Phylogenetic relationships of ancient brown bears ( Ursus arctos ) on Sakhalin Island, revealed by APLP and PCR-direct sequencing analyses of mitochondrial DNA

To investigate the phylogenetic relationships of brown bears (Ursus arctos) on Sakhalin Island in the Far East, mitochondrial DNA (mtDNA) sequences were analyzed for 27 ancient and five contemporary specimens of brown bears obtained from Sakhalin. We successfully determined partial sequences of the mtDNA control region (254–394 base-pairs) and identified six novel haplotypes. All sequences from bears on Sakhalin grouped phylogenetically with clade 3a but were not clearly distinguishable as to subclades 3a1 and 3a2. However, by application of APLP method for detecting single-nucleotide polymorphisms (SNPs) specific to clades, the samples from Sakhalin were all identified to clade 3a1, which is currently widespread in eastern continental Eurasia. Although the ancestors of brown bears on Hokkaido Island, Japan, migrated from continental Eurasia through Sakhalin, none of the clades previously found on Hokkaido (clades 3a2, 3b, and 4) were detected on Sakhalin. Our results suggest that an ancestral bear population from clade 3a1 migrated from continental Eurasia to Sakhalin, independently and after the migration of clade 3a2 to Hokkaido. Alternatively, clade 3a2 could have evolved from phylogenetically closely related clade 3a1 due to geographical isolation on Hokkaido. Our data confirm that bear skull remains from an Okhotsk Cultural archaeological site on small Rebun Island off the northwest coast of Hokkaido were transported from Hokkaido, rather than from Sakhalin.