RNA interference pathways display high rates of adaptive protein evolution across multiple invertebrates

Abstract

Conflict between organisms can lead to reciprocal adaptation that manifests itself as an increased evolutionary rate in the genes mediating the conflict. This adaptive signature has been observed in RNA interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked into an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species by using a formal meta-analytic framework to combine data across species, and by implementing a multispecies generalised linear mixed model of mutation counts. In all species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the subset of genes that are most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analysed insect species combined, perhaps due to concurrent parasite-mediated arms races.