Recurrent Adaptation in RNA Interference Genes Across the Drosophila Phylogeny

• Published in: Molecular biology and evolution Vol. 28; no. 2; pp. 1033 - 1042
• Main Authors: Kolaczkowski, Bryan, Hupalo, Daniel N., Kern, Andrew D.
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.02.2011
• Subjects: Adaptation; Adaptation, Biological; Adenosine Triphosphatases - chemistry; Adenosine Triphosphatases - genetics; Animals; Biological evolution; Drosophila; Drosophila - genetics; Drosophila melanogaster; Drosophila Proteins - chemistry; Drosophila Proteins - genetics; Evolution & development; Evolution, Molecular; Evolutionary genetics; Fruit flies; Gene regulation; Genes; Genomes; Insects; Models, Molecular; Phylogenetics; Phylogeny; Positive selection; Prediction models; Protein Structure, Tertiary; Proteins; Ribonuclease III - chemistry; Ribonuclease III - genetics; Ribonucleic acid; RNA; RNA Helicases - chemistry; RNA Helicases - genetics; RNA Interference; RNA-mediated interference; RNA-protein interactions; Structural Homology, Protein; adaptation; RNAi; positive selection; RNA interference
• ISSN: 0737-4038; 1537-1719; 1537-1719
• DOI: 10.1093/molbev/msq284

RNA interference (RNAi) is quickly emerging as a vital component of genome organization, gene regulation, and immunity in Drosophila and other species. Previous studies have suggested that, as a whole, genes involved in RNAi are under intense positive selection in Drosophila melanogaster. Here, we characterize the extent and patterns of adaptive evolution in 23 known Drosophila RNAi genes, both within D. melanogaster and across the Drosophila phylogeny. We find strong evidence for recurrent protein-coding adaptation at a large number of RNAi genes, particularly those involved in antiviral immunity and defense against transposable elements. We identify specific functional domains involved in direct protein–RNA interactions as particular hotspots of recurrent adaptation in multiple RNAi genes, suggesting that targeted coadaptive arms races may be a general feature of RNAi evolution. Our observations suggest a predictive model of how selective pressures generated by evolutionary arms race scenarios may affect multiple genes across protein interaction networks and other biochemical pathways.