ModEDI: An extendable software architecture for examining the effects of developmental interactions on evolutionary trajectories

Quantitative genetics is the study of complex biological traits, or traits controlled by more than one gene. A primary goal of quantitative genetic studies is the development of computational models for predicting the evolution of such traits in response to selection. Most models for analyzing the evolution of multiple traits employ a constant genetic variance-covariance matrix (G-matrix) to describe the distribution of genetic variation. While G-matrix based models provide a reasonable approximation of short term evolution, they may not sufficiently capture all important associations between traits. For example, nonlinear interactions between developmental factors underlying the production of traits can result in dramatic alteration of genetic variances and covariances as evolution proceeds. To aid in investigating this issue, we have developed an object-oriented code base, Models of Evolution with Developmental Interactions (ModEDI), that implements a powerful, general mathematical and conceptual framework developed by Sean Rice. This framework utilizes a phenotypic landscape to explicitly incorporate the effect of development in shaping heritable phenotypic variation. With our program, users can develop custom simulations for analyzing the evolution of multiple phenotypic traits that involve interactions between overlapping sets of developmental factors. Initial results from simulations performed with ModEDI indicate that developmental interactions may substantially alter evolutionary trajectories.