Climate change–mediated catastrophe exacerbates genomic vulnerability of a coastal cycad

Human-induced climate change severely threatens biodiversity, yet many studies focus on its direct effects on species maladaptation (e.g., genomic vulnerability), largely overlooking indirect impacts such as climate change-mediated catastrophic effects (CCCE). These CCCEs may be particularly profound for species susceptible to parasite attacks or habitat disturbances. We examined Cycas revoluta, a coastal species facing range-wide extirpation from two major CCCEs: sea-level rise and the recent invasion of a specialist scale insect. Using genome-wide SNP data and landscape analyses, we identified two temperature- and precipitation-structured conservation units (CUs) and assessed CCCEs on genomic vulnerability. Central Ryukyu populations (Okinawa) exhibited the highest maladaptation to future climate despite having less CCCEs. Conversely, in the northern Ryukyus, the CCCE is expected to devastate more climate-resilient populations, thereby exacerbating genomic vulnerability. Landscape analyses revealed inadequate natural genetic rescue, underscoring the need for assisted gene flow. Our findings are the first to demonstrate that overlooking indirect climate change effects biases genomic vulnerability assessments and misinforms conservation efforts. We proposed the CU-specific management for C. revoluta that accounts for threats of CCCE and emphasized the critical role of catastrophic events in evaluating genomic vulnerability for susceptible species.