Parallel phenotypic diversification in closely related species is a rigorous framework for testing the role of natural selection in evolution. Do parallel phenotypes always diversify by parallel genetic bases or does selection pave many alternative genomic routes to the same phenotypic ends? In this review, we show that the advent of next-generation sequencing technologies and the growing use of genomic approaches make it increasingly feasible to answer these fundamental questions using ecological and evolutionary 'non-model' populations of vertebrates in nature. While it is generally expected, and often observed, that closely related populations or species have parallel genetic bases to parallel phenotypes, exceptions are not rare and show that alternative genetic routes can result in similar phenotypes. Ultimately, this framework may illuminate the ecological conditions, evolutionary histories and genetic architectures that result in recurrent phenotypes and rapid adaptation.
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