Publications

@article{lenski2023,

title = {Revisiting the design of the long-term evolution experiment with \textit{Escherichia coli}},

author = {Richard E. Lenski},

url = {https://link.springer.com/epdf/10.1007/s00239-023-10095-3?sharing_token=zmDHuK0kbvnJBQq1k96fe_e4RwlQNchNByi7wbcMAY53KNkhv6F2YgRIeC8sZGNejxJrvlAGZWInruED5Dqdai5WeU2RAWL2PJNp0pL9QJO39B_ijCtRZcaW8jqM7PclDJfFwL_78U5zNlQYyCOsQwa1Yxha61uXUWhW-Buiq7o=},

doi = {10.1007/s00239-023-10095-3},

year  = {2023},

date = {2023-02-15},

journal = {Journal of Molecular Evolution},

abstract = {The long-term evolution experiment (LTEE) with \textit{Escherichia coli} began in 1988 and it continues to this day, with its 12 populations having recently reached 75,000 generations of evolution in a simple, well-controlled environment. The LTEE was designed to explore open-ended questions about the dynamics and repeatability of phenotypic and genetic evolution. Here I discuss various aspects of the LTEE’s experimental design that have enabled its stability and success, including the choices of the culture regime, growth medium, ancestral strain, and statistical replication. I also discuss some of the challenges associated with a long-running project, such as handling procedural errors (e.g., cross-contamination) and managing the expanding collection of frozen samples. The simplicity of the experimental design and procedures have supported the long-term stability of the LTEE. That stability—along with the inherent creativity of the evolutionary process and the emergence of new genomic technologies—provides a platform that has allowed talented students and collaborators to pose questions, collect data, and make discoveries that go far beyond anything I could have imagined at the start of the LTEE.},

keywords = {Citrate Evolution, Descendant Experiments, Fitness Trajectories, Genome Evolution, Methods and Miscellaneous, Review Articles},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{ascensao2023,

title = {Quantifying the adaptive potential of a nascent bacterial community},

author = {Joao A. Ascensao and Kelly M. Wetmore and Benjamin H. Good and Adam P. Arkin and Oskar Hallatschek},

url = {https://www.nature.com/articles/s41467-022-35677-5},

doi = {10.1038/s41467-022-35677-5},

year  = {2023},

date = {2023-01-16},

urldate = {2022-01-01},

journal = {Nature Communications},

volume = {14},

number = {1},

pages = {248},

publisher = {Cold Spring Harbor Laboratory},

abstract = {The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes (“L” and “S”) shortly after they emerged within the \textit{E. coli} Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.},

keywords = {Demography and Ecology, Descendant Experiments, Genome Evolution, Genotypes and Phenotypes},

pubstate = {published},

tppubtype = {article}

}

@article{Laurin2022,

title = {Extracellular Vesicles from 50,000 Generation Clones of the Escherichia coli Long-Term Evolution Experiment},

author = {David Laurin and Corinne Mercier and Nyamekye Quansah and Julie Suzanne Robert and Yves Usson and Dominique Schneider and Thomas Hindré and Béatrice Schaack },

url = {https://www.mdpi.com/1422-0067/23/23/14580},

doi = {10.3390/ijms232314580},

issn = {1422-0067},

year  = {2022},

date = {2022-11-01},

urldate = {2022-11-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

pages = {14580},

abstract = {Extracellular vesicles (EVs) are critical elements of cell–cell communication. Here, we characterized the outer membrane vesicles (OMVs) released by specific clones of Escherichia coli isolated from the Long-Term Evolution Experiment after 50,000 generations (50K) of adaptation to glucose minimal medium. Compared with their ancestor, the evolved clones produce small OMVs but also larger ones which display variable amounts of both OmpA and LPS. Tracking ancestral, fluorescently labelled OMVs revealed that they fuse with both ancestral- and 50K-evolved cells, albeit in different proportions. We quantified that less than 2% of the cells from one 50K-evolved clone acquired the fluorescence delivered by OMVs from the ancestral strain but that one cell concomitantly fuses with several OMVs. Globally, our results showed that OMV production in E. coli is a phenotype that varies along bacterial evolution and question the contribution of OMVs-mediated interactions in bacterial adaptation.},

