Range-wide pangenomics reveals vulnerability and adaptation in a sedentary bird

Structural genetic variants are known to underlie evolutionary adaptations, but have never been evaluated across the entire geographic range of a species. We constructed the first range-wide pangenome to evaluate how such variants may influence conservation efforts of the Montezuma quail (Cyrtonyx montezumae). Profiles of local adaptation, population structure, and genomic diversity all support a history of isolated glacial refugia and ring-like range expansion. Genomic offset analyses and forward-time simulations consistently indicated that isolated, peripheral populations are particularly vulnerable to climate change. Proactive management (e.g., translocations) could alleviate genetic erosion in fragmented, peripheral populations of this secretive bird. Our study demonstrates that in wild populations, structural variants can be both significant drivers of adaptive potential and genomic sentinels of sustainability.