Evolutionary constraints decouple genetic diversity from adaptive capacity under climate change

Climate change is expected to drive widespread biodiversity loss, and species persistence may depend on migration, phenotypic plasticity, or genetic adaptation. In long-lived species with constrained life histories, however, limited dispersal and slow demographic turnover restrict these alternatives, increasing reliance on adaptive genetic responses. Under this framework, adaptive capacity is often inferred from levels of standing genetic variation within populations. Genetic diversity is therefore widely assumed to buffer populations against environmental change, yet this assumption remains largely untested. Here, we integrate population genomics, genome-environment associations, and genomic vulnerability modelling to assess adaptive capacity across the range of a desert foundation species, the saguaro cactus (Carnegiea gigantea). We identify two genetically structured lineages occupying distinct climatic niches with contrasting evolutionary trajectories under future climates. Despite higher genetic diversity and stronger genome–environment associations, southern populations exhibit elevated genomic offset and are projected to undergo near-complete loss of suitable habitat. In contrast, northern populations show lower genomic offset but remain constrained by physiological limits and restricted recruitment. Across populations, environmental conditions explain substantially more variation in performance than genetic factors, indicating a limited contribution of standing genetic variation to persistence. Our results demonstrate that genetic diversity does not reliably predict adaptive capacity under rapid climate change. By showing that populations with greater genetic diversity can nonetheless experience higher genomic mismatch and increased collapse risk, we reveal that diversity-based metrics can misrepresent vulnerability. These findings call for conservation frameworks that explicitly integrate adaptive genomic variation with projected environmental change.