Genomic signatures of adaptive introgression in Chinese elm (Ulmus parvifolia) from subtropical broad-leaved forests and implications for climate-induced vulnerability

Adaptive introgression plays a pivotal role in mitigating the survival risks of subtropical broad-leaved forests (SBLFs) under climate change. In this study, we investigated genomic-wide adaptive introgression and its contribution to climate adaptation and vulnerability in SBLF trees. We performed whole-genome resequencing of 311 individuals from 44 natural populations of Ulmus parvifolia, a keystone SBLF species, and identified three distinct genetic lineages shaped by geographic isolation and ecological heterogeneity. By integrating population genomics, demographic modeling, and hybridization statistics, we uncovered substantial gene flow from both the southeastern and northern lineages into the central lineage (migration rates = 3.42 × 10 -5 and 8.57 × 10 -5 ). As a result, these central populations showed higher genetic diversity ( π = 0.0055) and lower genetic load, and genetic vulnerability analysis further demonstrated their increased adaptive potential and reduced genetic offsets. Furthermore, adaptively introgressed genes, such as ZFP3 and KUA1 , displayed complementary functions along geographic patterns in response to biotic and abiotic stress, which enhanced the adaptive capacity of the central lineage under complex subtropical ecology. Overall, our findings reveal adaptive introgression as a key mechanism for generating climate-resilient genetic variation, and we should prioritize naturally introgressed populations in conservation strategies to enhance the resilience of subtropical forests to climate change.