Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

Abstract

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that "replayed" evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 x 10(12) ancestral cells, nor among 9 x 10(12) cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

Fig. 1.

Population expansion during evolution of the Cit⁺ phenotype. Samples frozen at various times in the history of population Ara-3 were revived, and three DM25 cultures were established for each generation. Optical density (OD) at 420 nm was measured for each culture at 24 h. Error bars show the range of three values measured for each generation.

Fig. 2.

Growth of Cit⁻ (blue triangles) and Cit⁺ (red diamonds) cells in DM25 medium. Each trajectory shows the average OD for eight replicate mixtures of three clones, all from generation 33,000 of population Ara-3.

Fig. 3.

Alternative hypotheses for the origin of the Cit⁺ function. According to the rare-mutation hypothesis, the probability of mutation from Cit⁻ to Cit⁺ was low but constant over time. Under the historical-contingency hypothesis, the probability of this transition increased when a mutation arose that produced a genetic background with a higher mutation rate to Cit⁺.

Fig. 4.

Mutation rates from Ara⁻ to Ara⁺ (blue diamonds) and Cit⁻ to Cit⁺ (red squares) of the ancestor and a set of potentiated clones. Error bars are 95% confidence intervals. See text for details.

Fig. 5.

Frequency-dependent selection allows stable coexistence of Cit⁻ and Cit⁺ clones. Each trajectory shows the mean of five replicate cultures for seven different initial ratios of Cit⁻ and Cit⁺ clones from generation 33,000. Error bars are 95% confidence intervals.