Publications

@article{Blount2008,

title = {Historical contingency and the evolution of a key innovation in an experimental population of \emph{Escherichia coli}},

author = {Zachary D. Blount and Christina Z. Borland and Richard E. Lenski},

url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0803151105},

doi = {10.1073/pnas.0803151105},

issn = {0027-8424},

year  = {2008},

date = {2008-06-01},

urldate = {2008-06-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {105},

number = {23},

pages = {7899--7906},

abstract = {The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of \textit{Escherichia coli} were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which \textit{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 × 10^{12} ancestral cells, nor among 9 × 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.},

keywords = {Citrate Evolution, Demography and Ecology, Historical Contingency},

pubstate = {published},

tppubtype = {article}

}

@article{articled,

title = {Experimental Tests for an Evolutionary Trade-Off between Growth Rate and Yield in \textit{E. coli}},

author = {Maja Novak and Thomas Pfeiffer and Richard E. Lenski and Uwe Sauer and Sebastian Bonhoeffer},

url = {https://www.journals.uchicago.edu/doi/full/10.1086/506527},

doi = {10.1086/506527},

year  = {2006},

date = {2006-01-01},

urldate = {2006-01-01},

journal = {The American naturalist},

volume = {168},

pages = {242-51},

abstract = {Theoretical studies have predicted a trade-off between growth rate and yield in heterotrophic organisms. Here we test for the existence of this trade-off by analyzing the growth characteristics of 12 \textit{E. coli} B populations that evolved for 20,000 generations under a constant selection regime. We performed three different tests. First, we analyzed changes in growth rate and yield over evolutionary time for each population. Second, we tested for a negative correlation between rate and yield across the 12 populations. Finally, we isolated clones from four selected populations and tested for a negative correlation between rate and yield within these populations. We did not find evidence for a trade-off based on the first two tests. However, we did observe a trade-off based on the within-population correlation of yield and rate. Our results indicate that, at least for the populations studied here, an analysis of the within-population diversity might be the most sensitive test for the existence of a trade-off. The observation of a trade-off within, but not between, populations suggests that the populations evolved different genetic solutions for growth in the selective environment, which in turn led to different physiological constraints.},

keywords = {Demography and Ecology},

pubstate = {published},

tppubtype = {article}

}

@article{Rozen2005,

title = {Long-Term Experimental Evolution in \textit{Escherichia coli}. XIII. Phylogenetic History of a Balanced Polymorphism},

author = {Daniel E. Rozen and Dominique Schneider and Richard E. Lenski},

url = {http://link.springer.com/10.1007/s00239-004-0322-2},

doi = {10.1007/s00239-004-0322-2},

issn = {0022-2844},

year  = {2005},

date = {2005-08-01},

urldate = {2005-08-01},

journal = {Journal of Molecular Evolution},

volume = {61},

number = {2},

pages = {171--180},

abstract = {We investigated the phylogenetic history of a balanced polymorphism that evolved in an experimental population of \textit{Escherichia coli}. Previous work showed that two ecologically and morphologically distinct types, designated L (large) and S (small), arose by generation 6000 and coexisted for more than 12,000 generations thereafter. Here, we performed RFLP analyses using Insertion Sequence elements to resolve the phylogenetic history of L and S. Specifically, we sought to determine whether the derived S morph was monophyletic, indicating a long history of coexistence with L or, alternatively, S was repeatedly regenerated from L, indicating a series of periods with only transiently stable coexistence. Phylogenetic analysis of some 200 clones collected throughout the history of this population demonstrates that S is monophyletic. We then performed competition assays using clones of both morphs from different generations to determine whether either or both lineages continued to undergo genetic adaptation. Indeed, both lineages continued to adapt, and their continued evolution contributed to fluctuations in their relative abundance over evolutionary time. Based on their phylogenetic history and independent evolutionary trajectories, S and L fulfill Cohan's criteria for being different asexual species. },

keywords = {Demography and Ecology, Genome Evolution},

pubstate = {published},

tppubtype = {article}

}

@article{Rozen2000,

title = {Long-term experimental evolution in \textit{Escherichia coli}. VIII. Dynamics of a balanced polymorphism},

