Microevolution of the mitochondrial DNA control region in the Japanese brown bear (Ursus arctos) population

We investigated nucleotide sequences of the mitochondrial DNA control regio n to describe natural genetic variations and to assess the relationships be tween subpopulations of the brown bear Ursus arctos on Hokkaido Island, Jap an. Using the polymerase chain reaction product-direct sequencing technique , partial sequences (about 930 bases) of the control region were determined for 56 brown bears sampled throughout Hokkaido Island. A sequence alignmen t revealed that the brown bear control region included a variable sequence on the 5' side and a repetitive region on the 3' side. Phylogenetic trees r econstructed from the 5' variable region (696-702 bases) exhibited 17 haplo types, which were clustered into three groups (Clusters A, B, and C). The d istribution of each group did not overlap with those of the others, and the three different areas were located in separate mountainous forests of Hokk aido Island. Furthermore, most of the phylogenetically close haplotypes wit hin each group were distributed geographically close to each other. In addi tion, the 3' repetitive region (arrays of 10 bases) exhibited a much faster mutation rate than the 5' variable region, resulting in heteroplasmy. Such mitochondrial DNA divergence in each group could have occurred after the b rown bears migrated from the continent to Hokkaido and became fixed in the different areas.