Genomic structure and environmental adaptation in northern red oak: Foundations for climate-resilient forestry

Understanding genomic variation and adaptation of widespread tree species across their range is useful for predicting responses to environmental change and guiding sustainable forest management. Quercus rubra (Northern red oak) is a dominant hardwood species in eastern North America. Yet, its genomic diversity and adaptive structure remain poorly characterized. Using genotyping-by-sequencing (GBS), we generated 20,847 single nucleotide polymorphisms (SNPs) from 843 individuals sampled across 72 populations spanning the species’ native range. Population and landscape genomic analyses revealed a broadly homogenous pattern of genetic variation, with weak but significant population structure, predominantly shaped by neutral processes, including postglacial demographic history and extensive historical gene flow. To detect signatures of local adaptation, we combined F ST -based outlier detection with genotype–environment association (GEA) approaches. Across four genome scan methods, 142 SNPs were identified by at least two analytical approaches. Although temperature-related variables, particularly extreme minimum temperature (EMT), and moisture indices (MSP, SHM) showed significant associations with allele frequency variation, climate explained only a small fraction of total genomic variance. These results indicate that adaptive signals in Q. rubra are detectable but weak, consistent with polygenic adaptation involving small allele-frequency shifts. Together, our findings suggest that Q. rubra likely combines a polygenic genomic background with high within-population genetic diversity and inferred phenotypic plasticity rather than strict local adaptation to cope with environmental changes. This study provides a genomic foundation for Q. rubra and creates resources to support conservation planning, breeding programs, and the development of genomic traceability tools for provenance verification. • Continuous southwest-northeast genetic gradient within Quercus rubra. • Most genetic variation is shaped by neutral processes and demographic history. • Weak signal of local adaptation reflecting polygenic adaptation. • Plasticity and within-population genetic diversity likely drive adaptive response. • Foundational work for adaptive forest management strategies in northern red oak.