Foliar spectral signatures reveal adaptive divergence in live oaks (Quercus section Virentes) across species and environmental niches

Genomic tools have transformed our understanding of species and population genetic structure in landscapes. However, discerning the impacts of neutral and adaptive evolutionary forces remains challenging, largely due to the scarcity of tools capable of measuring a broad spectrum of phenotypic traits. We used spectroscopic data from preserved leaves to test for adaptive divergence among populations of live oaks (Quercus section Virentes) across genetic and phylogenetic levels. The monophyletic lineage includes seven species that diversified under sympatric, parapatric and allopatric speciation modes. We used 427 individuals to test for isolation-by-distance (IBD) and isolation-by-environment (IBE), as well as the influences of selection and phylogenetic inertia on traits. Finally and to examine how phylogenetic signals are distributed across their foliar reflectance spectra. Partial redundancy analyses (pRDA) revealed that (IBE explains more phenotypic variation than (IBD among sympatric species, particularly in certain spectral regions and traits derived from spectra. Across the phylogeny, phylogenetic generalized least squares (PGLS) models show that environmental variables—including minimum temperature of the coldest month and annual precipitation—predict traits related to stress tolerance across climatic gradients, such as lignin content and anthocyanin levels. These results demonstrate that leaf reflectance spectra can be used to capture adaptive differentiation and evolutionary history across scales, offering a powerful, non-destructive tool for linking phenotype, environment, and evolutionary processes in long-lived plant lineages.