Phylogeography of a Rare Serpentine Plant, Arenaria katoana Makino (Caryophyllaceae)

Arenaria katoana (Caryophyllaceae) is a rare endemic plant that occurs disjunctly on ultramafic rock sites in Japan. This study assessed the degree of genetic distinctness of small, disjunct, isolated populations of A. katoana in Japan. We sequenced several non-coding regions of the chloroplast DNA (trnL intron, trnL-trnF intergenic spacer, psbA-trnH intergenic spacer, and petG-trnP intergenic spacer) and nuclear ribosomal DNA (ITS1, 5.8S nrDNA, and ITS2) to determine the relationships between populations and to evaluate the level of intraspecific genetic variation. Eight different chloroplast DNA haplotypes were detected, and each population exhibited a unique cpDNA haplotype. Four different ITS types, which were shared between populations, were detected. The phylogeny and distribution patterns of the cpDNA haplotypes and the ITS types indicated that A. katoana can be divided into three groups; a central Hokkaido group (Mt. Yubari, Mt. Bozu, and Mt. Furano-nishi-dake), a Mt. Apoi and Mt. Shibutsu group, and a Mt. Hayachine group. The populations of A. katoana have been subjected to the effects of genetic drift and restricted gene flow, both of which promote population differentiation.