Genomic Insights Into Introgression Between <i>Quercus aquifolioides</i> and Its Sympatric Relatives Across Elevational Gradients

Geographically widespread species tend to have more opportunities to hybridise with different related species. However, the evolutionary consequences of such multi-species hybridisation are still poorly understood. In the Hengduan Mountains of southwest China, Quercus aquifolioides and its closely related species form two types of elevational hybrid zone in different geographical areas (i.e., Q. aquifolioides-Q. guyavaefolia-Q. longispica and Q. aquifolioides-Q. spinosa). Here, we investigated genome-wide patterns of introgression between Q. aquifolioides and its sympatric relatives to assess the evolutionary consequences of multi-species hybridisation. A new assembled genome of Q. longispica as a reference genome and whole-genome resequencing data of these focal oaks were used in this study. Our results showed that bidirectional gene flow occurred between Q. aquifolioides and its sympatric relatives, and candidate genomic regions derived from introgression were broadly distributed across the oak genome. Local introgression with different sympatric relatives has fuelled the intraspecific divergence of Q. aquifolioides between two regions with different species compositions. We found genomic signatures of positive selection in some candidate introgressed regions. Putative adaptation signals were detected in candidate introgressed genes with diverse functions, including stress response and organism development and growth. In addition, we identified the genomic targets of environment-associated selection in Q. aquifolioides, some of which were located in candidate introgressed regions. In sum, this study demonstrates that local introgression with relatives is a non-negligible mechanism facilitating intraspecific divergence and reveals putative adaptive introgression between Q. aquifolioides and its sympatric relatives.