Ammopiptanthus nanus 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 H_E = 0.09) and strong interpopulation genetic differentiation (mean F_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 A. nanus aimed at maintaining genetic diversity and facilitating gene flow.

Background: Fritillaria karelinii is an endangered medicinal herb mainly distributed in Central Asia, extending to northwestern China. Due to habitat fragmentation, overharvesting, and poor natural regeneration, this species has been designated as a Grade II national key protected species in China. Methods: To inform effective conservation strategies, we assessed the genetic diversity and population structure of F. karelinii using single nucleotide polymorphism (SNP) loci obtained via genotype-by-sequencing (GBS). A total of 87 individuals from 11 sampling sites across the Tacheng region in northern Xinjiang were genotyped, representing the species’ known extant distribution in China. Results: A relatively high level of genetic diversity (mean H_E = 0.1461) was detected in the species, and Bayesian assignment divided the sampled populations into two subtle but detectable genetic clusters. Conclusions: The relatively high diversity may be attributed to the edge-population effect and long-lived life-history traits, while the weak differentiation between the two groups may reflect restricted gene flow and genetic drift resulting from habitat isolation. Based on these findings, we propose conservation actions including immediate fencing of habitats to exclude livestock, ex situ germplasm collection separately from the two genetic groups as distinct management units, and cautious evaluation of potential germplasm introduction from Central Asia to broaden the genetic base while preserving local adaptation.

Helianthemum songaricum and H. ordosicum are two shrubs with a disjunctive distribution in Central Asia and northwestern China. For conservation purposes, we used genotyping by sequencing (GBS) to investigate their evolutionary history and population genetic structure. Based on the GBS data, H. songaricum populations showed considerable genetic difference from H. ordosicum populations, and H. songaricum populations are strongly genetically differentiated from each other within the isolated valleys in the Tianshan Mountains. We speculated that the lineage split between H. ordosicum and H. songaricum might be resulted from uplift of the northern Tibetan Plateau and the Tianshan Mountains in the late Tertiary, and the disjunctions between the two species may represent two co-temporal migration events between Middle East and Central Asia/Ordos Plateau. Based on our SNP data, we propose conservation strategies for the two species.