 0.236–0.080) Ma. The Hondo clade diverged into two subclades, and each was roughly distributed on the eastern or western area of the Japanese Archipelago. The effective population size of the Hondo red fox remained nearly constant until ~0.03–0.02 Ma; thereafter, it grew ~10-fold. The Kita red fox (Vulpes vulpes schrencki) distributed on Hokkaido Island formed a polyphyletic group, not including the Hondo clade. The completely different phylogenetic structures of the Hondo and Kita red fox indicate that they have independent evolutionary backgrounds. These findings provide crucial insights into the formation mechanisms of diversity and endemism of mammals on continental islands.