Data from: The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus

RNA viruses are the main source of emerging infectious diseases because of the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important property, which is usually neglected, is the topography of the fitness landscape. How many fitness maxima exist and how well they are connected is especially interesting, as this determines the number of accessible evolutionary pathways. To address this question, we have reconstructed a region of the fitness landscape of tobacco etch potyvirus constituted by mutations observed during the experimental adaptation of the virus to the novel host Arabidopsis thaliana. Fitness was measured for many genotypes, and showed the existence of multiple peaks and holes in the landscape. We found prevailing epistatic effects between mutations, with cases of reciprocal sign epistasis being common among pairs of mutations. We also found that high-order epistasis were as important as pairwise epistasis in their contribution to fitness. Therefore, results suggest that the landscape was rugged due to the existence of holes caused by lethal genotypes, that a very limited number of potential neutral paths exist, and that contained a single adaptive peak.

RNA病毒（RNA virus）是新发传染病的主要源头，这源于其快速复制、种群体量庞大、突变与重组频率高等特性所赋予的进化潜能。然而，一个通常被忽视的同等重要的特性是适合度景观（fitness landscape）的拓扑结构。存在多少个适合度峰值，以及这些峰值之间的连通性如何，是尤为值得关注的科学问题，因为这直接决定了可及的进化路径数量。为解答这一问题，我们基于病毒在实验中适应新型宿主拟南芥（Arabidopsis thaliana）过程中观测到的突变，重构了烟草蚀纹马铃薯Y病毒（tobacco etch potyvirus）适合度景观的一个区域。我们对大量基因型的适合度进行了测定，结果显示该景观中存在多个适合度峰值与适合度空洞。我们发现突变之间普遍存在上位效应（epistasis），且在突变位点对中，互反符号上位效应十分常见。此外，我们还发现高阶上位效应与成对上位效应对适合度的贡献程度相当。综上，研究结果表明，该适合度景观因致死基因型引发的适合度空洞而呈现崎岖特征，潜在的中性进化路径数量极为有限，且仅存在一个适应性峰值。