Microbial communities are comprised of many species that coexist on small spatial scales. This is difficult to explain because many interspecies interactions are competitive, and ecological theory predicts that one species will drive the extinction of another species that competes for the same resource. Conversely, evolutionary theory proposes that natural selection can lead to coexistence by driving competing species to use non-overlapping resources. However, evolutionary escape from extinction may be slow compared to the rate of competitive exclusion. Here, we use experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae to study the evolution of coexistence in species that compete for resources. We find that while E. coli usually outcompetes S. cerevisiae in co-culture, a few populations evolved stable coexistence after ~1000 generations of coevolution. We sequenced S. cerevisiae and E. coli populations, identified multi-hit genes, and engineered alleles from these genes into several genetic backgrounds, finding that some mutations modified interactions between E. coli and S. cerevisiae. Together, our data demonstrate that coexistence can evolve, de novo, from intense competition between two species with no history of coevolution.

微生物群落由许多在小空间尺度上共存的物种组成。这很难解释，因为许多种间的相互作用是竞争性的，而生态理论预测，一个物种将推动另一个物种的灭绝，而另一个物种竞争相同的资源。相反，进化论提出，自然选择可以通过驱使竞争物种使用非重叠资源而导致共存。然而，与竞争排斥的速度相比，从灭绝中进化逃逸的速度可能会很慢。在这里，我们使用大肠杆菌和酿酒酵母的实验性共培养来研究竞争资源的物种共存的进化。我们发现，虽然大肠杆菌通常在共培养中胜过酿酒酵母，少数种群在约 1000 代共进化后进化出稳定的共存。我们对S. cerevisiae和E. coli种群进行了测序，鉴定了多重打击基因，并将这些基因的等位基因改造为几个遗传背景，发现一些突变改变了E. coli和S. cerevisiae之间的相互作用。总之，我们的数据表明，从没有共同进化历史的两个物种之间的激烈竞争中，共存可以从头进化。