The Jinsha-Yalong River Divide: A Core Floristic Boundary Shaping Asymmetric Nuclear-Chloroplast Genetic Differentiation in Allium macranthum.

Abstract

The hypothesis that mountain uplift creates riverine barriers to alpine plant gene flow is widely accepted in biogeography, yet how these barriers drive species genetic differentiation remains poorly understood. Here, we tested this hypothesis using Allium macranthum (section Bromatorrhiza), a diploid-tetraploid alpine herb endemic to southwest China with a core distribution in the Jinsha-Yalong River basin. We genotyped 280 individuals from 22 range-wide populations (including sympatric cytotypes) using nuclear ITS and two chloroplast (cpDNA) fragments (trnL-F and rps16). Population karyotypic characteristics were investigated, and population genetic structure, differentiation and divergence time were estimated, with biogeographical history investigated. Our results reveal striking asymmetric genetic diversity, with biparentally inherited ITS showed far higher haplotype diversity (Hd = 0.95) than cpDNA markers (trnL-F: Hd = 0.54; rps16: Hd = 0.48). Meanwhile, significant population differentiation were revealed, with three deeply divergent phylogenetic clades detected, which corresponding to different geographic regions: the internal Hengduan Mountains between the Jinsha and Yalong Rivers (I), the external Hengduan Mountains (E), and Qinling Mountains (Q). Karyotypic analyses demonstrated that A. macranthumis characterized by pronounced polyploidy (coexisting diploid and tetraploid forms), and the tetraploid populations exhibited a significantly high level of karyotype asymmetry.Divergent time estimation showed that the intraspecific differentiation of A. macranthum was approximate at 6.72-1.91 Ma, coinciding with the intense uplift of the HMR and formation of the Jinsha-Yalong drainage system. Our findings suggest that Early Pleistocene mountain building might promote river incision, expediting the differentiation of A. macranthum, while riverine barriers, ploidy variation, and reproductive shifts may have synergistically shaped the observed asymmetric differentiation.