Correlated gene copy number changes in a seminal fluid protein network in Drosophila

In Drosophila melanogaster, the male seminal fluid protein Sex Peptide regulates persistent postmating changes in female physiology and behavior. The persistence of long-term postmating responses in females requires Sex Peptide binding to sperm, which is mediated by a network of other seminal fluid proteins. A recent study documented substantial copy number variation of Sex Peptide genes in Drosophila species. We hypothesized that, due to shared selective pressures and compensatory changes to maintain functionality, members of the Sex Peptide network should exhibit correlated patterns of gene duplication or loss. Using a computational pipeline pairing iterative genome searches with phylogenetic clustering to resolve homology relationships, we annotated among-species copy number variation of Sex Peptide network genes. We found that these genes are present in the common ancestor of Drosophila species and in many cases predated the origin of Sex Peptide itself. Furthermore, we observed statistically significant correlations in gene duplication or loss events among network members. Our results suggest that selection acting on copy number variation is an additional source of among-species variation of reproductive genes, and that this selection contributes to the maintenance of reproductive gene interactions. Using patterns of shared gene loss across the genus, we also identified and experimentally validated a network member, suggesting the utility of using correlated loss to identify functionally related genes. In contrast to the Sex Peptide seminal fluid network, female-derived proteins that modulate functions downstream of sperm bound Sex Peptide showed no correlation of gene turnover events with Sex Peptide network members.