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.

raw_competition_dataRaw competition colony counts and calculated fitness values for all competitionsraw_biologGENIII_dataRaw growth data of the bacterial strains in the biolog GENIII microplatebiolog_GENIII_dataFor all growth conditions in the Biolog GENIII microplates, growth yield of the 7 bacterial samples and growth yield ratio of the eight bacterial comparisons. Results of the clustering analyses and of the Wilcoxon sum-rank tests for the eight comparisons are also indicated.transcriptome_dataAnalysis of transcriptomic data. Average expression ration, p-values and q-values are indicated for the probe sets. For each probe set, gene ontology category, regulators, and results of the clustering analyses are indicated