Phenotypic plasticity is the major determinant of changes in phenotypic integration in Arabidopsis

•  The way in which novel genetic variation affects the patterns of phenotypic integration in natural populations is addressed here. •  An experimental study is presented of the variability in integration caused by interpopulation hybridization and consequent genetic reshuffling, as well as by changes in the physical environment in the model system Arabidopsis thaliana (Brassicaceae). •  Our results show a basic invariance of sets of covarying traits in A. thaliana, with changes in nutrient availability as the principal factor accounting for major departures from the general pattern and where differences in the genetic background of the recombinant lines are less important. In A. thaliana, the relationships among vegetative and reproductive traits form distinct clusters in multivariate space. A high degree of congruence was found between differences in the multivariate mean phenotype and the pattern of phenotypic integration, as expected on the basis of recent theoretical models. •  This relationship might indicate strong selective constraints acting on the specialized life history of these populations, which are spring ephemerals inhabiting ruderal habitats and prone to competition avoidance.