Biodiversity conservation calls for spatial explicit approaches to maximize the representation and persistence of genetic diversity given species idiosyncratic threats in mosaic landscapes, but conservation planning methodologies seldom account for this. Here, we introduce a novel approach that uses proxies of genetic diversity to identify conservation areas, applying systematic conservation planning tools to produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa specific tolerance to human-modified habitats and their extinction risk status. We illustrate our approach with crop wild relatives (CWR) because their intra- and interspecific diversity is important for crop breeding and food security. Although we focus on Mesoamerican CWR within Mexico, our methodology offers new opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.
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