Natural selection can remove maladaptive genotypic variance from populations, leaving reduced phenotypic variation as a signal of its action. Hybrid populations offer a unique opportunity to study phenotypic variance before selection purifies it, as these populations can have increased genotypic and phenotypic variance than can reveal trade-offs and selection conflicts not visible, or visible to a lesser extent, in unadmixed populations. Here, we study the interactions between a fungal leaf rust disease (Melampsora medusae) and stomata and ecophysiology traits in a set of hybrid and unadmixed individuals formed by natural matings between Populus balsamifera, P. trichocarpa, P. angustifolia, and P. deltoides. Phenotypes were measured on cloned genotypes grown in a common garden and genotyped at 227K SNPs with GBS.Our analyses indicate hybridization decreases disease resistance and increases the variance of stomatal ratio (SR), or the ratio of upper leaf surface stomata density to total stomata density. Heritability of SR was high in admixed populations (H 2 = 0.72) and covaries strongly with the proportion of P. balsamifera ancestry in a genome; thus, selection could effectively reduce disease by selecting for low values of stomatal ratio.However, selection conflicts present in some admixed populations may prevent adaptation to pathogens as a result of these populations being unable to occupy adaptive trait space along the growth-defense spectrum.These results suggest an important role for SR and stomatal patterning traits as a target of pathogen induced selection to achieve local fitness optima. Additionally, we demonstrate that hybridization is capable of generating, or magnifying maladaptive intermediate phenotypes to reveal trade-offs and selection conflicts.ABSTRACT 1 Natural selection can remove maladaptive genotypic variance from populations, leaving reduced phenotypic variation as a 2 signal of its action. Hybrid populations offer a unique opportunity to study phenotypic variance before selection purifies it, as 3 these populations can have increased genotypic and phenotypic variance than can reveal trade-offs and selection conflicts not 4 visible, or visible to a lesser extent, in unadmixed populations. Here, we study the interactions between a fungal leaf rust disease 5 (Melampsora medusae) and stomata and ecophysiology traits in a set of hybrid and unadmixed individuals formed by natural 6 matings between Populus balsamifera, P. trichocarpa, P. angustifolia, and P. deltoides. Phenotypes were measured on cloned 7 genotypes grown in a common garden and genotyped at 227K SNPs with GBS. Our analyses indicate hybridization decreases 8 disease resistance and increases the variance of stomatal ratio (SR), or the ratio of upper leaf surface stomata density to total 9 stomata density. Heritability of SR was high in admixed populations (H 2 = 0.72) and covaries strongly with the proportion 10 of P. balsamifera ancestry in a genome; thus, selection could effectively reduce disease by selecting for low values of st...