Phylogeographic study based on intraspecific sequence variation of chloroplast DNA for the conservation of genetic diversity in the Japanese endangered species Primula sieboldii

To gather information on intraspecific phylogeography for use in conservation programs for the endangered species Primula sieboldii in Japan, we analyzed sequence variation in five noncoding regions of chloroplast DNA. Twenty-two distinct haplotypes were recognized in total. The distribution of most haplotypes was geographically confined, but one haplotype was widely distributed throughout northern Japan, and several haplotypes were found in geographically distant regions. Three major clades were revealed by phylogenetic analysis of the haplotypes. Clade I was distributed in Kyushu and central Honshu, clade II in western Honshu and Hokkaido, and clade III from central Honshu to Hokkaido. According to analysis of molecular variance, 59.9% of the total cpDNA variation existed among regions, 32.5% among populations within regions, and 7.6% within populations. Therefore, if genetic conservation of the species is valued, transplanting of P. sieboldii among regions should be avoided. Multiple lineages often existed even in geographically narrow areas (e.g., within a 20-km range), so transplantation between adjacent populations in restoration activities should be carefully designed so as not to change the gene pool of local populations significantly. Also, the geographical distribution of cpDNA haplotypes may allow us to confirm the origin of plants collected for commercial purposes.