Data from: Parallel emergence of negative epistasis across experimental lineages

Epistatic interactions can greatly impact evolutionary phenomena, particularly the process of adaptation. Here, we leverage four parallel experimentally evolved lineages to study the emergence and trajectories of epistatic interactions in the social bacterium Myxococcus xanthus. A social gene (pilA) necessary for effective group swarming on soft agar had been deleted from the common ancestor of these lineages. During selection for competitiveness at the leading edge of growing colonies, two lineages evolved qualitatively novel mechanisms for greatly increased swarming on soft agar, whereas the other two lineages evolved relatively small increases in swarming. By reintroducing pilA into different genetic backgrounds along the four lineages, we tested whether parallel lineages showed similar patterns of epistasis. In particular, we tested whether a pattern of negative epistasis between accumulating mutations and pilA previously found in the fastest lineage would be found only in the two evolved lineages with the fastest and most striking swarming phenotypes, or rather was due to common epistatic structure across all lineages arising from the generic fixation of adaptive mutations. Our analysis reveals the emergence of negative epistasis across all four independent lineages. Further, we present results showing that the observed negative epistasis is not due exclusively to evolving populations approaching a maximum phenotypic value that inherently limits positive effects of pilA reintroduction, but rather involves direct antagonistic interactions between accumulating mutations and the reintroduced social gene.上位性互作（epistatic interactions）可对进化现象，尤其是适应性进化过程，产生极大影响。本研究借助四个平行实验进化谱系，探究社会细菌黄色粘球菌（Myxococcus xanthus）中上位性互作的出现与动态轨迹。这些谱系的共同祖先中，负责软琼脂表面有效群体群集运动的社交基因（pilA）已被敲除。在针对生长菌落前沿竞争能力的选择压力下，其中两个谱系进化出了可显著提升软琼脂群集运动能力的全新机制，而另外两个谱系的群集运动能力仅出现小幅提升。我们通过向四个谱系的不同遗传背景中重新引入pilA基因，检测平行进化谱系是否呈现相似的上位性模式。具体而言，我们验证了此前在最快进化谱系中发现的“累积突变与pilA间存在负上位性”这一模式，是否仅存在于群集速度最快、表型最显著的两个进化谱系中，抑或是源于所有谱系共有的上位性结构——该结构由适应性突变的普遍性固定所导致。分析结果显示，四个独立进化谱系中均出现了负上位性。此外，本研究结果表明，观测到的负上位性并非仅由进化种群趋近于固有限制pilA重新引入正向效应的最大表型值所导致，而是涉及累积突变与重新引入的社交基因之间直接的拮抗互作。