Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli

Abstract

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.

Fig. 1.

Evolutionary dynamics of global transcription profiles for L and S lineages during 40,000 generations. (A) Comparison of the ancestral strain (REL606) with the combined S and L samples at 6,500 generations [6.5K − (S + L)]. (B) Comparisons of S and L samples at 6,500, 17,000, and 40,000 generations. (C) Comparisons of S samples from different generations. (D) Comparisons of L samples from different generations. Each point corresponds to a gene, and the values are log₁₀-transformed expression levels. The number of genes with significantly different expression is shown for each comparison near the upper left corner. Gray symbols indicate genes without significant differences in expression in any of the eight comparisons. Those genes with significant differences in expression in at least one of the seven comparisons between two evolved samples were clustered according to their expression patterns, and the colored symbols indicate genes in expression clusters e1–e6 (Table S1). Black symbols indicate genes that either did not cluster or showed significant differences in expression only between the ancestor and evolved samples.

Fig. 2.

Evolutionary dynamics of growth abilities across 51 environments for L and S lineages during 40,000 generations, as described in Fig. 1. Each point corresponds to a different environment, and the values are log₁₀-transformed growth yields based on optical densities. The number of environments with significant differences in growth is shown for each comparison near the upper left corner. Gray symbols indicate environments without significant differences in growth in any of the eight comparisons. Those environments demonstrating significant differences in growth in at least one comparison between two evolved samples were clustered based on their growth patterns, and the different colored symbols indicate environments in growth clusters g1–g3 (Table S2). Black symbols indicate environments that either did not cluster or showed significant differences only between the ancestor and evolved samples.

Fig. 3.

 Changes in ecological interactions between L and S lineages during 40,000 generations. Sets of clones from the L (diamonds) and S (circles) lineages were sampled at 6,500, 17,000, and 40,000 generations. Each set from each time point competed against two or three other sets from the same or different generations. Black, red, and blue wedges indicate competitions between contemporary lineages, between later L and earlier S, and between earlier L and later S, respectively. Competitions were performed at two starting ratios, with each competitor either initially rare (10%) or common (90%). Wedges that expand (solid lines) or narrow (dashed lines) from each competitor indicate its advantage (fitness >1) or disadvantage (fitness <1) when initially rare. Values represent the mean fitness (with 95% confidence interval) of the rare competitor relative to the common competitor. With 15-fold replication of each competition, all values differ significantly from unity.