Hybridization is now recognized as a major driving force in the evolution of many organisms, particularly in the adaptive radiations of speciose plant and animal clades. Hybrid speciation differs from other modes of speciation in three distinct aspects: 1) the initial hybridization stage generates a swarm of extensive phenotypic and genetic diversity, 2) the invasion of a new niche by some of this diversity in response to an ecological opportunity, and 3) environment-specific sorting and optimization of the admixed gene pool to manifest a new adaptive peak. Exactly how the variations are generated and sorted spatially in this evolutionary process is not fully understood. This project investigates these processes by utilizing a unique hybrid pine system that allows us to explore evolutionary trajectories in transcriptome profile and genome divergence from initial stage of hybridization to stabilized hybrid lineage. By scrutinizing gene expression profile along with whole exome sequence divergence over diverse genetic background and landscapes, the project has the potential to assemble a more complete picture of the dynamic processes of hybrid speciation and adaptation to novel habitats.