In our study, we performed a population genetic analysis in all three native oak species of Cyprus and addressed whether two intermediate individuals arose from intersectional hybridization between Quercus coccifera ssp. calliprinos and Q. infectoria ssp. veneris. For this purpose, we successfully tested chloroplast and nuclear microsatellites initially developed for other oak species. We identified a set of markers that can be efficiently used for species identification and study of hybridization. Haplotypes based on the chloroplast microsatellites could resolve different maternal lineages and distinguish between the two sections represented in the study area. Using the nuclear microsatellites, we described patterns of genetic diversity across species with the endemic Q. alnifolia exhibiting reduced genetic diversity. Additionally, we employed a multivariate analysis, which could clearly differentiate among the three species. The two intermediate individuals clustered within the point cloud of Q. infectoria ssp. veneris and also possessed a chloroplast haplotype typical for this species. Therefore, we rejected the hypothesis of intersectional hybridization and interpreted their phenotypic appearance as the result of high phenotypic plasticity within Q. infectoria ssp. veneris.
