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Neofunctionalization of young duplicate genes in Drosophila

Significance Gene duplication is thought to play an important role in the evolution of complex phenotypes. Although studies have revealed that duplicate genes are abundant, there is considerable controversy about how they are maintained throughout evolution. In this study, we develop an approach for comparing genome-wide expression profiles of closely related species to disentangle the evolutionary forces operating on duplicate genes. Application of our approach to pairs of young duplicate genes in Drosophila reveals that nearly all duplicates are retained by the evolution of a novel function in one copy. Further analysis reveals that, although young genes are primarily expressed in testes, their expression broadens as they age, illustrating how new genes become integrated into diverse functional networks over time. Gene duplication is a key source of genetic innovation that plays a role in the evolution of phenotypic complexity. Although several evolutionary processes can result in the long-term retention of duplicate genes, their relative contributions in nature are unknown. Here we develop a phylogenetic approach for comparing genome-wide expression profiles of closely related species to quantify the roles of conservation, neofunctionalization, subfunctionalization, and specialization in the preservation of duplicate genes. Application of our method to pairs of young duplicates in Drosophila shows that neofunctionalization, the gain of a novel function in one copy, accounts for the retention of almost two-thirds of duplicate genes. Surprisingly, novel functions nearly always originate in younger (child) copies, whereas older (parent) copies possess functions similar to those of ancestral genes. Further examination of such pairs reveals a strong bias toward RNA-mediated duplication events, implicating asymmetric duplication and positive selection in the evolution of new functions. Moreover, we show that young duplicate genes are expressed primarily in testes and that their expression breadth increases over evolutionary time. This finding supports the “out-of-testes” hypothesis, which posits that testes are a catalyst for the emergence of new genes that ultimately evolve functions in other tissues. Thus, our study highlights the importance of neofunctionalization and positive selection in the retention of young duplicates in Drosophila and illustrates how duplicates become incorporated into novel functional networks over evolutionary time.