Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population

• Published in: PloS one Vol. 10; no. 11; p. e0142050
• Main Authors: Turner, Caroline B, Blount, Zachary D, Lenski, Richard E
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 18.11.2015; Public Library of Science (PLoS)
• Subjects: Adaptation; Bacteria; Biological evolution; Carbon; Citric acid; Citric Acid - metabolism; Demographics; Directed Molecular Evolution; E coli; Ecosystem biology; Ecosystems; Ecotype; Ecotypes; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli - physiology; Evolution; Evolution (Biology); Evolutionary biology; Experiments; Extinction; Extinction, Biological; Frequency dependence; Genetic aspects; Genetics; Genotype; Genotypes; Glucose; Health aspects; Innovations; Mutation; Phenotype; Population; Population number; Predation; Science; Stochasticity; Studies; United States; United States > US; East Lansing Michigan; Michigan
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0142050

In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit-) ecotypes, with Cit-bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit-lineage went extinct; cells with the Cit-phenotype dropped to levels below detection, and the Cit-clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ ecotype that competitively excluded the Cit-ecotype. We tested this hypothesis by re-evolving the population from a frozen population sample taken within 500 generations of the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit-type did not go extinct in any of these replays, and Cit-cells also persisted in a single replicate that was propagated for 2,500 generations. Even more unexpectedly, we showed that the Cit-ecotype could reinvade the Cit+ population after its extinction. Taken together, these results indicate that the extinction of the Cit-ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ ecotype. The extinction also cannot be explained by demographic stochasticity alone, as the population size of the Cit-ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.