Lack of association between winter coat colour and genetic population structure in the Japanese hare,Lepus brachyurus (Lagomorpha: Leporidae)

Seasonal changes in fur colour in some mammalian species have long attracted the attention of biologists, especially in species showing population variation in these seasonal changes. Genetic differences among populations that show differences in seasonal changes in coat colour have been poorly studied. Because the Japanese hare (Lepus brachyurus) has two allopatric morphotypes that show remarkably different coat colours in winter, we examined the population genetic structure of the species using partial sequences of the SRY gene and six autosomal genes: three coat colour‐related genes (ASIP, TYR, and MC1R) and three putatively neutral genes (TSHB, APOB, and SPTBN1). The phylogenetic tree of SRY sequences exhibited two distinct lineages that diverged approsimately 1 Mya. Although the two lineages exhibited a clear allopatric distribution, it was not consistent with the distribution of morphotypes. In addition, six nuclear gene sequences failed to reveal genetic differences between morphotypes. Population network trees for 11 expedient populations divided the populations into four groups. Genetic structure analysis revealed an admixture of four genetic clusters in L. brachyurus, two of which showed large genetic differences. Our results suggest ancient vicariance in L. brachyurus, and we detected no genetic differences between the two morphotypes. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 761–776.