Adaptive Genomic Divergence Across Altitudes in <i>Capsella bursa‐pastoris</i>

ABSTRACT Understanding how natural selection drives local adaptation is fundamental to evolutionary biology. Capsella bursa‐pastoris , a close relative of Arabidopsis thaliana , is widely distributed across diverse habitats worldwide. However, the genetic basis underlying its local adaptation remains unclear. Here, we analyzed 40 individuals from 14 populations across China using population genomic approaches to investigate genetic structure and adaptive selection. Our results revealed a clear genomic divergence between western high‐altitude and eastern low‐altitude populations of C. bursa‐pastoris . We identified 54 candidate genes under positive selection associated with altitudinal divergence, including energy metabolism, photosynthesis, signal transduction, growth regulation, and membrane transport. Most of these genes were located in subgenome CbpB, suggesting that this subgenome harbors an enrichment of loci potentially involved in adaptive differentiation. Moreover, genotype‐environment association and partial redundancy analyses highlighted a strong influence of ecological factors on genetic variation. Notably, loci associated with environmental variables were primarily linked to responses to light, temperature, and water availability, indicating their likely roles in local adaptation. Overall, our findings indicate that ecological selection is an important driver of population divergence in C. bursa‐pastoris and provide a robust genomic framework for understanding its adaptation across heterogeneous environments.