Abstract
Tamarix austromongolica is a native species widely used for ecological restoration in the Yellow River basin. Its natural distribution aligns with the river's strong environmental gradients. Previous research based on traditional molecular markers suggested that the Yellow River acts as an efficient corridor for gene flow, leading to weak genetic differentiation in the species. However, a recent genotyping-by-sequencing study indicates a more complex genetic structure. This discrepancy reveals the limitations of low-resolution genetic markers in resolving genetic differentiation against a background of strong gene flow. Here, we utilized whole-genome resequencing to analyze genomic variation data from 112 samples collected from 20 populations in the Yellow River Basin. Our results revealed three distinct genetic lineages, each corresponding to a specific habitat: the Liujiaxia lineage (high-altitude), the Hetao lineage (arid), and the Sanmenxia lineage (saline-alkali). Demographic modeling indicated that the Liujiaxia lineage diverged first, approximately 470,000 years ago, likely due to glaciation-induced isolation. Furthermore, significant asymmetric gene flow was detected between the Hetao and Sanmenxia lineages, highlighting the role of the river as a corridor for genetic exchange. Genome-wide scans identified candidate genes associated with local adaptation in each lineage, with functions primarily related to diverse environmental stress responses, DNA damage repair, and pathogen defense. These results provide a foundation and resources for understanding the mechanisms of river-driven plant differentiation and the stress-resistant breeding of T. austromongolica.