Climate change is likely to alter the selective pressures that drive shifts in adaptive variation. For species with long life histories and low dispersion capacities, rapid climate change could impede the migration of beneficial alleles and their ability to track changing environments. Disentangling the processes of adaptive genetic variation in tree species has important implications for conservation and forest management. In this study, we used landscape genomic approaches and phenotypic data from range-wide sampling to investigate the adaptive genetic and phenotypic variation of the oak Quercus longinux, which is endemic in Taiwan. Among 2,000 single-nucleotide polymorphisms (SNPs) generated by double-digested restriction-site associated DNA (ddRAD) sequencing from 205 individuals, 35 drought- and freeze-resistance genes exhibited signatures of natural selection driven by various environmental pressures. GradientForest and redundancy analysis showed that these putative adaptive SNPs had elevated associations with climate and soil variations. The proportion of joint effects of demography, geology, and environments was high, indicating covariation of environmental gradients and colonization history. Compared with other populations, Q. longinux var. kuoi, a unique variety limited to southern Taiwan, exhibited substantial phenotypic, ecological, and adaptive divergence. Finally, we used the environmentally associated SNPs to estimate the genetic offset for each individual under different climate change scenarios, which revealed that edge populations in northern and southeastern Taiwan may be threatened by rising temperatures and reallocation of precipitation. Our study shed light on the pattern of environment-driven adaptation and provides prediction for future vulnerability of island oaks in subtropical and tropical regions.

climate change, genetic offset, landscape genomics, local adaptation, natural selection, Quercus