Although genetic diversity ultimately determines the ability of organisms to adapt to environmental changes, conservation assessments like the widely used International Union for Conservation of Nature (IUCN) Red List Criteria do not explicitly consider genetic information. Including a genetic dimension into the IUCN Red List Criteria would greatly enhance conservation efforts, because the demographic parameters traditionally considered are poor predictors of the evolutionary resilience of natural populations to global change. Here we perform the first genomic assessment of genetic diversity, gene flow, and patterns of local adaptation in tropical plant species belonging to different IUCN Red List Categories. Employing RAD-sequencing we identified tens of thousands of single-nucleotide polymorphisms in an endangered narrow-endemic and a least concern widespread morning glory (Convolvulaceae) from Amazonian savannas, a highly threatened and under-protected tropical ecosystem. Our results reveal greater genetic diversity and less spatial genetic structure in the endangered species. Whereas terrain roughness affected gene flow in both species, forested and mining areas were found to hinder gene flow in the endangered plant. Finally we implemented environmental association tests and genome scans for selection, and identified a higher proportion of candidate adaptive loci in the widespread species. These mainly contained genes related to pathogen resistance and physiological adaptations to life in nutrient-limited environments. Our study emphasizes that IUCN Red List Criteria do not always prioritize species with low genetic diversity or whose genetic variation is being affected by habitat loss and fragmentation, and calls for the inclusion of genetic information into conservation assessments. More generally, our study exemplifies how landscape genomic tools can be employed to assess the status, threats and adaptive responses of imperiled biodiversity.

Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species’ entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (FST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.