2023
Lenski R E
Revisiting the design of the long-term evolution experiment with Escherichia coli Journal Article
Journal of Molecular Evolution, 91 (3), pp. 241-253, 2023.
Abstract | Links | BibTeX | Altmetric | Tags: Citrate Evolution, Descendant Experiments, Fitness Trajectories, Genome Evolution, Methods and Miscellaneous, Review Articles
@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 = {2023-06-01},
urldate = {2023-02-15},
journal = {Journal of Molecular Evolution},
volume = {91},
number = {3},
pages = {241-253},
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 = {published},
tppubtype = {article}
}
The long-term evolution experiment (LTEE) with 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.
2018
Blount Z D; Lenski R E; Losos J B
Contingency and determinism in evolution: Replaying life's tape Journal Article
Science, 362 (6415), pp. eaam5979, 2018, ISSN: 0036-8075.
Abstract | Links | BibTeX | Altmetric | Tags: Historical Contingency, Parallelism and Divergence, Review Articles
@article{Blount2018,
title = {Contingency and determinism in evolution: Replaying life's tape},
author = {Zachary D. Blount and Richard E. Lenski and Jonathan B. Losos},
url = {https://www.sciencemag.org/lookup/doi/10.1126/science.aam5979},
doi = {10.1126/science.aam5979},
issn = {0036-8075},
year = {2018},
date = {2018-11-01},
urldate = {2018-11-01},
journal = {Science},
volume = {362},
number = {6415},
pages = {eaam5979},
abstract = {Historical processes display some degree of "contingency," meaning their outcomes are sensitive to seemingly inconsequential events that can fundamentally change the future. Contingency is what makes historical outcomes unpredictable. Unlike many other natural phenomena, evolution is a historical process. Evolutionary change is often driven by the deterministic force of natural selection, but natural selection works upon variation that arises unpredictably through time by random mutation, and even beneficial mutations can be lost by chance through genetic drift. Moreover, evolution has taken place within a planetary environment with a particular history of its own. This tension between determinism and contingency makes evolutionary biology a kind of hybrid between science and history. While philosophers of science examine the nuances of contingency, biologists have performed many empirical studies of evolutionary repeatability and contingency. Here, we review the experimental and comparative evidence from these studies. Replicate populations in evolutionary "replay" experiments often show parallel changes, especially in overall performance, although idiosyncratic outcomes show that the particulars of a lineage's history can affect which of several evolutionary paths is taken. Comparative biologists have found many notable examples of convergent adaptation to similar conditions, but quantification of how frequently such convergence occurs is difficult. On balance, the evidence indicates that evolution tends to be surprisingly repeatable among closely related lineages, but disparate outcomes become more likely as the footprint of history grows deeper. Ongoing research on the structure of adaptive landscapes is providing additional insight into the interplay of fate and chance in the evolutionary process.},
keywords = {Historical Contingency, Parallelism and Divergence, Review Articles},
pubstate = {published},
tppubtype = {article}
}
Historical processes display some degree of "contingency," meaning their outcomes are sensitive to seemingly inconsequential events that can fundamentally change the future. Contingency is what makes historical outcomes unpredictable. Unlike many other natural phenomena, evolution is a historical process. Evolutionary change is often driven by the deterministic force of natural selection, but natural selection works upon variation that arises unpredictably through time by random mutation, and even beneficial mutations can be lost by chance through genetic drift. Moreover, evolution has taken place within a planetary environment with a particular history of its own. This tension between determinism and contingency makes evolutionary biology a kind of hybrid between science and history. While philosophers of science examine the nuances of contingency, biologists have performed many empirical studies of evolutionary repeatability and contingency. Here, we review the experimental and comparative evidence from these studies. Replicate populations in evolutionary "replay" experiments often show parallel changes, especially in overall performance, although idiosyncratic outcomes show that the particulars of a lineage's history can affect which of several evolutionary paths is taken. Comparative biologists have found many notable examples of convergent adaptation to similar conditions, but quantification of how frequently such convergence occurs is difficult. On balance, the evidence indicates that evolution tends to be surprisingly repeatable among closely related lineages, but disparate outcomes become more likely as the footprint of history grows deeper. Ongoing research on the structure of adaptive landscapes is providing additional insight into the interplay of fate and chance in the evolutionary process.
