Pinus densata Mast. is considered a homoploid hybrid species that originated from the putative parent species Pinus tabuliformis Carr. and Pinus yunnanensis Franch., but the mechanism of the adaptive differentiation of P. densata and its parents in native habitats has not been reported. Therefore, the overlapping distribution areas between P. densata and P. yunnanensis in the heart of the Hengduan Mountains were chosen. The adaptive differentiation mechanism of the homoploid hybrids and their parents with respect to the elevational gradient was studied based on the morphological features and the different strategies of recruiting endophytic microbial communities from the rhizosphere soil. The results showed that (1) the height and diameter at breast height were the greatest at 2600 m and 2900 m, and from 2700 m to 2900 m, three-needle pines (P. yunnanensis-like type) transitioned into two-needle pines (P. densata-like type). (2) The recruitment of rhizosphere microbial communities was driven by the C, N, P and pH values which showed significant elevation features. (3) There was a significant difference in the recruitment strategies of endophytes between the P. yunnanensis-like type and P. densata-like type. Pinus densata mainly reduced the recruitment of Mucoromycota (fungi) and increased the recruitment of Proteobacteria (bacteria), which may be related to environmental adaptability, quorum sensing and the metabolism of auxiliary factors and vitamins at high elevations. (4) The root endophytic microbiome was enriched in the rare groups from the rhizosphere soil microbial pool. The results of this study provide new insights and new ideas for environmental adaptability and differentiation in homoploid hybrid speciation.
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