Data from: Eco-evolutionary genomics reveal mountain range-specific adaptation and intraspecific variation in vulnerability to climate change of alpine endemics

Alpine chasmophytes exhibit intraspecific diversification due to range fragmentation during Holocene warming, complicating predictions of their climate vulnerability. A lack of understanding of eco-evolutionary mechanisms driving their response to climate change results in ineffective conservation efforts. To uncover the genomic basis of their diversification and explain spatial patterns of their vulnerability, we combine landscape genomics and species distribution modeling. Our model, the Campanula lehmanniana complex, occurs in three distinct central Asian mountain ranges, considered both a biodiversity hotspot and a vascular plant diversity darkspot. Genome-environment association confirmed the adaptive basis of intraspecific diversification, driven by numerous loci of small effect. Genomic and ecological data indicate mountain range-specific climate sensitivity driven by altitude, temperature, and precipitation. The cold-dry adapted group from Zeravshan-Hissar Mts will face niche decline but show a higher degree of preadaptation to future climate, while the temperate-humid group from Tian Shan shows an opposite response, with a higher risk of maladaptation despite predicted niche expansion. Maladapted populations at northern margins may require an influx of adaptive variation to cope with predicted changes. However, limited landscape connectivity between sky island habitats, combined with long migration distances required to minimize genotype-environment disruption, highlights the role of human-assisted migration in enabling evolutionary rescue. These results underscore the need to facilitate gene flow from pre- to maladapted populations and the importance of population-specific approaches to inform effective conservation strategies in heterogeneous mountain ecosystems. The results may be relevant to numerous Central Asian mountain species that show similar phylogeographic patterns.