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. 1. Introduction Gene duplication plays a major role in evolution by expanding？？gene families and facilitating the diversification of？？gene function. Following？？duplication, gene copies can diverge in function. Retroduplication occurs when mRNA from a parent gene is reverse-transcribed and inserted into the genome, producing a new retrogene copy that lacks the regulatory elements and introns of the parent [1, 2]. The lack of parental regulatory elements in a new retrogene is often associated with a lack of function and pseudogenization; however, those retrogenes that are transcribed presumably lack the expression pattern of their parents and may therefore acquire novel functions [3]. Genome-wide studies have provided insights into the evolutionary outcome of this initial asymmetry between parent gene and retrogene regulatory elements and expression patterns, including several studies focusing on protein-coding parent genes and retrogenes in Drosophila. Expression data from Drosophila melanogaster show that retrogenes tend to be expressed at a lower level and in fewer tissues than their parents, with the exception that retrogenes tend to be more represented in testes than parent genes [4, 5]. The mean expression levels of
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