Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis) despite extensive hybridization in subtropical China

Understanding how natural selection sustains genetic differentiation despite ongoing hybridization remains a central question in evolutionary biology. Here, we integrated range-wide whole-genome resequencing data and ecological niche modeling to elucidate the evolutionary history, local adaptation, and hybridization patterns of Juglans cathayensis, a walnut species widely distributed across subtropical China. Our analyses revealed that Chinese walnut comprised two genetic clusters corresponding to its two recognized varieties, which were further subdivided into three lineages: the East lineage, consisting exclusively of J. cathayensis var. formosana individuals; and the West and Admixed lineages, comprising genetically pure and admixed individuals of J. cathayensis var. cathayensis, respectively. The admixed populations formed a hybrid zone in the ecotone between the East and West lineages. Divergence between the East and West lineages dates to the Middle Pliocene, with persistent bidirectional gene flow until the mid-Pleistocene, likely driven by long-term local adaptation to niche differences between eastern and western China. Genomic regions of differentiation may result from divergent selection under gene flow and divergent sorting of ancient polymorphisms. Moreover, we identified positively selected genes and environment-associated loci involved in ecological adaptation, underscoring their role in promoting intraspecific differentiation. Bayesian genomic cline analysis detected limited introgression of adaptive loci in the hybrid zone, suggesting that natural selection sustains divergence in genomic regions associated with local adaptation, while neutral loci are homogenized through hybridization. Together, these findings provide novel insights into the evolutionary mechanisms shaping plant diversity in subtropical China, a region recognized as an evolutionary cradle.