Data for: The central Alps comprise a major dispersal barrier between western and eastern populations of two butterfly species

<p><strong>Aim:</strong> Environmental and species-specific factors shape spatial patterns in genetic diversity and population structure. Comparing different species within the same area helps to disentangle more general from species-specific factors affecting such geographic patterns. Here, we examined genetic diversity and population structuring through geographic features in two alpine butterfly species.</p> <p><strong>Location:</strong> European Alps.</p> <p><strong>Taxon:</strong> Copper butterflies (<em>Lycaena</em> spp.).</p> <p><strong>Methods:</strong> We sampled 21 <em>Lycaena hippothoe</em> and 14 <em>L. virgaureae</em> populations with 18 individuals per population. We analysed the genetic diversity and structure<a> </a>of these populations by using 14 and nine microsatellite markers for <em>L. hippothoe</em> and <em>L. virgaureae</em> , respectively.</p> <p><strong>Results:</strong> We found higher number of alleles, allelic richness, observed heterozygosity, F_ST values  and more genetic clusters in <em>L. hippothoe</em> than in <em>L. virgaureae</em>. Both species displayed a major genetic barrier in the central Alps. Western and eastern <em>L. hippothoe</em> populations but central <em>L. virgaureae</em> populations showed the highest genetic diversity.</p> <p><strong>Main Conclusions:</strong> The population genetic structures of both Copper butterflies seemed to be strongly affected by population history and demography. Patterns indicate for both species a western and an eastern glacial refuge. The high genetic diversity and pronounced population structure found in <em>L. hippothoe</em> seems to be related to a low dispersal ability and closed populations with high local abundances as opposed to <em>L. virgaureae</em>. The higher dispersal of the latter likely caused hybridisation in the central alpine contact zone boosting genetic diversity, which was not the case in <em>L. hippothoe</em>. These findings suggest that different conservation strategies are needed for these closely related species.</p>