Intraspecific sequence variation of chloroplast DNA inPedicularis chamissonis Steven (Scrophulariaceae) and geographic structuring of the Japanese “Alpine” plants

In order to clarify evolutionary patterns and processes of intraspecific diversification ofPedicularis chamissonis Steven, we analyzed intraspecific variation of the nucleotide sequences of non-coding regions of chloroplast DNA: the intergenic spacers betweentrnT (UGU) andtrnL (UAA) 5′exon,trnL (UAA) 3′exon andtrnF (GAA), andatpB andrbcL. In 24 populations ofP. chamissonis, 33 nucleotide substitutions and 12 insertions/deletions were inferred, and their genetic distances ranged from 0.001 to 0.014. Seventeen distinct cpDNA haplotypes could be recognized and each haplotype was found to be geographically structured. Two major clades (the Northern and Southern clades) were revealed in phylogenetic analyses of cpDNA haplotypes. The haplotypes of the Northern clade had a wider distribution area in the populations of Mts. lide of central Honshu in Japan, northward to Unalaska Island in the Aleutians. Relationships among most haplotypes were unresolved polytomies. On the other hand, the haplotypes of the Southern clade occurred from the populations of Mt. Gassan southwards to Mt. Arakawa of central Honshu. Within this clade, three subclades were clearly recognized. From these results, we concluded that the haplotypes of the Northern and Southern clades inP. chamissonis might have traveled down to Japanese Archipelago from the north in not a single glacial period.