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Gene flow is one of the main factors shaping genetic diversity within and among tree populations, and occurs through pollen and seed dispersal. Recent findings of pollen-release asynchronies in distant populations of Scots pine (Pinus sylvestris L.) within Scotland suggest that gene dispersal among more distant populations might be less effective than previously thought. Limited gene dispersal is one of the major factors causing genetic structure for neutral markers, and pollen-release asynchrony could have driven isolation by distance (IBD) among Scottish populations. Previous studies of neutral markers found little differentiation among Scottish populations of Scots pine, however they did not consider IBD over the full Scottish range. We analysed data from 6 nuclear simple sequence repeats (SSR) and 5 chloroplast SSR loci in a total of 540 individuals of Scots pine from 18 populations across Scotland. Our aim was to assess contemporary levels and distribution of genetic variation and to test if the distribution of genetic diversity was consistent with IBD. We also analysed patterns of gene flow that could have contributed to the observed patterns of variation. Levels of genetic diversity were high, for both nuclear and chloroplast markers within populations, and there was no significant differentiation among populations. A weak signal of IBD was present. We found an increase in nuclear diversity towards the East along with greater gene flow in a West-East direction commensurate with the prevailing winds. Our findings suggest that this wind-driven gene flow is dominant over genetic drift and prevents differentiation among the Scottish populations. It may also counteract any pollen-release asynchronies among populations.

Weak isolation by distance and geographic diversity gradients persist in Scottish relict pine forest