keywords = {Cell Morphology, Genotypes and Phenotypes},

pubstate = {published},

tppubtype = {article}

}

@article{favate2022,

title = {The landscape of transcriptional and translational changes over 22 years of bacterial adaptation},

author = {John S. Favate AND Shun Liang AND Alexander L. Cope AND Srujana S. Yadavilli AND Premal Shah},

editor = {Detlef Weigel},

url = {https://elifesciences.org/articles/81979},

doi = {10.7554/eLife.81979},

year  = {2022},

date = {2022-10-10},

urldate = {2022-10-10},

journal = {eLife},

volume = {11},

pages = {e81979},

abstract = {Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the \textit{Escherichia coli} long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.},

howpublished = {eLife},

keywords = {Genotypes and Phenotypes, Parallelism and Divergence},

pubstate = {published},

tppubtype = {article}

}

@article{izutsu2022,

title = {Experimental test of the contributions of initial variation and new mutations to adaptive evolution in a novel environment},

author = {Minako Izutsu and Richard E. Lenski},

url = {https://www.frontiersin.org/articles/10.3389/fevo.2022.958406/full},

doi = {10.3389/fevo.2022.958406},

issn = {2296-701X},

year  = {2022},

date = {2022-10-06},

urldate = {2022-10-01},

journal = {Frontiers in Ecology and Evolution},

volume = {10},

pages = {958406},

abstract = {Experimental evolution is an approach that allows researchers to study organisms as they evolve in controlled environments. Despite the growing popularity of this approach, there are conceptual gaps among projects that use different experimental designs. One such gap concerns the contributions to adaptation of genetic variation present at the start of an experiment and that of new mutations that arise during an experiment. The primary source of genetic variation has historically depended largely on the study organisms. In the long-term evolution experiment (LTEE) using \textit{Escherichia coli}, for example, each population started from a single haploid cell, and therefore, adaptation depended entirely on new mutations. Most other microbial evolution experiments have followed the same strategy. By contrast, evolution experiments using multicellular, sexually reproducing organisms typically start with preexisting variation that fuels the response to selection. New mutations may also come into play in later generations of these experiments, but it is generally difficult to quantify their contribution in these studies. Here, we performed an experiment using \textit{E. coli} to compare the contributions of initial genetic variation and new mutations to adaptation in a new environment. Our experiment had four treatments that varied in their starting diversity, with 18 populations in each treatment. One treatment depended entirely on new mutations, while the other three began with mixtures of clones, whole-population samples, or mixtures of whole-population samples from the LTEE. We tracked a genetic marker associated with different founders in two treatments. These data revealed significant variation in fitness among the founders, and that variation impacted evolution in the early generations of our experiment. However, there were no differences in fitness among the treatments after 500 or 2,000 generations in the new environment, despite the variation in fitness among the founders. These results indicate that new mutations quickly dominated, and eventually they contributed more to adaptation than did the initial variation. Our study thus shows that preexisting genetic variation can have a strong impact on early evolution in a new environment, but new beneficial mutations may contribute more to later evolution and can even drive some initially beneficial variants to extinction.},

keywords = {Descendant Experiments, Historical Contingency, Parallelism and Divergence},

pubstate = {published},

tppubtype = {article}

}

@article{smith2022,

title = {Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns},

author = {Chelsea E. Smith AND Adam N. H. Smith AND Tim F. Cooper AND Francisco B.-G. Moore},

url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2022.1292},

doi = {10.1098/rspb.2022.1292},

year  = {2022},

date = {2022-09-14},

journal = {Proceedings of the Royal Society B: Biological Sciences},

volume = {289},

number = {1982},

pages = {20221292},

abstract = {Long-term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments and chance events, all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2000 generations of evolution of four natural isolates of \textit{Escherichia coli} bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.},

keywords = {Descendant Experiments, Fitness Trajectories, Genotypes and Phenotypes, Historical Contingency},

