The set of genes in the genome of a species is the result of a dynamic net balance between gain and loss events that happen over evolutionary time. The origination and divergence of new genes are major sources of genomic novelty, and has the potential to generate substantial raw material for the evolution of functional innovations. It has been recently recognized that young genes can take over fundamental functions in basic cellular processes and be essential for the survival of an organism, even when they are restricted to a few species in a phylogeny. It is not clear, however, how newly duplicated genes are integrated into ancestral networks or to what extent they diverge from their parents at the functional level. In the two study cases reported here, I investigate the evolution of three relatively young duplicated genes with regulatory functions, and only found in some fly species. Using computational analyses and experimental assays, I show that a diverse suite of factors was responsible for the functional divergence of the duplicated genes after their origination from their conserved parental genes. After their origination through retrotransposition events in different branches of the Drosophila phylogeny, the genes acquired a restrict expression pattern, and rapidly diverged in sequence from their parents, which remained essentially conserved. I further show their phenotypic importance for viability and male fertility, and demonstrate that the duplicated genes diverged in several aspects from their parents, including their protein interactions, genomic binding pattern and impact on global gene regulation. Our results show how young elements can be integrated into conserved processes in different ways, and illustrate the complex nature of evolution driven by new gene origination.