2017
Lenski R E
What is adaptation by natural selection? Perspectives of an experimental microbiologist Journal Article
PLOS Genetics, 13 (4), pp. e1006668, 2017, ISSN: 1553-7404.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{Lenski2017,
title = {What is adaptation by natural selection? Perspectives of an experimental microbiologist},
author = {Richard E. Lenski},
editor = {W. Ford Doolittle},
url = {https://dx.plos.org/10.1371/journal.pgen.1006668},
doi = {10.1371/journal.pgen.1006668},
issn = {1553-7404},
year = {2017},
date = {2017-04-01},
urldate = {2017-04-01},
journal = {PLOS Genetics},
volume = {13},
number = {4},
pages = {e1006668},
abstract = {Use of at least three potent antiretroviral agents has become the standard of care in the management of HIV infection. The potential toxicities associated with highly active antiretroviral therapy (HAART) however, may limit a patient's ability to adhere to and tolerate these agents. Although a comprehensive discussion of all toxicities associated with HAART is beyond the scope of this article, selected short-term and long-term significant toxicities will be reviewed. Short-term toxicities that will be discussed include abacavir-induced hypersensitivity reactions, efavirenz-associated central nervous system side effects and rash associated with the non-nucleoside reverse transcriptase inhibitors (NNRTIs) and the protease inhibitor (PI) amprenavir. Several long-term toxicities associated with the nucleoside reverse transcriptase inhibitors (NRTIs) are hypothesized to be due to mitochondrial toxicity. These toxicities include myositis and lactic acidosis with hepatic steatosis, pancreatitis and peripheral neuropathy. Some experts also hypothesize that mitochondrial toxicity is responsible for the lipodystrophy syndrome, which includes hyperglycemia, abnormal fat redistribution and dyslipidemia. Finally, indinavir-associated nephrolithiasis, which may present with either short term or long term use will be discussed. This article will provide the practicing pharmacist with a review of these significant toxicities, the implicated agents, incidence, usual clinical presentation, and recommendations for management.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
Use of at least three potent antiretroviral agents has become the standard of care in the management of HIV infection. The potential toxicities associated with highly active antiretroviral therapy (HAART) however, may limit a patient's ability to adhere to and tolerate these agents. Although a comprehensive discussion of all toxicities associated with HAART is beyond the scope of this article, selected short-term and long-term significant toxicities will be reviewed. Short-term toxicities that will be discussed include abacavir-induced hypersensitivity reactions, efavirenz-associated central nervous system side effects and rash associated with the non-nucleoside reverse transcriptase inhibitors (NNRTIs) and the protease inhibitor (PI) amprenavir. Several long-term toxicities associated with the nucleoside reverse transcriptase inhibitors (NRTIs) are hypothesized to be due to mitochondrial toxicity. These toxicities include myositis and lactic acidosis with hepatic steatosis, pancreatitis and peripheral neuropathy. Some experts also hypothesize that mitochondrial toxicity is responsible for the lipodystrophy syndrome, which includes hyperglycemia, abnormal fat redistribution and dyslipidemia. Finally, indinavir-associated nephrolithiasis, which may present with either short term or long term use will be discussed. This article will provide the practicing pharmacist with a review of these significant toxicities, the implicated agents, incidence, usual clinical presentation, and recommendations for management.
2016
Blount Z D
A case study in evolutionary contingency Journal Article
Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 58 , pp. 82–92, 2016, ISSN: 13698486.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{Blount2016,
title = {A case study in evolutionary contingency},
author = {Zachary D. Blount},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1369848615001806},
doi = {10.1016/j.shpsc.2015.12.007},
issn = {13698486},
year = {2016},
date = {2016-08-01},
urldate = {2016-08-01},
journal = {Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences},
volume = {58},
pages = {82--92},
publisher = {Elsevier Ltd},
abstract = {Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the \textit{Escherichia coli} Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of \textit{E. coli} have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit+), a novel trait for \textit{E. coli}, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit+ trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit+), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit+ trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.
2015
Fox J W; Lenski R E
From Here to Eternity—The Theory and Practice of a Really Long Experiment Journal Article
PLOS Biology, 13 (3), pp. e1002185, 2015, ISSN: 1545-7885.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{nokey,
title = {From Here to Eternity—The Theory and Practice of a Really Long Experiment},
author = {Jeremy W. Fox and Richard E. Lenski},
url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002185},
doi = {10.1371/journal.pbio.1002185},
issn = {1545-7885},
year = {2015},
date = {2015-06-23},
urldate = {2015-06-23},
journal = {PLOS Biology},
volume = {13},
number = {3},
pages = { e1002185},
abstract = {In February 1988, Richard Lenski set up 12 replicate populations of a single genotype of \textit{Escherichia coli} in a simple nutrient medium. He has been following their evolution ever since. Here, Lenski answers provocative questions from Jeremy Fox about his iconic "Long-Term Evolution Experiment" (LTEE). The LTEE is a remarkable case study of the interplay of determinism and chance in evolution—and in the conduct of science.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
In February 1988, Richard Lenski set up 12 replicate populations of a single genotype of Escherichia coli in a simple nutrient medium. He has been following their evolution ever since. Here, Lenski answers provocative questions from Jeremy Fox about his iconic "Long-Term Evolution Experiment" (LTEE). The LTEE is a remarkable case study of the interplay of determinism and chance in evolution—and in the conduct of science.
