Detection of genetic segregation in sika deer (Cervus nippon) by tandem repeat variations in the mitochondrial DNA D-loop region

Abstract

ABSTRACTThe browsing habits of sika deer (Cervus nippon) in Japan have caused serious damage to forest vegetation. In Southern Kanto areas such as Tokyo, Saitama, Yamanashi, and Kanagawa Prefectures, sika deer disturb reforestation in logged areas by feeding on planted trees. To appropriately manage sika deer populations in these regions, a genetic marker is required to understand their movement. We previously identified the segregation of sika deer populations between the Kanto Mountain and Tanzawa Mountain areas based on the mitochondrial D-loop region. Here, we aimed to identify an informative genetic marker by focusing on tandem repeat sequences in the D-loop region. The tandem repeat sequences of 145 sika deer sampled in our previous study in Southern Kanto were examined. We revealed that 16 tandem repeat haplotypes existed in Southern Kanto. These tandem repeat haplotypes subdivided five of nine D-loop haplotypes identified in our previous study. Further, they geographically separated one of the D-loop haplotypes, and thus, tandem repeat haplotypes can detect spatial genetic structure with higher sensitivity than flanking D-loop haplotypes. Moreover, the number of tandem repeats ranged from four to eleven. This unusually high variation in the number of repeats might be due to a unique historical background of the Kanto Mountain population. Thus, the tandem repeat haplotype was found to be highly polymorphic, and it can be a useful index to understand sika deer movement in the Southern Kanto area. Furthermore, this marker can be used to analyze the genetic structure of sika deer in other areas.