Ecophysiological transition mediated by hybridization in a hybrid pine species complex

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of <i>Pinus densata</i>, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide <i>in situ</i> assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between <i>P. densata</i> and its putative parental species <i>P. tabuliformis</i> and <i>P. yunnanensis</i>, with <i>P. densata</i> demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled <i>P. densata</i> in most traits. Gene expression revealed 19%-10% of 34,000 examined genes as differentially expressed in <i>P. densata</i> and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%-6% in F1s, 10%-12% in <i>P. densata</i>) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of <i>P. densata</i> to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.