Hybridization studies are important to advance our understanding of the interspecific gene flow and its evolutionary consequences in closely related species. Hybridization and admixture patterns were assessed in a contact zone and reference populations of European pine species using sequence data from 26 nuclear genes and a species-diagnostic cpDNA marker. Reference populations formed three distinct genetic clusters comprising Pinus sylvestris, Pinus mugo/Pinus uliginosa, and Pinus uncinata. Evidence of population structure was found only in P. uliginosa. Based on phenotypic characteristics and molecular data, we identified five groups of individuals in the contact zone in Poland, comprising forms of the parental species and intermediates that were most probably the result of interspecific crosses. A combination of nuclear gene sequence data and a diagnostic organelle marker were used to show that hybridization is frequent in the contact zone and results in hybrid trees with distinct phenotypic identity. The influence of selection in maintaining hybrid phenotypes in environments unsuited to parental species was inferred from nucleotide polymorphism data. A lack of admixture in reference populations suggests that hybridization has not occurred during post-glacial migration and so the contact zone represents a distinct, active example of ongoing evolution. Pine populations in this zone will be a valuable system for studying the genetic basis of hybrid advantage in environmental conditions untypical of pure parental species.

This study of nuclear microsatellite loci demonstrates genetic relationships between twenty four Scots pine populations from Europe and Asia Minor. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation between distant populations, for instance in central and northern Europe. Despite the signs of isolation found in peripheral stands, a similar level of genetic variation and no evidence of a recent bottleneck was found across the populations.

Polymorphisms at a set of eighteen nuclear (nSSR) and chloroplast (cpSSR) microsatellite loci were investigated in sixteen populations of Scots pine (Pinus sylvestris L.) derived from the provenance trial experiment and representative of the species distribution range and climatic zones in Poland. The patterns of genetic variation were compared to the reference samples from the species distribution in Europe and Asia. A similar level of genetic variation and no evidence of population structure was found among the Polish stands. They showed genetic similarity and homogenous patterns of allelic frequency spectra compared to the Northern European populations. Those populations were genetically divergent compared to the marginal populations from Turkey, Spain and Scotland. The population structure patterns reflect the phylogeography of the species and the divergence of populations that most likely do not share recent history. As the analysed provenance trial populations from Poland are diverged in phenotypic traits but are genetically similar, they could be used to test for selection at genomic regions that influence variation in quantitative traits.

The NERC and CEH trademarks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. Polish populations share the same genetic background at the analysed nuclear gene markers.However, the populations showed a much closer genetic relationship with North European samples than other regional groups of populations. Across the very uniform genetic background of the populations we identified several genes with outlier patterns of haplotype, polymorphism frequency variation and departures from compound neutrality tests. Our data indicate that the Central and NorthEuropean parts of the Scots pine distribution seem particularly suitable for association genetic studies to link phenotypic and genetic variation at a large geographical scale.

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With the current rate of biodiversity loss, conservation management practices require a comprehensive understanding of eco‐evolutionary relationships, history, and genetic structure of species. Assessments of genetic diversity are crucial, especially in rare, endemic, or threatened forest tree species with small and isolated populations, such as peat bog pine (Pinus uliginosa N.). Here, we used a novel approach, combining genetic diversity assessment, ecological niche modeling, and population demography inference to explore the complex history of a few remnant populations of this endangered pine. To asses the relative influence of isolation and fragmentation on genetic diversity in the taxonomic context, the patterns of genetic variation found in P. uliginosa were contrasted with those observed in its close relatives with much bigger distribution ranges and larger populations (Pinus sylvestris, Pinus mugo, and Pinus uncinata). We found a similar level of genetic diversity across the species at nuclear loci but contrasting patterns of variability distribution at chloroplast markers. We detected the signatures of an ancient genetic bottleneck dated at around 26 400 years ago, indicating a drastic reduction in the population size of P. uligionosa during the Last Glacial Maximum. In addition, we found substantial differentiation between current populations as a result of enhanced genetic drift during long‐lasting isolation. The research suggests potential conservation management strategies for peat bog pine and emphasizes the importance of using complementary approaches for their successful development.

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