A complete understanding of the evolutionary process has long been impeded by limited knowledge about the genetic and developmental basis of functionally relevant phenotypic variation. This situation has changed with the advent of genomic and developmental tools, making possible integrative research linking molecular variation to fitness-relevant phenotypic variation in some model organisms. The aim of the present proposal is to carry out such an integrative study in Swiss populations of threespine stickleback fish. I will focus on populations that have repeatedly and independently evolved highly divergent foraging morphologies (gill raker apparatus) in response to contrasting foraging conditions between limnetic and benthic habitats (parallel evolution). These populations will be subject to powerful molecular genetic experiments, including QTL mapping, candidate and comparative gene expression analysis, and selective sweep analysis. These molecular experiments will uncover the genetic architecture of phenotypic variation, identify key genes and developmental pathways in morphogenesis, and determine the role natural selection in driving molecular shifts. The proposed study will shed light on mechanisms underlying parallel evolution, and thereby contribute to our understanding of adaptation and biological diversification.