A major goal in evolutionary genetics is to understand the molecular changes underlying adaptations and the evolutionary processes that have shaped adaptation and biodiversity. To this end, the ability to pinpoint the genetic basis of complex adaptive phenotypes has been a major advancement in current biology, establishing crucial links between genotypes, phenotypes, and evolutionary processes. Classic biological systems are being revisited with a genomics lens, building on traditional approaches in evolution, ecology, and natural history. By applying new genomic methods to classic biological questions, we are making progress along two major fronts: uncovering the genes, molecular mechanisms, and genetic architectures that generate adaptive phenotypes, and exploring the evolutionary processes that give rise to these adaptations. Through the work included in this dissertation, I have sought to explore the evolutionary processes that generate and maintain adaptive biodiversity in two focal systems. First, I reviewed new insights based on genomic analyses of a classic system, Darwin’s finches, and connected these findings to the growing literature on adaptive introgression and its contributions to phenotypic evolution (Chapter 1). I then looked to another classic system in evolutionary biology with a long tradition of theoretical and empirical research: polymorphic wing pattern mimicry in Papilio swallowtail butterflies. In Papilio, I studied i) natural selection on polymorphic wing pattern phenotypes in the field (Chapter 2), and ii) the genetic basis and evolution of convergent polymorphic wing pattern mimicry (Chapter 3).