Correlated Gene Copy Number Changes in a Seminal Fluid Protein Network in Drosophila

Abstract Reproductive proteins often diverge rapidly between species, yet network function must be maintained. Shared selective pressures on network members and compensatory changes between members can drive their parallel evolutionary trajectories. Indeed, correlated evolutionary rates of amino acid sequence change have been observed for interacting reproductive proteins. But whether gene copy number changes also correlate has not been widely studied. Here, we investigated copy number variation (CNV) of genes in the Drosophila Sex Peptide Seminal Fluid Protein (Sfp) network. Previous research analyzed CNV of the Sfp Sex Peptide (SP) in Drosophila species. We focus on 9 other Sfps whose function is required to mediate the binding of SP to sperm in D. melanogaster which is required for persistence of female post-mating responses. To exhaustively annotate CNV of genes, we developed a computational pipeline pairing iterative protein queries to genome sequence searches with phylogenetic clustering to resolve homology relationships. We observed that the Sfp network’s genes are ancestral to Drosophila and that there were repeated duplications and losses of network members across the genus. We detect statistically significant correlations in gene duplication or loss events among network proteins, and show this can be used to identify new members of the network. We also investigated CNV of female-derived proteins that act downstream of the SP sperm-binding network to modulate SP function, these proteins showed no significant correlation of gene turnover events with SP or its network. Our results provide insight into how evolving reproductive genes tolerate duplication and loss, and how network relationships could constrain reproductive protein evolution. Significance Statement Reproductive proteins often diverge rapidly between species, yet network function must be maintained. Shared selective pressures on network members and compensatory changes between members can drive their parallel evolutionary trajectories. We report correlated gene duplication and loss among members of the Drosophila Sex Peptide seminal fluid protein network, suggesting that duplication or loss events may drive corresponding events in other network genes. This work is a natural extension of the idea of evolutionary rate covariation, but instead of scoring rates of substitution it tracks correlated duplication and loss events on the phylogeny. Applied to the Sex Peptide network, the method reveals striking patterns, especially for coordinated loss, and identifies a new network gene that is experimentally confirmed.