Genomic variation of a keystone forest tree species reveals patterns of local adaptation and future maladaptation

Local adaptation is key for ecotypic differentiation and species evolution. Understanding the underlying genomic patterns allows the prediction of future maladaptation and ecosystem stability. Here we report the whole-genome resequencing of 865 individuals from 100 range-wide populations of European beech (Fagus sylvatica), which is one of the most important forest tree species in Europe. We show that genetic variation closely mirrors geography. Adaptive variation identified by genotype-environment associations exhibits highly polygenic architectures, involving thousands of associated sequence variants across the genome. By modelling the ‘genomic offset’ of these sequence variants under projected future climate conditions, we identify broad- and fine-scale variation highlighting geographic regions as well as populations at potential elevated risk of mortality or local extinction. Our results emphasize the importance of considering natural genetic variation for forest conservation under climate change conditions.