Geographical Variation and Migration History for Japanese Populations of the Masked Palm Civet (Paguma larvata), Revealed by Ddrad-Seq Analysis

in Japan and Taiwan by using genome-wide SNP (single nucleotide polymorphism) data generated through ddRAD-seq. We found the previously unstudied population in western Honshu to be genetically closely related to that in central Honshu, with low genetic diversity due to a recent range expansion. The populations in Japan were genetically differentiated among Shikoku, western and central Honshu, and eastern Honshu. By admixture analysis, the Honshu and Shikoku populations showed affinity with one or two of them. Overall, the genetic diversity in Japan was lower than that in Taiwan, suggesting a founder effect during introduction from Taiwan. Within Japan, relatively higher variation in the eastern Honshu (especially Gunma Prefecture) populations indicated multiple introductions and/or different genetic lineages from those in Taiwan. Our study provides insights into the introduction history and migration routes of this alien species that can enhance management plans.