Repeated Evolutionary Changes of Leaf Morphology Caused by Mutations to a Homeobox Gene

Elucidating the genetic basis of morphological changes in evolution remains a major challenge in biology [1–3]. Repeated independent trait changes are of particular interest because they can indicate adaptation in different lineages or genetic and developmental constraints on generating morphological variation [4–6]. In animals, changes to “hot spot” genes with minimal pleiotropy and large phenotypic effects underlie many cases of repeated morphological transitions [4–8]. By contrast, only few such genes have been identified from plants [8–11], limiting cross-kingdom comparisons of the principles of morphological evolution. Here, we demonstrate that the REDUCED COMPLEXITY (RCO) locus [12] underlies more than one naturally evolved change in leaf shape in the Brassicaceae. We show that the difference in leaf margin dissection between the sister species Capsella rubella and Capsella grandiflora is caused by cis-regulatory variation in the homeobox gene RCO-A, which alters its activity in the developing lobes of the leaf. Population genetic analyses in the ancestral C. grandiflora indicate that the more-active C. rubella haplotype is derived from a now rare or lost C. grandiflora haplotype via additional mutations. In Arabidopsis thaliana, the deletion of the RCO-A and RCO-B genes has contributed to its evolutionarily derived smooth leaf margin [12], suggesting the RCO locus as a candidate for an evolutionary hot spot. We also find that temperature-responsive expression of RCO-A can explain the phenotypic plasticity of leaf shape to ambient temperature in Capsella, suggesting a molecular basis for the well-known negative correlation between temperature and leaf margin dissection. •Leaf shape evolution in Capsella is due to altered expression of a homeobox gene•The high-lobing allele likely arose by novel mutation in Capsella rubella•RCO-A mediates phenotypic plasticity of leaf shape to ambient temperature Leaf shape varies greatly among plant species and is modulated by the environment. Sicard et al. demonstrate that altered expression of a homeobox gene underlies different leaf shapes between two species of shepherd’s purse (Capsella). The temperature-responsive expression of this gene mediates plasticity of leaf shape to ambient temperature.