Understanding the processes that accompany or facilitate the origin of phenotypic novelty in nature has always been of great interest to biology, but the molecular and computational tools required to address these long-standing questions have become available only recently. The advent of genomic and post-genomic science holds great promise for students of organismal evolution. We focus on plants as the preferred model organisms for our research, because plants are often more amenable to evolutionary genetics studies, e.g. plants can be crossed rather easily and their sessile nature facilitates the estimation of fitness effects (the ‘adaptive value’) of individual traits, chromosomal segments, or even individual genes in the wild. An important motivation for our work also lies in the immense potential conservation value of phenotypes and genotypes we study, especially in ecologically important ´foundation species´, and in wild relatives of domesticated taxa.