Data from: Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly

Background. While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ thoroughly characterized, well- integrated systems of proteins and organic constituents to immobilize prey via paralysis, hypotension, or both. Venoms are optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Results. Using next-generation transcriptome sequencing and mass spectrometry, we examined protein expression and microevolution in two pitvipers, allopatrically separated for at least 1.6 million years (Protobothrops flavoviridis and P. elegans), and their hybrids. Parental venoms had generally similar compositions at the protein family level, but homologs present and concentrations thereof, differed dramatically. For instance, a phospholipase A2 comprising 73.4% of the P. elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05%). Hybrids produced most gene products found in both parental venoms. There was a positive correlation between protein evolutionary rates and their transcriptomic and proteomic abundances, with the most abundant proteins showing positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at the genus Protobothrops, we show that the rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptive evolution. Conclusions. Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components.