Using an integrative approach that combines lab and fieldwork and applies the tools of molecular phylogenetics, ecological genetics, and population genomics, I am linking genotype and phenotype in two systems: the deer mouse, Peromyscus maniculatus, and the pine-sawfly genus Neodiprion (order Hymenoptera; family Diprionidae). Deer mice and sawflies share several features that make them excellent study organisms, including: they are abundant and easy to find in nature; they can be kept under controlled laboratory conditions; crosses can be made between divergent populations and species; and they have many traits that are variable within and between species. To gain insight into how organisms adapt to their environment and why this process sometimes leads to the formation of new species, I specifically focus on those traits that impact the ability of individuals to survive and reproduce (e.g., cryptic coat color in deer mice) and/or contribute to reproductive barriers between populations and species (e.g., host use in sawflies). My long-term research goals in both systems are to: (1) identify the genes, mutations, and molecular mechanisms responsible for phenotypic differences between populations and species, (2) measure the strength of natural selection acting on those phenotypes and their underlying genes, (3) reconstruct the histories of ecologically important genes (gene trees) and the populations in which they occur (population/species trees), and (4) determine the extent to which the course of evolution varies across different organisms and traits.