Genetic variation is an important attribute of forest tree populations enabling them to adapt to spatial and temporal variations in environmental conditions. In particular, Scots pine (Pinus sylvestris L.) has an exceptionally broad area of dispersal covering different climates and soil conditions, but the genetic variability in extreme conditions has not been studied. We hypothesized that the genetic variability of P. sylvestris is enhanced at its soil fertility limit in bogs where stunted trees form a sparse canopy with reduced light competition, but in highly turbulent conditions generating ideal conditions for distant pollen dispersal. A total of 180 individuals were studied from three bog populations using five nuclear (nSSR) and five chloroplastic (cpSSR) polymorphic microsatellite loci (simple sequence repeats, SSR). According to both marker systems, high and similar level of genetic diversity (ca. 99 % within the populations and 1 % among the populations) was observed for nuclear (F ST = 0.007 and R ST = 0.022) and chloroplast (F ST = 0.015 and R ST = 0.023) genomes. Despite the low genetic differentiation among the populations, there was evidence of geographic genetic differentiation in the chloroplast genomes, suggesting that isolation by distance might be a possible mechanism shaping the present distribution of genetic variability. In addition, significant but low spatial genetic structure along habitat wetness gradient was found in nuclear genomes in one site. Significant cyto-nuclear linkage disequilibrium was shown between one of the cpSSR loci to all nSSR loci. The results demonstrate a huge within-population genetic variability in these sites and underscore the importance of pollen gene flow in homogenizing populations on these geographic scales.
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