The impact of Quaternary climate change on the historical population dynamics of Psammochloa villosa, a typical desert herb from northwest China

Climatic oscillations and geographic barriers since the Quaternary have profoundly influenced plant distribution patterns, driving substantial species differentiation through range fragmentation. Investigating the interplay between genetic structure divergence and population dynamics under climatic forcing remains a central challenge in evolutionary biology. Psammochloa villosa (Poaceae), a dominant perennial grass endemic to the Inner Mongolian Plateau's desert steppe, serves critical functions in grassland restoration and livestock forage provision. Notably, its wind-pollination strategy and distant hybridization capacity establish this species as a model system for studying panmictic population equilibrium. This study employs a dual-marker approach, combining 10 low-copy nuclear gene loci (LCNG) with 13 SSR markers, to elucidate the population genetic architecture across 43 natural populations ( n  = 210 individuals) spanning the distribution range of P. villosa . The results showed that the populations of P. villosa were distinctly divided into two major branches, Group 1 and Group 2, separated by the Yinshan Mountains, with Group 2 exhibiting higher genetic diversity ( H _d = 0.990, π  = 0.00145). The populations showed significant diversity and phylogeographic structure, with the majority of genetic variation originating from differences between populations ( F _ST (LCNG) = 0.766; F _ST (SSR) = 0.577). The Mantel test revealed a positive correlation between genetic distance and geographic distance. Subsequent correlation analysis of genetic differentiation (measured by F _ST ) with climatic factors demonstrated an overall positive association, although only elevation showed a statistically significant correlation with F _ST values. Demographic history analyses revealed that both Group 1 and Group 2 exhibited smaller effective population sizes compared with N _A . Phylogenetic divergence analysis estimated that P. villosa and Achnatherum splendens diverged approximately 3.26 Ma, whereas the differentiation between Group 1 and Group 2 initiated around 0.38 Ma. Notably, bidirectional yet asymmetric gene flow was detected between the two groups. Geographical barrier analysis identified significant genetic discontinuities corresponding to major mountain ranges, including the Yinshan, Helan, Ordos Plateau, and Yabulai mountains. These findings collectively suggest that Quaternary uplift of the Tibetan Plateau, coupled with the divergent monsoon influences east and west of the Yinshan Mountains and progressive habitat fragmentation, have driven the observed genetic differentiation in P. villosa populations through environmental adaptation.