Habitat and Haplotype‐Specific Genetic Vulnerability Analysis Combined With a Multidimensional Scoring System Provides a New Insight for Conservation Prioritization of <i>Ephedra przewalskii</i>

<i>Ephedra przewalskii</i> is a key species in arid regions recognized for its remarkable ecological, economic, and medicinal importance. However, climate change and anthropogenic activities have severely threatened their survival, reduced genetic diversity, and increased the risk of extinction. Nonclimatic variables lack systematic integration in current modeling frameworks, and intraspecific genetic variation is similarly poorly explored. This study assessed the vulnerability and adaptive capacity of <i>E. przewalskii</i> populations by applying ensemble species distribution models (ESDMs) and Climate-Niche Factor Analysis (CNFA), incorporating climate scenarios and human activity data. Additionally, we calculated the haplotype genetic vulnerability and constructed a multidimensional scoring system that combined habitat and genetic vulnerabilities. High vulnerability was observed in regions such as Nilka County and Hotan, whereas regions such as the Ejina Banner-Hami-Heiying Mountain-Jiuquan range area exhibited reduced vulnerability for <i>E. przewalskii</i>. The habitat vulnerability decreased over time under Shared Socioeconomic Pathways 1-2.6 (SSP1-2.6) but significantly increased by the 2090s under Shared Socioeconomic Pathways 5-8.5 (SSP5-8.5). Haplotypes G, E, and A were identified as being at high risk for genetic diversity loss under SSP5-8.5. Application of the multidimensional scoring system successfully identified and prioritized key conservation hotspots-including populations in Wuheshalu, Qiemo, and Ruoqian (Tarim Basin) as well as Karamay, Wuchang, and Burqin (Junggar Basin)-based on their high haplotype diversity and vulnerability. The approach thereby offers an adaptable framework for vulnerability assessment and supporting broader conservation efforts.