Linking together biological models from both the molecular and population levels has the potential to provide insights that cannot be gained from the study of either level in isolation. Computational modeling provides the means to integrate and test theories which span different temporal and spatial scales, and thus provides an ideal platform for forging this link. This paper describes a preliminary model that links together three key levels of biological theory. A computational model of gene regulation is integrated with a model of early land plant morphology, and placed in an evolutionary environment of competing fitness pressures. This work provides a methodological scaffold upon which increasingly complex models at each level of genotype, phenotype and environment can be built.