Abstract
Genomic tools have advanced our understanding of species and population structure, but distinguishing neutral from adaptive evolution remains challenging due to limited methods for 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), a monophyletic group of seven species that diversified under sympatric, parapatric, and allopatric speciation. 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, we examined how phylogenetic signals are distributed across their foliar reflectance spectra. Partial redundancy analyses revealed that IBE explains more phenotypic variation than IBD among sympatric species, particularly in certain spectral regions and traits derived from spectra. Phylogenetic generalized least squares 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 concentration and anthocyanin levels. These results demonstrate that foliar reflectance spectra can be used to capture adaptive differentiation and evolutionary history across scales, offering a powerful, nondestructive tool for linking phenotype, environment, and evolutionary processes in long-lived plant lineages.