Progress in molecular technology is opening unprecedented opportunities for unraveling the mechanisms of evolutionary diversification. One promising avenue is to enrich organismal systems for which detailed background information about ecology and adaptive diversification is available with insights from developmental genetics. Another attractive opportunity is to transfer the power of genomic approaches established in well-developed research models to organisms offering fascinating ecological backgrounds, yet remaining unexplored at the molecular level. In this proposal, I describe two subprojects taking up these challenges. The first subproject focuses on my long-term research model, threespine stickleback fish. Populations of this species exhibit striking evolutionary reduction in skeletal traits in response to acidic waters on the island of North Uist, Scotland. Applying methodology from developmental genetics (fine-mapping using genome-wide association; developmental series and histological analyses; gene expression analysis based on RNA sequencing and in situ hybridization; genome editing), my objective is to elucidate how genetic variation modifies developmental pathways to produce the phenotypic diversity seen in nature. The second subproject will uncover the genomic underpinnings of rapid range expansion across Europe in a butterfly. This contemporary biological invasion will be examined at the whole-genome level by building a high-quality reference genome, dissecting the colonization history based on dozens of samples across the ancestral and new range, and finally by performing genome scans to search for genome regions and associated candidate genes promoting the rapid colonization of new territory. I anticipate that the proposed work will make strong contributions to understanding the developmental basis of vertebrate morphological evolution, and ecological and evolutionary responses of organisms to global change.