Genetic variation of the relict maple Acer miyabei: uncovering its history of disjunct occurrence and the role of mountain refugia in shaping genetic diversity

Premise Relict species provide valuable insights into the origin and formation of extant vegetation. Here, we aimed to elucidate the genetic structure and diversity of a riparian relic, Acer miyabei, in Japan. Once widely distributed, it now occurs in three isolated regions. The most northern regional group is located at low elevation on Hokkaido Island, whereas the southernmost group in central Honshu Island is at high elevation in a mountainous landscape. This contrastive distribution enables us to examine the effects of climate oscillations on genetic diversity in relation to topographic variation. Methods We collected 604 individuals of A. miyabei from 43 sites. Their genetic structure and diversity were analyzed using 12 microsatellite markers and cpDNA sequences. Results According to structure analyses, ∆K was lowest at K = 2; the clustering essentially separated many of the individuals in the most northern regional group from the others. In contrast, the two southern groups were not clearly differentiated from each other, despite their geographic discontinuity. The proportion of private alleles was high in populations from the mountain terrain in the southern group although the number of extant populations is limited. Conclusions Genetic clustering of A. miyabei is not perfectly congruent with the current patterns of geographic distribution. We infer that disjunction of the two southern groups occurred more recently than that between these groups and the northern group. The mountainous landscape in the most southern region likely provided multiple refugia and contributed to the retention of distinctive genetic variation.