One of the fundamental goals in evolution is to understand the process of speciation and adaptation. In this dissertation, we explore this long-lasting question by addressing the genetic basis of species adaptation, and the geological and environmental factors that promote both population differentiation and speciation. To answer these questions, we focused on three model systems. (1) The genetic basis of the remarkable adaptations of the African wild dog (Lycaon pictus). We found unique mutations associated with cursoriality, hypercanivory, and coat color variation in this species. These mutations evolved ~1.7 million years ago, coinciding with the diversification of large-bodied ungulates. (2) The diversification of one of the most rapid speciation in carnivores, the South American canids. We found that this group is derived from a single ancestral population that likely colonized South America three million years ago when the Panama land bridge was formed. In South America, we found that the Andes promote early diversifications in the eastern region, followed by recent diversification in the west of the Andes. We detected extensive historical gene flow among the youngest lineages, which could have augmented species adaption to different niches. Finally, we found a complex history of adaptive diversification throughout a sequence of past climatic cycles in South America, compounded by recent population declines caused by humans. (3) The effect of island isolation and species introduction in the genetic differentiation and diversity of Galapagos rails. We found that the separation of a central landmass in the archipelago around 400 thousand years ago shaped the diversification of rail populations. Our findings show that the eradication of goats was critical to avoiding episodes of severe inbreeding in most populations.