As the field of evolutionary biology pivots away from a gene-centric view of how adaptive evolution proceeds, renewed emphasis is placed on the origin of phenotypic variation. Understanding the developmental processes that underlie the production of novel traits, and how they might influence evolvability, is considered a primary goal in the on-going “extended evolutionary synthesis”. The following dissertation explores these questions in the context of adaptive radiations in fish, with a focus on morphological variation in the craniofacial skeleton. Specifically, the first chapter investigates the genetic and developmental basis of shape (co-)variation in the feeding apparatus of African cichlid fishes, and uncovers a common signaling pathway that underlies the adaptive evolution of multiple elements in a complex functional structure. The second chapter presents a new method that is capable of evaluating phenotypic integration on the individual level, and demonstrates its utility in genetic mapping studies. The third chapter characterizes the pattern of morphological diversification in the Antarctic notothenioid fishes, and discusses how integration might have facilitated their adaptive radiation in the Southern Ocean.