Topographic fragmentation shapes maternal lineage divergence and plastome variation in the seed dispersal limited alpine herb Rhodiola bupleuroides

The fragmented landscape of the Qinghai–Xizang Plateau (QXP) is widely recognized as a driver of speciation. However, the relative contributions of physical topographic barriers versus environmental heterogeneity in shaping the fine-scale genetic structure of alpine plants remain debated. Particularly for species with limited seed dispersal, population plastomic evidence remains limited regarding the extent to which topographic fragmentation restricts seed-mediated gene flow and contributes to maternal lineage differentiation. Here, we employed Rhodiola bupleuroides as a model system, sequencing whole-chloroplast genomes of 468 individuals from 19 populations across its known range to investigate the relative roles of geographic isolation and environmental heterogeneity in shaping plastome genetic structure. Phylogenetic and molecular clock analyses recovered four maternal lineages, indicating that intraspecific divergence initiated at 3.88 Ma [2.83–5.31 Ma], with subsequent lineage splits extending into the Early Quaternary. Spatial genetic analyses showed a stronger association of plastome genetic structure with geographic isolation than with environmental heterogeneity (IBD > IBE; geographic distance: Mantel r = 0.578, P = 0.0001; environmental distance: Mantel r = 0.275, P = 0.0001). The major genetic discontinuities were spatially aligned with the mountain–canyon–river configuration of the QXP and adjacent mountains, suggesting that topographic barriers provide a primary spatial template for the long-term restriction of seed-mediated maternal gene flow. Beyond spatial isolation, lineage-specific plastome variation was also evident: the high-diversity Hengduan Mountain lineage was characterized by elevated chloroplast DNA diversity and enriched complex SSR motifs, whereas the southwestern plateau lineage combined stronger codon usage bias with lower nucleotide diversity and reduced retention of complex SSR motifs. These contrasts indicate that geographically isolated lineages have embarked on distinct plastome evolutionary trajectories associated with their specific topographic and habitat contexts. Together, these results suggest that while topographic fragmentation and restricted dispersal primarily shape maternal lineage divergence, environmental heterogeneity and lineage-specific demographic history further shape fine-scale plastome variation. This study provides high-resolution plastome-based evidence for geography-associated maternal lineage divergence in a seed-limited alpine herb on the QXP.