Understanding the mechanisms of speciation and adaptation is a fundamental question in biology that also provides an opportunity to uncover new gene functions of clinical relevance. Highly conserved genetic regulatory pathways shared across diverse vertebrate species have been shaped by adaptive evolution to produce spectacular morphological, behavioral, and ecological diversity. Here I review a decade of my lab’s work investigating the rapid evolutionary transition from generalist algae-eating pupfishes to trophic specialists endemic to hypersaline lakes of San Salvador Island in the Bahamas and Laguna Chichancanab, Mexico. We show that colonizing these niches occurred in stages, beginning with selection on standing genetic variation for feeding behavior, then aided by adaptive introgression from diverse sources, and ending with selection on de novo mutations in key craniofacial genes. We discovered that only 157 single-nucleotide polymorphisms (SNPs) and 87 deletions are fixed between scale-eating and molluscivore specialists despite extensive phenotypic divergence in their craniofacial morphology, metabolism, and behavior. These few differences resulted in major transitions in ecological niches and the colonization of new fitness peaks and novel performance optima for scale-biting. Overall, our work provides a new microevolutionary framework for investigating how major ecological transitions occur in nature and illustrates how both shared and unique genetic variation contributes to diversification and provides a path through complex fitness landscapes for access to novel ecological niches.