Genetic diversity and differentiation of the endangered Japanese endemic tree Magnolia stellata using nuclear and chloroplast microsatellite markers

Abstract

Genetic diversity and differentiation were analyzed in 11 populations of Magnolia stellata (Sieb. and Zucc.) Maxim. (Magnoliaceae) in the Tokai district, Japan. Variation at four nuclear microsatellite (nSSR) loci was examined, three chloroplast microsatellite (cpSSR) markers were developed and 13 haplotypes identified. The 11 populations were divided into three groups (A, B and C). Each population within the group was separated less than 40 km. Group B harbored the highest gene diversity (H) and allelic richness (Ar) for nSSR (H=0.74 and Ar=8.02). Group C had the highest diversity of chloroplast haplotypes (H=0.79 and Ar=6.8): 2.5 times more haplotypes than the other groups. Each population contributed differently to the total diversity, with respect to nSSR and cpSSR. AMOVA revealed that 58% of haplotypic and 15% of nSSR variation was partitioned among populations within groups. A Mantel test revealed significant correlations between population pairwise geographic ln(distance) and F ST /(1)F ST ) for both nSSR (r=0.479; P=0.001) and cpSSR (r=0.230; P=0.040). Dendrograms of populations for nSSR, based on Nei's genetic distance, were constructed using UPGMA and the neighbor-joining method. These results suggest that populations in group C have diverged from the other populations, while those in group B are similar to each other. For group B, fragmentation between populations should be avoided in order to maintain gene flow. For group C, the uniqueness of each population should be given the highest priority when planning genetic conservation measures for the species.

Genetic variation and differentiation in populations of a threatened tree, Magnolia stellata: factors influencing the level of within-population genetic variation

“…Within-and among-population genetic variation The level of within-population genetic variation tended to be higher for populations in region A than for populations in regions B and C, in accordance with the results of previous studies (Kawahara and Yoshimaru, 1995;Ueno et al, 2005). This trend may be partly due to region A being central to the species' range, while regions B and C are marginal, and partly due to the populations in regions B and C being more isolated from one another than those in region A.…”

“…The value of F ST obtained in this study is very similar to that obtained by Ueno et al (2005) using nuclear microsatellites (F SC , an analog to F ST ¼ 0.18), but lower than that found by Kawahara and Yoshimaru (1995) using allozymes (G ST , an analog to F ST ¼ 0.254). Values of F ST and G ST cannot be simply compared between loci if the loci to be compared exhibit different levels of within-population genetic variation (Hedrick, 2005), as in the material examined here, since there were considerably higher values of H S at microsatellite loci (0.719, this study; 0.58, Ueno et al, 2005) than at allozyme loci (0.092, Kawahara and Yoshimaru, 1995). Hedrick (2005) addressed this problem, and proposed a standardized measure (G 0 ST ), which allows more appropriate comparisons between loci that have different levels of genetic variation.…”

“…Interestingly, although the Tabika population was highly isolated and did not have a large population size, it showed the highest within-population genetic variation. High genetic variation in this population has also been revealed by nuclear microsatellite analyses in a previous study (in which it was called the Komono population; Ueno et al, 2005). Ueno et al (2005) also examined cpDNA variation in 11 populations, and found that the level of variation was unusually high in the Tabika population.…”

“…High genetic variation in this population has also been revealed by nuclear microsatellite analyses in a previous study (in which it was called the Komono population; Ueno et al, 2005). Ueno et al (2005) also examined cpDNA variation in 11 populations, and found that the level of variation was unusually high in the Tabika population. The unusually high genetic variation in the population could not be explained by contemporary gene flow due to its isolated distribution and its modest current size.…”

“…Second, Nakashima and Sakai (2003) investigated 14 populations sampled solely from the Tono region (southeastern Gifu Prefecture) using 10 allozyme markers, but did not identify the factors influencing the level of within-population genetic variation. Third, Ueno et al (2005) investigated 11 populations, including the nine examined by Kawahara and Yoshimaru (1995), using four microsatellite markers developed in M. obovata, and also failed to identify Mie Pref.…”