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To investigate genetic diversity among populations of the Japanese giant flying squirrel Petaurista leucogenys, the mitochondrial DNA control region sequences (1,052–1,054 bases) were determined in 37 specimens from 17 localities on the Honshu, Shikoku, and Kyushu Islands of Japan. Of the 37 animals examined, 24 haplotypes were identified. All haplotypes from Kyushu consisted of 1,052 bases, whereas those from Honshu and Shikoku consisted of 1,054 bases including two insertions, except for three haplotypes (which had 1,052 or 1,053 bases). Phylogenetic relationships reconstructed using neighbor-joining and maximum parsimony methods indicated that P. leucogenys is essentially separated into three major lineages: Group A consisting of a single haplotype from Kyushu, Group B consisting of some haplotypes from Kyushu and one haplotype from Honshu, and Group C consisting mostly of haplotypes from Honshu and Shikoku. Animals with the Kyushu haplotypes were split into two lineages (Groups A and B), suggesting that Group A diverged at an earlier point from the other groups. Genetic distances in Group C were not related to geographic distances between sampling localities, indicating that ancestral populations of this group recently expanded their distribution in a short time, possibly after the last glacial stage.

Phylogeography of the Japanese Giant Flying Squirrel, Petaurista leucogenys, Based on Mitochondrial DNA Control Region Sequences