Small Population Size and Low Levels of Genetic Diversity in an Endangered Species Endemic to the Western Tianshan Mountains

<i>Ammopiptanthus nanus</i> is an endangered evergreen shrub endemic to the western Tianshan Mountains. Genetic diversity and population structure of this species were assessed using single-nucleotide polymorphism (SNP) loci identified via double-digest restriction site-associated DNA (ddRAD) sequencing. In this study, a total of 42 individuals were sampled from seven populations located in valley habitats across the western Tianshan Mountains. A low level of genetic diversity (mean <i>H</i>_E = 0.09) and strong interpopulation genetic differentiation (mean <i>F</i>_ST = 0.4832) were observed in the species, indicating substantial genetic structuring among populations. Population structure analyses using Admixture analysis, principal coordinate analysis (PCA), and maximum likelihood trees yielded congruent patterns, supporting four genetically distinct groups within the western Tianshan Mountains. Genetic drift and inbreeding, likely induced by habitat fragmentation, appear to be primarily responsible for the low genetic diversity, while restricted gene flow probably shaped the pronounced genetic structure. Based on our findings, we recommend specific conservation strategies for <i>A. nanus</i> aimed at maintaining genetic diversity and facilitating gene flow.