Abstract

Background and Objectives: The hyperarid–semiarid gradient of the western Andes, from the coastal Atacama Desert to central Mediterranean Chile, hosts exceptional plant endemism driven by palaeoclimatic oscillations, rugged topography and long-term isolation. Here, we use the columnar cactus genus Leucostele as a model to (1) quantify the influence of geographic isolation and topographic heterogeneity on genome-wide divergence, and (2) test whether zones of secondary contact foster genetic admixture. Methods: We genotyped 151 individuals from 20 populations of Leucostele using 9397 SNPs to assess spatial genetic structure, isolation by distance and the influence of terrain ruggedness and geographic isolation on admixture. Key Results: Spatial ancestry analyses delineated ten latitudinal genetic clusters, with 8 populations exhibiting >75 % ancestry assignment to a single cluster and 12 showing varying degrees of admixture. Genetic differentiation increased with geographic distance, revealing strong isolation by distance across the Atacama Desert to southern central Chile. Admixture, quantified as Shannon entropy, varied among populations and decreased significantly with both increasing terrain ruggedness and greater geographic isolation. Conclusions: Our study reveals that rugged topography and spatial isolation promote genomic divergence by limiting gene flow and fostering distinct genetic clusters while less rugged terrain facilitates secondary contact and admixture, showing that these barriers remain permeable and reproductive isolation is incomplete. This dual influence of topographic heterogeneity underpins the dynamic evolutionary mosaic observed across the coastal Atacama Desert–central Chile gradient. © The Author(s) 2025. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For commercial re-use, please contact [email protected] for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact [email protected].