History of Population Formation for the Red Fox Around the Japanese Archipelago, Revealed by Ddrad-Seq Analysis

The red fox (Vulpes vulpes), which is widely distributed across the Northern Hemisphere, including Japan, has been studied for its distribution patterns and migration timing, but its population demography remains poorly understood. To solve it, this study conducted double-digest restriction-site-associated DNA sequencing (ddRAD-seq) on 118 samples from Japan, continental Eurasia, and Sakhalin. Based on single nucleotide polymorphisms (SNPs) detected by ddRAD-seq, this study revealed large genetic differentiation among populations of western Eurasia and four Japanese islands (Hokkaido, Honshu, Shikoku, and Kyushu). The eastern Eurasian population, including Sakhalin, was admixed with the western Eurasian and Hokkaido populations. Our results are consistent with previous reports based on mitochondrial DNA analyses that the Hokkaido and Honshu/Shikoku/Kyushu populations migrated from the continent independently. Demographic simulations showed that the Honshu/Shikoku/Kyushu population could have diverged first from the eastern continental Eurasian population, and that subsequently the Hokkaido population diverged. The simulation results are consistent with the geological record in that Honshu/Shikoku/Kyushu islands were the first to separate from continental Eurasia, followed by the isolation of Hokkaido. We propose a scenario in which the two fox populations in the Japanese archipelago became differentiated genetically as the result of geographical isolation from continental Eurasia by straits. In addition, a clustering analysis showed that foxes on Hokkaido could have become genetically divided into two subpopulations, northeastern and southwestern, suggesting that the Ishikari Lowland located between the two subpopulations served as a barrier to fox dispersal.