Evolution of the reproductive interactome: proteomic divergence and the origins of postmating-prezygotic reproductive incompatibilities

Reproductive proteins evolve rapidly, making them strong candidates for driving postmating-prezygotic (PMPZ) reproductive incompatibilities between populations. While most previous studies have focused on protein sequence divergence as a likely driver of PMPZ incompatibilities, reproductive proteomes may also diverge compositionally and/or quantitatively. Here, we combine quantitative proteomics, molecular evolutionary analyses, and protein-protein interaction (PPI) modeling to predict the molecular basis of reproductive incompatibilities between Drosophila mojavensis and D. arizonae. We demonstrate multidimensional divergence in reproductive proteomes including changes at the sequence, compositional, and quantitative levels. We further demonstrate that three divergent male seminal fluid proteins affect the size of the insemination reaction mass and/or fertilization success in D. arizonae. Despite high sequence divergence, predicted protein-protein interactions involving a conserved set of proteases and/or protease inhibitors were predicted to be maintained in heterospecific crosses. In contrast, predicted interspecies protein incompatibilities arose from proteome compositional divergence, suggesting that such changes may play a disproportionate role in PMPZ incompatibilities, at least for the subset of the interactome that we tested. Furthermore, extensive quantitative divergence, particularly for proteases and inhibitors, suggests pervasive stoichiometric mismatches in heterospecific matings. Altogether, our findings indicate that reproductive proteins are evolutionarily labile at multiple levels, and that compositional and quantitative divergence, rather than sequence changes alone, may be central to the early evolution of reproductive isolation.