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

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.     

Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environment

Replicate populations of the social bacterium Myxococcus xanthus underwent extensive evolutionary adaptation to an asocial selective environment (liquid batch culture). All 12 populations showed partial or complete loss of their social (S) motility function after 1,000 generations of evolution. Mutations in the pil gene cluster (responsible for type IV pilus biogenesis and function) were found to be at least partially responsible for the loss of S motility in the majority of evolved lines. Restoration (partial or complete) of S motility in the evolved lines by genetic complementation with wild-type pil genes positively affected their fruiting body development and sporulation while negatively affecting their competitive fitness in the asocial regime. This genetic tradeoff indicates that mutations in the pil region were adaptive in the asocial selective environment. This finding was confirmed by experiments showing that defined deletions of pil gene regions conferred a competitive advantage under asocial conditions. Moreover, an amino acid substitution in an evolved genotype was located in a region predicted by genetic complementation analysis to bear an adaptive mutation.     

Genomic comparisons among <Emphasis Type="Italic">Escherichia coli</Emphasis> strains B,K-12, and O157:H7 using IS elements as molecular markers

Background  

Insertion Sequence (IS) elements are mobile genetic elements widely distributed among bacteria. Their activities cause mutations, promoting genetic diversity and sometimes adaptation. Previous studies have examined their copy number and distribution in Escherichia coli K-12 and natural isolates. Here, we map most of the IS elements in E. coli B and compare their locations with the published genomes of K-12 and O157:H7.     

EXPERIMENTAL STUDIES OF PLEIOTROPY AND EPISTASIS IN ESCHERICHIA COLI. II. COMPENSATION FOR MALADAPTIVE EFFECTS ASSOCIATED WITH RESISTANCE TO VIRUS T4

Mutations in Escherichia coli that confer resistance to virus T4 also have maladaptive effects that reduce competitive fitness. After resistant populations had evolved for 400 generations in the absence of T4, their fitness approached that of sensitive populations allowed to evolve under identical conditions. However, the resistant populations had not reverted to sensitivity. Instead, this convergence in fitness resulted from genetic changes that compensated for maladaptive pleiotropic effects of the resistance mutations. An allele selected in an evolving resistant population reduced the competitive disadvantage associated with resistance by almost half. Interestingly, this allele was also beneficial in sensitive populations, although its fitness advantage was only about one-fifth as great as it was in the resistant population. These results run counter to a commonly held view that trade-offs between components of fitness should become more pronounced as populations approach their “selective equilibria.” If a trade-off derives from some limiting energetic or material currency, then it is likely to become more pronounced as a population becomes more finely adapted. If a trade-off derives from the disruption of genetic integration, then it is likely to be diminished with further adaptation.     

EVOLUTIONARY ADAPTATION TO TEMPERATURE. I. FITNESS RESPONSES OF ESCHERICHIA COLI TO CHANGES IN ITS THERMAL ENVIRONMENT

We used bacteria to study experimentally the process of genetic adaptation to environmental temperature. Replicate lines of Escherichia coli, founded from a common ancestor, were propagated for 2,000 generations in 4 different thermal regimes as 4 experimental groups: constant 32, 37, or 42°C (thermal specialists), or a daily alternation between 32 and 42°C (32/42°C: thermal generalists). The ancestor had previously been propagated at 37°C for 2,000 generations. Adaptation of the groups to temperature was measured by improvement in fitness relative to the ancestor, as estimated by competition experiments. All four experimental groups showed improved relative fitness in their own thermal environment (direct response of fitness). However, rates of fitness improvement varied greatly among temperature groups. The 42°C group responded most rapidly and extensively, followed by the 32 and 32/42°C groups, whose fitness improvements were indistinguishable. The 37°C group, which experienced the ancestral temperature, had the slowest and least extensive fitness improvement. The correlated fitness responses of each group, again relative to the common ancestor, were measured over the entire experimental range of temperatures. No necessary tradeoff between direct and correlated responses of fitness was apparent: for example, the improved fitness of the 42°C group at 42°C was not accompanied by a loss of fitness at 37°C or 32°C. However, the direct fitness responses were usually greater than the correlated responses, judged both by comparing direct and correlated responses of a single group at different temperatures and by comparing direct and correlated responses of different groups at a single temperature. These comparisons indicate that the observed adaptation was, in fact, largely temperature specific. Also, the fitness responses of the generalist group across a range of temperatures were less variable than those of the thermal specialist groups considered as whole.     