pubstate = {published},

tppubtype = {article}

}

@article{maddamsetti2022,

title = {Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations},

author = { Rohan Maddamsetti and Nkrumah A. Grant},

editor = {Jianzhi Zhang},

url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010324},

doi = {10.1371/journal.pgen.1010324},

issn = {1553-7404},

year  = {2022},

date = {2022-08-18},

urldate = {2022-08-18},

journal = {PLOS Genetics},

volume = {18},

number = {8},

pages = {e1010324},

abstract = {A general method to infer both positive and purifying selection during the real-time evolution of hypermutator pathogens would be broadly useful. To this end, we introduce a simple test to infer mode of selection (STIMS) from metagenomic time series of evolving microbial populations. We test STIMS on metagenomic data generated by simulations of bacterial evolution, and on metagenomic data spanning 62,750 generations of Lenski’s long-term evolution experiment with \textit{Escherichia coli} (LTEE). This benchmarking shows that STIMS detects positive selection in both nonmutator and hypermutator populations, and purifying selection in hypermutator populations. Using STIMS, we find strong evidence of ongoing positive selection on key regulators of the \textit{E. coli} gene regulatory network, even in some hypermutator populations. STIMS also detects positive selection on regulatory genes in hypermutator populations of \textit{Pseudomonas aeruginosa} that adapted to subinhibitory concentrations of colistin—an antibiotic of last resort—for just twenty-six days of laboratory evolution. Our results show that the fine-tuning of gene regulatory networks is a general mechanism for rapid and ongoing adaptation. The simplicity of STIMS, together with its intuitive visual interpretation, make it a useful test for positive and purifying selection in metagenomic data sets that track microbial evolution in real-time.},

key = {Maddamsetti2022},

keywords = {Genome Evolution, Mutation Rates},

pubstate = {published},

tppubtype = {article}

}

@article{marshall2021,

title = {Long-term experimental evolution decouples size and production costs in \emph{Escherichia coli}},

author = {Dustin J. Marshall and Martino Malerba and Thomas Lines and Aysha L. Sezmis and Chowdhury M. Hasan and Richard E. Lenski and Michael J. McDonald},

editor = {Ruth Shaw},

url = {https://pnas.org/doi/full/10.1073/pnas.2200713119},

doi = {10.1073/pnas.2200713119},

year  = {2022},

date = {2022-05-20},

urldate = {2021-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {119},

number = {21},

pages = {e2200713119},

abstract = {Body size covaries with population dynamics across life’s domains. Metabolism may impose fundamental constraints on the coevolution of size and demography, but experimental tests of the causal links remain elusive. We leverage a 60,000-generation experiment in which \textit{Escherichia coli} populations evolved larger cells to examine intraspecific metabolic scaling and correlations with demographic parameters. Over the course of their evolution, the cells have roughly doubled in size relative to their ancestors. These larger cells have metabolic rates that are absolutely higher, but relative to their size, they are lower. Metabolic theory successfully predicted the relations between size, metabolism, and maximum population density, including support for Damuth’s law of energy equivalence, such that populations of larger cells achieved lower maximum densities but higher maximum biomasses than populations of smaller cells. The scaling of metabolism with cell size thus predicted the scaling of size with maximum population density. In stark contrast to standard theory, however, populations of larger cells grew faster than those of smaller cells, contradicting the fundamental and intuitive assumption that the costs of building new individuals should scale directly with their size. The finding that the costs of production can be decoupled from size necessitates a reevaluation of the evolutionary drivers and ecological consequences of biological size more generally.},

howpublished = {bioRxiv},

keywords = {Cell Morphology, Demography and Ecology},

pubstate = {published},

tppubtype = {article}

}

@article{mathe-hubert2022,

title = {Evolution of bacterial persistence to antibiotics during a 50,000-generation experiment in an antibiotic-free environment},

author = {Hugo Mathé-Hubert and Rafika Amie and Mikaël Martin and Joël Gaffé and Dominique Schneider},

url = {https://www.mdpi.com/2079-6382/11/4/451},

doi = {10.3390/antibiotics11040451},

issn = {2079-6382},

year  = {2022},

date = {2022-03-27},

urldate = {2022-03-27},

journal = {Antibiotics},

volume = {11},

number = {4},

pages = {451},

abstract = {Failure of antibiotic therapies causes >700,000 deaths yearly and involves both bacterial resistance and persistence. Persistence results in the relapse of infections by producing a tiny fraction of pathogen survivors that stay dormant during antibiotic exposure. From an evolutionary perspective, persistence is either a ‘bet-hedging strategy’ that helps to cope with stochastically changing environments or an unavoidable minimal rate of ‘cellular errors’ that lock the cells in a low activity state. Here, we analyzed the evolution of persistence over 50,000 bacterial generations in a stable environment by improving a published method that estimates the number of persister cells based on the growth of the reviving population. Our results challenged our understanding of the factors underlying persistence evolution. In one case, we observed a substantial decrease in persistence proportion, suggesting that the naturally observed persistence level is not an unavoidable minimal rate of ‘cellular errors’. However, although there was no obvious environmental stochasticity, in 11 of the 12 investigated populations, the persistence level was maintained during 50,000 bacterial generations.},

