Population genetic structure reveals asymmetric hybridization between Pinus pumila and P. parviflora var. Pentaphylla in the Hakkoda Mountains, Northern Japan.

Interspecific hybridization can facilitate rapid adaptation to novel environments despite potential fitness reductions. The genomic regions of Pinus parviflora var. pentaphylla inhabiting higher temperatures could increase the fitness of the recipient alpine species Pinus pumila, which has adapted to lower temperatures, particularly under global warming. Using exome-capture techniques to overcome challenges of large Pinus genomes, we investigate the genome-wide hybridization patterns between these species in the Hakkoda Mountains, Japan. Hybrids predominantly occurred at mid-elevation and contained P. pumila chloroplasts, suggesting P. pumila is the most recent pollen parent. Genome-wide introgression patterns suggested frequent backcrossing with P. pumila and limited backcrossing with P. parviflora var. pentaphylla, likely owing to geographic isolation, phenological differences in flowering time, and natural selection favoring hybrids in specific environmental contexts. Specifically, tall hybrids may be advantageous in light competition at mid-elevations covered with moorland vegetation, whereas shorter pure P. pumila individuals may be favored in high-altitude wind-exposed fellfields. Hybrids with shorter heights may be disadvantaged in deciduous broad-leaved forests at lower altitudes compared to taller pure P. parviflora var. pentaphylla. Our findings provide insights for future functional analyses of introgressed genes to elucidate the adaptive significance of such hybridization patterns along elevational and environmental gradients.