Abstract
This study explores the population structure, hybridization, and adaptation of Juniperus communis sensu lato in the context of its current habitat fragmentation, using inter-primer binding site markers and needle morphometry. Three native juniper taxa in Slovakia were analyzed: J. communis ssp. communis, J. communis ssp. nana, and their putative hybrid, J. communis nothovar. intermedia. The results reveal a moderate overall structure (Φ(PT) = 0.115, p = 0.001), indicating high gene flow within ssp. communis and low gene flow between ssp. communis and ssp. nana. However, after correcting for non-neutral loci, the inter-subspecies differentiation dropped significantly, suggesting adaptive divergence despite substantial gene flow. This conclusion was further supported using admixture regression of needle morphometry and Φ(PT)-Q(ST) comparison. We show that adaptive genetic differentiation may play a more significant role than phenotypic plasticity in these traits, a key consideration in preventing outbreeding depression in conservation management. Importantly, we also provide evidence for intermediate admixture and distinct selection pressures within two populations of nothovar. intermedia (Stolica, Kralova Studna), which may qualify their recognition as evolutionarily significant units (ESUs).