author = {Daniel E. Rozen and Richard E. Lenski},

url = {https://www.journals.uchicago.edu/doi/full/10.1086/303299},

doi = {10.1086/303299},

issn = {00030147},

year  = {2000},

date = {2000-01-01},

urldate = {2000-01-01},

journal = {American Naturalist},

volume = {155},

number = {1},

pages = {24--35},

abstract = {We describe the short- and long-term dynamics of a phenotypic polymorphism that arose in a population of \textit{Escherichia coli} while it was serially propagated for almost 20,000 generations in a glucose-limited minimal medium. The two types, designated \textit{L} and \textit{S}, differ conspicuously in the size of the colonies they form on agar plates as well as the size of their individual cells, and these differences are heritable. The \textit{S} type reached a detectable frequency (>1%) at generation 6,000, and it remained above that frequency throughout the subsequent generations. In addition to morphological differences, \textit{L} and \textit{S} diverged in important ecological properties. With clones isolated at 18,000 generations, \textit{L} has a maximal growth rate in fresh medium that is ~20% higher than that of \textit{S}. However, experiments with conditioned media demonstrate that \textit{L} and \textit{S} secrete one or more metabolites that promote the growth of \textit{S} but not of \textit{L}. The death rate of \textit{L} during stationary phase also increases when \textit{S} is abundant, which suggests that \textit{S} may either secrete a metabolite that is toxic to \textit{L} or remove some factor that enables the survival of \textit{L}. One-day competition experiments with the clones isolated at generation 18,000 show that their relative fitness is frequency dependent, with each type having an advantage when rare. When these two types are grown together for a period of several weeks, they converge on an equilibrium frequency that is consistent with the 1-d competition experiments. Over the entire 14,000-generation period of coexistence, however, the frequency of the \textit{S} type fluctuated between approximately 10% and 85%. We offer several hypotheses that may explain the fluctuations in this balanced polymorphism, including the possibility of coevolution between the two types.},

keywords = {Demography and Ecology},

pubstate = {published},

tppubtype = {article}

}

@article{Elena1997,

title = {Long-term experimental evolution in \textit{Escherichia coli}. VII. Mechanisms maintaining genetic variability within populations.},

author = {Santiago F. Elena and Richard E. Lenski},

url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1997.tb03953.x},

doi = {10.1111/j.1558-5646.1997.tb03953.x},

issn = {0014-3820},

year  = {1997},

date = {1997-08-01},

urldate = {1997-08-01},

journal = {Evolution},

volume = {51},

number = {4},

pages = {1058--1067},

abstract = {Six replicate populations of the bacterium \textit{Escherichia coli} were propagated for more than 10,000 generations in a defined environment. We sought to quantify the variation among clones within these populations with respect to their relative fitness, and to evaluate the roles of three distinct population genetic processes in maintaining this variation. On average, a pair of clones from the same population differed from one another in their relative fitness by approximately 4%. This within-population variation was small compared with the average fitness gain relative to the common ancestor, but it was statistically significant. According to one hypothesis. The variation in fitness is transient and reflects the ongoing substitution of beneficial alleles. We used Fisher's fundamental theorem to compare the observed rate of each population's change in mean fitness with the extent of variation for fitness within that population, but we failed to discern any correspondence between these quantities. A second hypothesis supposes that the variation in fitness is maintained by recurrent deleterious mutations that give rise to a mutation-selection balance. To test this hypothesis, we made use of the fact that two of the six replicate populations had evolved mutator phenotypes, which gave them a genomic mutation rate approximately 100-fold higher than that of the other populations. There was a marginally significant correlation between a population's mutation rate and the extent of its within-population variance for fitness, but this correlation was driven by only one population (whereas two of the populations had elevated mutation rates). Under a third hypothesis, this variation is maintained by frequency-dependent selection, whereby genotypes have an advantage when they are rare relative to when they are common. In all six populations, clones were more fit, on average, when they were rare than when they were common, although the magnitude of the advantage when rare was usually small (~1% in five populations and ~45% in the other). These three hypotheses are not mutually exclusive, but frequency-dependent selection appears to be the primary force maintaining the fitness variation within these experimental populations.},

keywords = {Demography and Ecology, Fitness Trajectories, Mutation Rates, Theory and Simulations},

pubstate = {published},

tppubtype = {article}

}

@article{Vasi1994,

title = {Long-Term Experimental Evolution in \textit{Escherichia coli}. II. Changes in Life-History Traits During Adaptation to a Seasonal Environment},

author = {Farida K. Vasi and Michael Travisano and Richard E. Lenski},

url = {https://www.journals.uchicago.edu/doi/10.1086/285685},

doi = {10.1086/285685},

issn = {0003-0147},

year  = {1994},

date = {1994-09-01},

urldate = {1994-09-01},

journal = {The American Naturalist},

volume = {144},

number = {3},

pages = {432--456},

abstract = {Twelve populations of the bacterium \textit{Escherichia coli} were propagated for 2,000 generations in a seasonal environment, which consisted of alternating periods of feast and famine. The mean fitness of the derived genotypes increased by ∼35% relative to their common ancestor, based on competition experiments in the same environment. The bacteria could have adapted, in principle, by decreasing their lag prior to growth upon transfer to fresh medium (L), increasing their maximum growth rate (V_{m}), reducing the concentration of resource required to support growth at half the maximum rate (K_{s}), and reducing their death rate after the limiting resource was exhausted (D). We estimated these parameters for the ancestor and then calculated the opportunity for selection on each parameter. The inferred selection gradients for V_{m} and L were much steeper than for K_{s} and D. The derived genotypes showed significant improvement in V_{m} and L but not in K_{s} or D. Also, the numerical yield in pure culture of the derived genotypes was significantly lower than the yield of the common ancestor, but the average cell size was much larger. The independently derived genotypes are somewhat more variable in these life-history traits than in their relative fitnesses, which indicates that they acquired different genetic adaptations to the seasonal environment. Nonetheless, the evolutionary changes in life-history traits exhibit substantial parallelism among the replicate populations.},

keywords = {Demography and Ecology, Parallelism and Divergence},

pubstate = {published},

tppubtype = {article}

}