Transposable elements are entangled in rapid adaptation to climate change

Biodiversity conservation is urged at biodiversity hotspots that are under constant threat from anthropogenic development, yet a careful examination of the adaptive potential is a prerequisite for action. The Levant is considered a biodiversity hotspot and the distribution edge for many species, including important crop wild relatives. This region is under accelerated desertification and constantly disturbed by human activities, thus urging intervenient action. We collected and sequenced 300 wild barley plants along an eco-geographic gradient following a unique ecological-genetic sampling design. This scheme enabled to overcome the tight correlation between environmental and geographic distances. Phenotypic data was collected from 3600 progeny plants over three years and enabled to identify adaptive haplotype blocks comprised of phenological regulating genes tightly linked to drought and heat responsive genes. These haplotype blocks were highly enriched for transposable elements insertions, likely regulating genetic variation around adaptive genes, especially in stressed populations. Ecological and evolutionary models using over 2600 observations were combined to predict maladaptive risk, indicating that populations will be funneled into higher water availability refugia habitats while increasing isolation. Our findings highlight the main factors affecting rapid local adaptation and provide important recommendations for biodiversity management and conservation.