A mitochondrial control region and cytochrome b phylogeny of sika deer (Cervus nippon) and report of tandem repeats in the control region

Sika deer (Cervus nippon Temminck) are endemic to mainland and insular Asia. Numerous subspecies have been named, but they are not quantitatively well defined. Portions of the mitochondrial cytochrome b gene (450 bp) and control region (512 bp) were sequenced from 28 individuals belonging to five sika subspecies and two Cervus elaphus subspecies. Phylogenetic trees constructed using these sequences clearly demonstrated that sika are monophyletic with respect to C. elaphus. A survey of variation in the control region showed that approximately half the variation occurred in a 100-base segment between positions 150 and 250 in the left domain of the control region. Within this region there were three tandemly repeated copies of a 39-base motif. In addition, two of the samples (C. n. aplodontus and C. n. hortulorum) contained, respectively, two and four additional copies of the repeated motif.