EPISTATIC INTERACTIONS CAN LOWER THE COST OF RESISTANCE TO MULTIPLE CONSUMERS

It is widely assumed that resistance to consumers (e.g., predators or pathogens) comes at a “cost,” that is, when the consumer is absent the resistant organisms are less fit than their susceptible counterparts. It is unclear what factors determine this cost. We demonstrate that epistasis between genes that confer resistance to two different consumers can alter the cost of resistance. We used as a model system the bacterium Escherichia coli and two different viruses (bacteriophages), T4 and Λ, that prey upon E. coli. Epistasis tended to reduce the costs of multiple resistance in this system. However, the extent of cost savings and its statistical significance depended on the environment in which fitness was measured, whether the null hypothesis for gene interaction was additive or multiplicative, and subtle differences among mutations that conferred the same resistance phenotype.     

EVOLUTIONARY ADAPTATION TO TEMPERATURE. III. ADAPTATION OF ESCHERICHIA COLI TO A TEMPORALLY VARYING ENVIRONMENT

Six lines of the bacterium Escherichia coli were propagated for 2,000 generations in a temporally varying environment. The imposed environmental regime consisted of alternating days at 32°C and 42°C, with rapid transitions between them. These derived lines are competitively superior to their ancestor in this variable temperature regime. We also measured changes in the fitness of these lines, relative to their common ancestor, in both the constant (32°C and 42°C) and transition (from 32°C to 42°C and from 42°C to 32°C) components of this temporally varying environment, to determine whether the bacteria had adapted to the particular constant temperatures or the transitions between them, or both. The experimentally evolved lines had significantly improved fitness in each of the constant environmental components (32°C and 42°C). However, the experimental lines had not improved in making the sudden temperature transitions that were a potentially important aspect of the temporally variable environment. In fact, fitness in making at least one of the transitions (between 32°C and 42°C) unexpectedly decreased. This reduced adaptation to the abrupt transitions between these temperatures is probably a pleiotropic effect of mutations that were responsible for the increased fitness at the component temperatures. Among the six experimental lines, significant heterogeneity occurred in their adaptation to the constant and transition components of the variable environment.     

Cryptic population dynamics: rapid evolution masks trophic interactions

Trophic relationships, such as those between predator and prey or between pathogen and host, are key interactions linking species in ecological food webs. The structure of these links and their strengths have major consequences for the dynamics and stability of food webs. The existence and strength of particular trophic links has often been assessed using observational data on changes in species abundance through time. Here we show that very strong links can be completely missed by these kinds of analyses when changes in population abundance are accompanied by contemporaneous rapid evolution in the prey or host species. Experimental observations, in rotifer-alga and phage-bacteria chemostats, show that the predator or pathogen can exhibit large-amplitude cycles while the abundance of the prey or host remains essentially constant. We know that the species are tightly linked in these experimental microcosms, but without this knowledge, we would infer from observed patterns in abundance that the species are weakly or not at all linked. Mathematical modeling shows that this kind of cryptic dynamics occurs when there is rapid prey or host evolution for traits conferring defense against attack, and the cost of defense (in terms of tradeoffs with other fitness components) is low. Several predictions of the theory that we developed to explain the rotifer-alga experiments are confirmed in the phage-bacteria experiments, where bacterial evolution could be tracked. Modeling suggests that rapid evolution may also confound experimental approaches to measuring interaction strength, but it identifies certain experimental designs as being more robust against potential confounding by rapid evolution.