keywords = {Correlated Responses, Genotypes and Phenotypes},

pubstate = {published},

tppubtype = {article}

}

@article{Jordan2022.02.06.479266,

title = {Idiosyncratic fitness costs of ampicillin-resistant mutants derived from a long-term experiment with \textit{Escherichia coli}},

author = {Jalin A. Jordan and Richard E. Lenski and Kyle J. Card},

url = {https://www.biorxiv.org/content/10.1101/2022.02.06.479266v1},

doi = {10.3390/antibiotics11030347},

issn = {2079-6382},

year  = {2022},

date = {2022-03-13},

urldate = {2022-03-13},

journal = {Antibiotics},

volume = {11},

number = {3},

pages = {347},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Antibiotic resistance is a growing concern that has prompted a renewed focus on drug discovery, stewardship, and evolutionary studies of the patterns and processes that underlie this phenomenon. A resistant strain’s competitive fitness relative to its sensitive counterparts in the absence of drug can impact its spread and persistence in both clinical and community settings. In a prior study, we examined the fitness of tetracycline-resistant clones that evolved from five different Escherichia coli genotypes, which had diverged during a long-term evolution experiment. In this study, we build on that work to examine whether ampicillin-resistant mutants are also less fit in the absence of the drug than their sensitive parents, and whether the cost of resistance is constant or variable among independently derived lines. Like the tetracycline-resistant lines, the ampicillin-resistant mutants were often less fit than their sensitive parents, with significant variation in the fitness costs among the mutants. This variation was not associated with the level of resistance conferred by the mutations, nor did it vary across the different parental backgrounds. In our earlier study, some of the variation in fitness costs associated with tetracycline resistance was explained by the effects of different mutations affecting the same cellular pathway and even the same gene. In contrast, the variance among the ampicillin-resistant mutants was associated with different sets of target genes. About half of the resistant clones suffered large fitness deficits, and their mutations impacted major outer-membrane proteins or subunits of RNA polymerases. The other mutants experienced little or no fitness costs and with, one exception, they had mutations affecting other genes and functions. Our findings underscore the importance of comparative studies on the evolution of antibiotic resistance, and they highlight the nuanced processes that shape these phenotypes.},

keywords = {Descendant Experiments},

pubstate = {published},

tppubtype = {article}

}

@article{Consuegra2021,

title = {Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria},

author = {Jessika Consuegra and Joël Gaffé and Richard E. Lenski and Thomas Hindré and Jeffrey E. Barrick and Olivier Tenaillon and Dominique Schneider},

url = {http://www.nature.com/articles/s41467-021-21210-7},

doi = {https://doi.org/10.1038/s41467-021-21210-7},

issn = {2041-1723},

year  = {2021},

date = {2021-12-01},

urldate = {2021-12-01},

journal = {Nature Communications},

volume = {12},

number = {1},

pages = {980},

publisher = {Springer US},

abstract = {Insertion sequences (IS) are ubiquitous bacterial mobile genetic elements, and the mutations they cause can be deleterious, neutral, or beneficial. The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with \textit{Escherichia coli}. IS elements account for ~35% of the mutations that reached high frequency through 50,000 generations in those populations that retained the ancestral point-mutation rate. In mutator populations, IS-mediated mutations are only half as frequent in absolute numbers. In one population, an exceptionally high ~8-fold increase in IS 150 copy number is associated with the beneficial effects of early insertion mutations; however, this expansion later slowed down owing to reduced IS 150 activity. This population also achieves the lowest fitness, suggesting that some avenues for further adaptation are precluded by the IS 150 -mediated mutations. More generally, across all populations, we find that higher IS activity becomes detrimental to adaptation over evolutionary time. Therefore, IS-mediated mutations can both promote and constrain evolvability.},

