Plant species around the world are negatively affected by habitat fragmentation and climate change. Montane willow populations in the UK have declined primarily due to grazing, as well as climate change and muirburn in certain areas. Only small, isolated populations remain, scattered across steep ledges where shrubs escape most grazing animals. We explored the genetic effects of habitat fragmentation on gene flow and genetic diversity in the largest remaining patches in the UK, which lie in Scotland, for two now restricted and rare montane willow species—Salix myrsinites and Salix lapponum. Using ten microsatellite loci and an almost complete genetic inventory in the central Cairngorms area (S. myrsinites n = 186, S. lapponum n = 91) we showed that genetic diversity (heterozygosity and allelic richness) is relatively high in both species, particularly high for the decaploid S. myrsinites, and clonal reproduction low. Historic gene flow between populations could be demonstrated. Significant inbreeding was detected in both species and observed seed set and numbers of juveniles in the field are low, possibly indicating signs of inbreeding depression. Both species have extremely low numbers of individuals at each site, with many being smaller than ten, and in some cases combined with skewed sex-ratios (mainly female biased). This will likely cause more severe reproductive failures in the next generations unless population numbers are increased. Reinforcing populations of both species under low grazing pressure with new, unrelated individuals, as well as creating new stepping-stone populations will be necessary to help the recovery of these species. Results from this study will inform restoration work in Scotland aiming to create continuous woodland habitats from pinewoods at lower altitudes through to higher altitude downy birch woodlands merging with montane willows.
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