Abstract

Karst tiankengs—giant enclosed sinkholes—harbor humid, shaded forests that may buffer climate stress yet isolate populations. Here, we generated a near telomere-to-telomere genome assembly for the endangered karst tree Magnolia aromatica and resequenced 26 populations across tiankeng interiors and surrounding habitats in southwest China. Population genomics resolved four lineages and indicated a history of divergence with gene flow constrained by strong dispersal barriers. At the lineage scale, tiankeng-associated populations exhibited intermediate genomic diversity and mutation load relative to non-tiankeng lineages. At fine spatial scales, however, tiankeng-interior populations showed reduced diversity and elevated deleterious burden compared with nearby exterior populations, consistent with demographic isolation and strong genetic drift. We detected lineage-specific selection signals in genes related to photosynthesis and carbon fixation, and shading experiments revealed that seedlings exhibited high mortality under strong light but survived and grew well under deep shade. Forecasts combining species distribution models, genomic offset, and mutation-load prediction identified future risk hotspots near barriers and suggested that genomic erosion may compound climate vulnerability in parts of the range. Together, these results indicate that karst tiankengs can function as nested microrefugia that promote persistence while constraining connectivity and long-term evolutionary potential, with important implications for conserving edaphic specialists under climate change.