Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Juglans cathayensis Dode) 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. We sequenced 30 individuals of Juglans cathayensis from 2021 to 2023 in subtropical China. All fresh leaf samples were dried with silica gel and stored at -20 °C in the Lushan Botanical Garden (Jiujiang, Jiangxi). Total genomic DNA was extracted from leaf tissue using a modified CTAB method. Paired-end sequencing libraries were constructed with an insert size of 400 bp and whole-genome resequencing (> 15× coverage) was performed on the MGI DNBSEQ-T7 platform.