keywords = {Fitness Trajectories, Genome Evolution, Mutation Rates},

pubstate = {published},

tppubtype = {article}

}

@article{DEATHERAGE2021,

title = {High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing},

author = {Daniel E. Deatherage and Jeffrey E. Barrick},

url = {https://www.sciencedirect.com/science/article/pii/S2405471221003343 

https://linkinghub.elsevier.com/retrieve/pii/S2405471221003343},

doi = {10.1016/j.cels.2021.08.011},

issn = {24054712},

year  = {2021},

date = {2021-09-01},

urldate = {2021-09-01},

journal = {Cell Systems},

abstract = {Understanding how cells are likely to evolve can guide medical interventions and bioengineering efforts that must contend with unwanted mutations. The adaptome of a cell—the neighborhood of genetic changes that are most likely to drive adaptation in a given environment—can be mapped by tracking rare beneficial variants during the early stages of clonal evolution. We used multiplex adaptome capture sequencing (mAdCap-seq), a procedure that combines unique molecular identifiers and hybridization-based enrichment, to characterize mutations in eight \textit{Escherichia coli} genes known to be under selection in a laboratory environment. We tracked 301 mutations at frequencies as low as 0.01% and inferred the fitness effects of 240 of these mutations. There were distinct molecular signatures of selection on protein structure and function for the three genes with the most beneficial mutations. Our results demonstrate how mAdCap-seq can be used to deeply profile a targeted portion of a cell's adaptome.},

keywords = {Descendant Experiments, Fitness Trajectories, Methods and Miscellaneous},

pubstate = {published},

tppubtype = {article}

}

@article{Grant2021b,

title = {Maintenance of Metabolic Plasticity despite Relaxed Selection in a Long-Term Evolution Experiment with \textit{Escherichia coli}},

author = {Nkrumah A. Grant and Rohan Maddamsetti and Richard E. Lenski},

url = {https://www.journals.uchicago.edu/doi/10.1086/714530},

doi = {10.1086/714530},

issn = {0003-0147},

year  = {2021},

date = {2021-07-01},

urldate = {2021-07-01},

journal = {The American Naturalist},

volume = {198},

number = {1},

pages = {93--112},

abstract = {Traits that are unused in a given environment are subject to processes that tend to erode them, leading to reduced fitness in other environments. Although this general tendency is clear, we know much less about why some traits are lost while others are retained and about the roles of mutation and selection in generating different responses. We addressed these issues by examining populations of a facultative anaerobe, \textit{Escherichia coli}, that have evolved for 130 years in the presence of oxygen, with relaxed selection for anaerobic growth and the associated metabolic plasticity. We asked whether evolution led to the loss, improvement, or maintenance of anaerobic growth, and we analyzed gene expression and mutational data sets to understand the outcomes. We identified genomic signatures of both positive and purifying selection on aerobic-specific genes, while anaerobic-specific genes showed clear evidence of relaxed selection. We also found parallel evolution at two interacting loci that regulate anaerobic growth. We competed the ancestor and evolved clones from each population in an anoxic environment, and we found that anaerobic fitness had not decayed, despite relaxed selection. In summary, relaxed selection does not necessarily reduce an organism's fitness in other environments. Instead, the genetic architecture of the traits under relaxed selection and their correlations with traits under positive and purifying selection may sometimes determine evolutionary outcomes.},

keywords = {Correlated Responses, Fitness Trajectories, Genome Evolution, Genotypes and Phenotypes},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/molbev/msab077,

title = {Historical Contingency Causes Divergence in Adaptive Expression of the lac Operon},

author = {Kedar Karkare and Huei-Yi Lai and Ricardo B. R. Azevedo and Tim F. Cooper},

