Abstract
The study investigates the population structure, hybridization, and adaptation of Juniperus communis sensu lato in the context of recent habitat fragmentation across Europe, using inter-Primer Binding Site (iPBS) markers and needle morphometry. Three operational taxonomic units, all native to Slovakia, are analyzed: J. communis ssp. communis, J. communis ssp. nana, and their putative hybrid, J. communis ssp. communis var. intermedia. The results show a moderate overall structure (𝛷𝑃𝑇=0.115, 𝑝=0.001), indicating high gene flow within ssp. communis and low gene flow between ssp. communis and ssp. nana. However, the inter-subspecies differentiation dropped significantly after correcting for non-neutral loci, which implies adaptive divergence despite substantial gene flow. This conclusion is further supported by admixture regression and 𝛷𝑃𝑇-𝑄𝑆𝑇 comparison. In needle morphometry, we find genetic differentiation by selection to be relatively important compared to phenotypic plasticity. This can be highly relevant for conservation measures due to the risk of outbreeding depression. Finally, we identify var. intermedia as the hybrid of the two subspecies, suggesting it as an evolutionary significant unit.