Abstract: The elucidation of relationships between biodiversity and ecosystem processes has been limited by the definition of metrics of biodiversity and their integration into experimental design. Functional trait screening can strengthen the performance of these designs. We suggest the use of Rao's quadratic entropy to measure both functional diversity and phylogenetic diversity of species mixtures proposed for an experimental design, and demonstrate how they can provide complementary information. We also present an index assessing the statistical performance of these independent variables in different experimental designs. Measurement of independent variables as continuous vs. discrete variables reduces statistical performance, but improves the model by quantifying species differences masked by group assignments. To illustrate these advances, we present an example from a tropical forest tree community in which we screened 38 species for nine functional traits. The proposed TropiDEP design is based on the relative orthogonality of two multivariate trait axes defined using principal component analysis. We propose that independent variables describing functional diversity might be grouped to calculate independent variables describing suites of different traits with potentially different effects on particular ecosystem processes. In other systems these axes may differ from those reported here, yet the methods of analysis integrating functional and phylogenetic diversity into experimental design could be universal.