Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution

Most experimental studies of epistasis in evolution have focused on adaptive changes—but adaptation accounts for only a portion of total evolutionary change. Are the patterns of epistasis during adaptation representative of evolution more broadly? We address this question by examining a pair of protein homologs, of which only one is subject to a well-defined pressure for adaptive change. Specifically, we compare the nucleoproteins from human and swine influenza. Human influenza is under continual selection to evade recognition by acquired immune memory, while swine influenza experiences less such selection due to the fact that pigs are less likely to be infected with influenza repeatedly in a lifetime. Mutations in some types of immune epitopes are therefore much more strongly adaptive to human than swine influenza—here we focus on epitopes targeted by human cytotoxic T lymphocytes. The nucleoproteins of human and swine influenza possess nearly identical numbers of such epitopes. However, mutations in these epitopes are fixed significantly more frequently in human than in swine influenza, presumably because these epitope mutations are adaptive only to human influenza. Experimentally, we find that epistatically constrained mutations are fixed only in the adaptively evolving human influenza lineage, where they occur at sites that are enriched in epitopes. Overall, our results demonstrate that epistatically interacting substitutions are enriched during adaptation, suggesting that the prevalence of epistasis is dependent on the underlying evolutionary forces at play.现有针对进化中上位性（epistasis）的实验研究大多聚焦于适应性演化——但适应性变化仅占总演化改变的一部分。那么，适应性演化过程中的上位性模式，是否能广泛代表整体演化的上位性特征？本研究通过比对一对蛋白质同源物（protein homologs）解答该问题：二者中仅有一种受到明确的适应性演化选择压力。具体而言，我们比对了人类流感与猪流感的核蛋白（nucleoprotein）。人类流感持续受到选择压力，以逃逸获得性免疫记忆的识别；而猪流感面临的此类选择压力更弱，原因在于猪一生中重复感染流感的概率更低。因此，部分免疫表位（immune epitope）的突变对人类流感的适应性贡献远强于猪流感——本研究聚焦于人类细胞毒性T淋巴细胞（cytotoxic T lymphocyte）所靶向的表位。人类与猪流感的核蛋白所拥有的此类表位数量几乎一致。但此类表位突变在人类流感中的固定频率显著高于猪流感，推测原因是这类表位突变仅对人类流感具有适应性优势。实验结果显示，受上位性约束的突变仅在经历适应性演化的人类流感谱系中被固定，且这些突变均发生在表位富集的位点。综上，本研究结果表明，存在上位性互作的氨基酸替换在适应性演化过程中显著富集，提示上位性的普遍程度取决于其所对应的核心演化动力。