Isolation by environment overrides isolation by distance in Asterothamnus centraliasiaticus across the Qinghai–Tibet Plateau

The relative roles of isolation by distance (IBD) and isolation by environment (IBE) in shaping the genetic differentiation of species remain a central debate in plant ecology and evolutionary biology, particularly in highly heterogeneous landscapes such as the Qinghai–Tibet Plateau (QTP). Disentangling the contributions of IBD and IBE in keystone species populations is essential for elucidating the mechanistic drivers of the spatial genetic structure, local adaptation patterns, and ecosystem resilience in desert ecosystems of the plateau. This study investigated 21 typical populations of Asterothamnus centraliasiaticus , a keystone species widely distributed across desert ecosystems on the QTP. Using inter-simple sequence repeat molecular markers, we assessed the genetic diversity and examined the effects of environmental filtering on gene flow across different climatic zones. By integrating geographical and environmental data, we evaluated the relative contribution of IBD and IBE to genetic differentiation. The results demonstrated substantial genetic diversity in A. centraliasiaticus populations, with a mean number of alleles of 1.86 and Nei’s genetic diversity of 0.31. Population genetic structure analysis revealed distinct geographic clustering patterns in most populations. However, notable exceptions were observed, in which certain individuals exhibited genetic similarities with geographically distant populations. Moderate levels of genetic exchange (1.42–2.15) were observed among populations distributed across different climatic zones in the study area. IBE accounted for 21.34 % of the observed genetic variation. Among the variables, soil available phosphorus and mean annual temperature emerged as the most influential drivers of genetic differentiation, contributing 88.63 % and 79.04 % of the explained environmental variance, respectively. In contrast, IBD accounted for less than 2 % of the genetic variation. Mantel tests further confirmed the absence of statistically significant correlations between genetic differentiation and both horizontal and vertical geographic distance matrices. These findings collectively highlight that within the extreme heterogeneity of the QTP, environmental selection, rather than geographic isolation, predominantly influences the genetic structure of the keystone species. This indicates that future conservation strategies should prioritize the protection of key environmental factors rather than focus solely on habitat connectivity. • we tested the hypothesis that IBE overrides IBD in keystone species across the QTP. • We used an interdisciplinary approach that integrates population ecology with molecular genetic markers. • IBE predominantly governs genetic differentiation in A. centraliasiaticus on the QTP, significantly exceeding IBD. • Soil available phosphorus and mean annual temperature are the principal determinants of genetic structure. • Protection strategies must prioritize key environmental factors over habitat connectivity.