editor = {Patricia Wittkopp},

url = {https://academic.oup.com/mbe/article/38/7/2869/6179336},

doi = {10.1093/molbev/msab077},

issn = {1537-1719},

year  = {2021},

date = {2021-06-01},

urldate = {2021-06-01},

journal = {Molecular Biology and Evolution},

volume = {38},

number = {7},

pages = {2869--2879},

abstract = {Populations of \textit{Escherichia coli} selected in constant and fluctuating environments containing lactose often adapt by substituting mutations in the lacI repressor that cause constitutive expression of the lac operon. These mutations occur at a high rate and provide a significant benefit. Despite this, eight of 24 populations evolved for 8,000 generations in environments containing lactose contained no detectable repressor mutations. We report here on the basis of this observation. We find that, given relevant mutation rates, repressor mutations are expected to have fixed in all evolved populations if they had maintained the same fitness effect they confer when introduced to the ancestor. In fact, reconstruction experiments demonstrate that repressor mutations have become neutral or deleterious in those populations in which they were not detectable. Populations not fixing repressor mutations nevertheless reached the same fitness as those that did fix them, indicating that they followed an alternative evolutionary path that made redundant the potential benefit of the repressor mutation, but involved unique mutations of equivalent benefit. We identify a mutation occurring in the promoter region of the uspB gene as a candidate for influencing the selective choice between these paths. Our results detail an example of historical contingency leading to divergent evolutionary outcomes.},

keywords = {Descendant Experiments},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Idiosyncratic variation in the fitness costs of tetracycline-resistance mutations in \textit{Escherichia coli}},

author = {Kyle J. Card and Jalin A. Jordan and Richard E. Lenski},

url = {https://onlinelibrary.wiley.com/doi/10.1111/evo.14203},

doi = {10.1111/evo.14203},

issn = {0014-3820},

year  = {2021},

date = {2021-02-25},

urldate = {2021-02-25},

journal = {Evolution},

volume = {75},

number = {5},

pages = {1230-1238},

abstract = {A bacterium's fitness relative to its competitors, both in the presence and absence of antibiotics, plays a key role in its ecological success and clinical impact. In this study, we examine whether tetracycline-resistant mutants are less fit in the absence of the drug than their sensitive parents, and whether the fitness cost of resistance is constant or variable across independently derived lines. Tetracycline-resistant lines suffered, on average, a reduction in fitness of almost 8%. There was substantial among-line variation in the fitness cost. This variation was not associated with the level of resistance conferred by the mutations, nor did it vary significantly across several genetic backgrounds. The two resistant lines with the most extreme fitness costs involved functionally unrelated mutations on different genetic backgrounds. However, there was also significant variation in the fitness costs for mutations affecting the same pathway and even different alleles of the same gene. Our findings demonstrate that the fitness costs of antibiotic resistance do not always correlate with the phenotypic level of resistance or the underlying genetic changes. Instead, these costs reflect the idiosyncratic effects of particular resistance mutations and the genetic backgrounds in which they occur.},

keywords = {Descendant Experiments},

pubstate = {published},

tppubtype = {article}

}

@article{Card2021,

title = {Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with \textit{Escherichia coli}},

author = {Kyle J. Card and Misty D. Thomas and Joseph L. Graves and Jeffrey E. Barrick and Richard E. Lenski},

url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2016886118},

doi = {10.1073/pnas.2016886118},

issn = {0027-8424},

year  = {2021},

date = {2021-02-01},

urldate = {2021-02-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {118},

number = {5},

pages = {e2016886118},

abstract = {Antibiotic resistance is a growing health concern. Efforts to control resistance would benefit from an improved ability to forecast when and how it will evolve. Epistatic interactions between mutations can promote divergent evolutionary trajectories, which complicates our ability to predict evolution. We recently showed that differences between genetic backgrounds can lead to idiosyncratic responses in the evolvability of phenotypic resistance, even among closely related \textit{Escherichia coli} strains. In this study, we examined whether a strain's genetic background also influences the genotypic evolution of resistance. Do lineages founded by different genotypes take parallel or divergent mutational paths to achieve their evolved resistance states? We addressed this question by sequencing the complete genomes of antibiotic-resistant clones that evolved from several different genetic starting points during our earlier experiments. We first validated our statistical approach by quantifying the specificity of genomic evolution with respect to antibiotic treatment. As expected, mutations in particular genes were strongly associated with each drug. Then, we determined that replicate lines evolved from the same founding genotypes had more parallel mutations at the gene level than lines evolved from different founding genotypes, although these effects were more subtle than those showing antibiotic specificity. Taken together with our previous work, we conclude that historical contingency can alter both genotypic and phenotypic pathways to antibiotic resistance.},

keywords = {Descendant Experiments, Genome Evolution, Historical Contingency},

pubstate = {published},

tppubtype = {article}

}