Morphological and genetic variations of Sophora davidii populations originating from different altitudes in the mountains of southwestern China

•Leaf morphological and genetic variability of S. davidii varied across altitudes.•Leaf area and leaf thickness increased linearly with increasing altitude.•Genetic diversity exhibited an increasing trend with increasing altitude.•Altitude lead to diverse genetic differentiation pattern within and among populations.

Sophora davidii Franch. is a multipurpose shrub with significant economic and ecological importance in karst mountainous regions of southeastern China. These mountainous ecosystems are associated with altitudinal gradients that can lead to major morphological and genetic differences in the species. We examined the morphological and genetic variation of this species at six sites with different altitudes (600 m–1950 m asl). Significant morphological variations (p < 0.01) were observed for leaf area and leaf thickness across the populations, with linear increasing trends along increasing altitude. Genetic diversity exhibited an increasing trend with increasing altitude, and the highest diversity (PPB = 87.66%; h = 0.2765; I = 0.4206) was observed at 1950 m asl, whereas the lowest genetic diversity (PPB = 75.97%; h = 0.2428; I = 0.3701) existed at 870 m asl. AMOVA analyses indicated that variation existed mainly within populations (89.49%), in line with the high level of gene flow (Nm = 4.6629). In addition, altitude correlated with percentage of polymorphic bands (PPB) and Shannon’s information index (I); PPB and I correlated with leaf length and leaf thickness. Our results provided strong evidence that variations in morphological and genetic parameters of S. davidii populations reflected morphological and genetic adaptations to native habitats, and highlighted its ecological and evolutionary implications along altitudinal gradients of karst mountainous ecosystems.