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Retrogenes form a class of gene duplicate lacking the regulatory sequences found outside of the mRNA-coding regions of the parent gene. It is not clear how a retrogene's lack of parental regulatory sequences affects the evolution of the gene pair. To explore the evolution of parent genes and retrogenes, we investigated three such gene pairs in the family Drosophilidae; in  Drosophila melanogaster , these gene pairs are  CG8331  and  CG4960 ,  CG17734  and  CG11825 , and  Sep2  and  Sep5 . We investigated the embryonic expression patterns of these gene pairs across multiple  Drosophila  species. Expression patterns of the parent genes and their single copy orthologs are relatively conserved across species, whether or not a species has a retrogene copy, although there is some variation in  CG8331  and  CG17734 . In contrast, expression patterns of the retrogene orthologs have diversified. We used the genome sequences of 20  Drosophila  species to investigate coding sequence evolution. The coding sequences of the three gene pairs appear to be evolving predominantly under negative selection; however, the parent genes and retrogenes show some distinct differences in amino acid sequence. Therefore, in general, retrogene expression patterns and coding sequences are distinct compared to their parents and, in some cases, retrogene expression patterns diversify.

Evolution of Three Parent Genes and Their Retrogene Copies inDrosophilaSpecies