Data from: Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli

Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.亲缘关系较近的生物通常占据相似的生态位（ecological niche），进而引发激烈的种间竞争，甚至导致其中一方灭绝。此类竞争还可推动快速的表型进化（phenotypic evolution）与生态位分化。这一演化过程最终可能以不同生态位的稳定占据告终，或是反复经历多轮演化循环。 本研究聚焦于两个源自共同祖先、分化后共存超过30000代的大肠杆菌（Escherichia coli）谱系，分别命名为L与S。两个谱系均基于全局转录谱与资源利用谱持续发生表型进化，且随着时间推移，L谱系似乎逐渐侵占了S谱系的分解代谢谱。针对相同或不同世代的L、S克隆株开展的相互入侵实验揭示了二者互作关系的演化变化，其中包括一项不对称性特征，证实了L谱系对S谱系生态位的侵占行为。 总体而言，同一世代的L与S克隆株呈现出负频率依赖效应，与二者稳定共存的理论预期相符。但值得注意的是，L克隆株可入侵来自更早或更晚世代的S克隆株，而S克隆株仅能入侵来自更早世代的L克隆株。在该实验体系中，竞争谱系的长期共存显然依赖于多轮连续的演化过程，而非初始分化后便维持静态平衡的状态。