"As we learn more about the mechanisms of development, it remains a challenge to understand the relationship between molecular processes and functional characteristics of the organism. The complexity of the networks that link genes and phenotypes is nearly ignored by evolutionary theory, which builds on simple phenomenological models of the genotype-phenotype relationship. These models treat development as a black box, leaving mainstream evolutionary theory ill-equipped to explain how molecular mechanisms evolve. In order to resolve this problem, the current proposal develops a framework for understanding the evolution of complex traits and their genetic basis, integrating methods from systems biology and evolutionary genetics. This novel strategy is first applied to bacterial chemotaxis, a prototype for studying the molecular basis of emergent behavior and its response to selection. A second project examines evolutionary diversification by modeling the origin of distinct ecotypes observed in evolution experiments with Escherichia coli. In both cases, I employ systems-biology models to reconstruct the relationship between molecular mechanisms and phenotypic characters under selection and then apply population-genetic techniques to study how populations evolve on these landscapes. The work on microbial model systems is complemented by conceptual analyses that examine how sexual populations evolve on complex adaptive landscapes. I will study whether higher organisms differ from bacteria in the way they realize evolutionary innovations and whether the high rate of recombination in sexual species has an effect on the structure of molecular interactions. This research will also clarify what signatures of selection are likely to be found in molecular networks. A final research aim is to delineate under what conditions phenotypic evolution can be studied without knowledge of molecular details, which is still the common situation in evolutionary biology."