2013
Barrick J E; Lenski R E
Genome dynamics during experimental evolution Journal Article
Nature Reviews Genetics, 14 (12), pp. 827–839, 2013, ISSN: 1471-0056.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{Barrick2013,
title = {Genome dynamics during experimental evolution},
author = {Jeffrey E. Barrick and Richard E. Lenski},
url = {http://www.nature.com/articles/nrg3564},
doi = {10.1038/nrg3564},
issn = {1471-0056},
year = {2013},
date = {2013-12-01},
urldate = {2013-12-01},
journal = {Nature Reviews Genetics},
volume = {14},
number = {12},
pages = {827--839},
abstract = {Evolutionary changes in organismal traits may occur either gradually or suddenly. However, until recently, there has been little direct information about how phenotypic changes are related to the rate and the nature of the underlying genotypic changes. Technological advances that facilitate whole-genome and whole-population sequencing, coupled with experiments that 'watch' evolution in action, have brought new precision to and insights into studies of mutation rates and genome evolution. In this Review, we discuss the evolutionary forces and ecological processes that govern genome dynamics in various laboratory systems in the context of relevant population genetic theory, and we relate these findings to evolution in natural populations.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
Evolutionary changes in organismal traits may occur either gradually or suddenly. However, until recently, there has been little direct information about how phenotypic changes are related to the rate and the nature of the underlying genotypic changes. Technological advances that facilitate whole-genome and whole-population sequencing, coupled with experiments that 'watch' evolution in action, have brought new precision to and insights into studies of mutation rates and genome evolution. In this Review, we discuss the evolutionary forces and ecological processes that govern genome dynamics in various laboratory systems in the context of relevant population genetic theory, and we relate these findings to evolution in natural populations.
2011
Lenski R E
Evolution in Action: a 50,000-Generation Salute to Charles Darwin Journal Article
Microbe Magazine, 6 (1), pp. 30–33, 2011, ISSN: 1558-7452.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{Lenski2011,
title = {Evolution in Action: a 50,000-Generation Salute to Charles Darwin},
author = {Richard E. Lenski},
url = {https://www.semanticscholar.org/paper/Evolution-in-Action%3A-a-50%2C000-Generation-Salute-to-Lenski/a75187b9d6e968c3f80dbfd949f19b8c333e7540
https://www.researchgate.net/publication/270690851_Evolution_in_Action_a_50000-Generation_Salute_to_Charles_Darwin},
doi = {https://doi.org/10.1128/MICROBE.6.30.1},
issn = {1558-7452},
year = {2011},
date = {2011-01-01},
urldate = {2011-01-01},
journal = {Microbe Magazine},
volume = {6},
number = {1},
pages = {30--33},
abstract = {Like cuneiform on clay tablets, the history of life itself is written in minerals and in code. The minerals are fossils of long-dead organisms, while the code is the language of DNA shared by all organisms, revealing the family tree of life.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
Like cuneiform on clay tablets, the history of life itself is written in minerals and in code. The minerals are fossils of long-dead organisms, while the code is the language of DNA shared by all organisms, revealing the family tree of life.
2008
Lenski R E
Chance and necessity in evolution Book Chapter
Morris, Simon Conway (Ed.): The deep structure of biology:is convergence sufficiently ubiquitous to give a directional signal?, Chapter 1, pp. 3–16, Templeton Foundation Press, West Conshohocken, 2008, ISBN: 9781599471723.
Abstract | Links | BibTeX | Tags: Review Articles
@inbook{Lenski2008,
title = {Chance and necessity in evolution},
author = {Richard E. Lenski},
editor = {Simon Conway Morris},
url = {https://searchworks.stanford.edu/view/13022746},
isbn = {9781599471723},
year = {2008},
date = {2008-01-01},
urldate = {2008-01-01},
booktitle = {The deep structure of biology:is convergence sufficiently ubiquitous to give a directional signal?},
pages = {3--16},
publisher = {Templeton Foundation Press},
address = {West Conshohocken},
chapter = {1},
abstract = {We humans have long recognized the profound tension that exists in our world between chance and necessity, between things that seem to happen by accident and those that seem inevitable or even purposeful. Democritus said that “everything existing in the universe is the fruit of chance and necessity.” The aphorism that “necessity is the mother of invention” finds its counterpoint in Mark Twain’s quip that “necessity is the mother of taking chances.” Even in our most goal-directed endeavors, we see the tension between accident and purpose, as Louis Pasteur did in saying that “chance favors only the prepared mind.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {inbook}
}
We humans have long recognized the profound tension that exists in our world between chance and necessity, between things that seem to happen by accident and those that seem inevitable or even purposeful. Democritus said that “everything existing in the universe is the fruit of chance and necessity.” The aphorism that “necessity is the mother of invention” finds its counterpoint in Mark Twain’s quip that “necessity is the mother of taking chances.” Even in our most goal-directed endeavors, we see the tension between accident and purpose, as Louis Pasteur did in saying that “chance favors only the prepared mind.
2007
Philippe N; Crozat E; Lenski R E; Schneider D
Evolution of global regulatory networks during a long-term experiment with Escherichia coli Journal Article
BioEssays, 29 (9), pp. 846-860, 2007, ISSN: 02659247.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{nokey,
title = {Evolution of global regulatory networks during a long-term experiment with \textit{Escherichia coli}},
author = {Nadège Philippe and Estelle Crozat and Richard E. Lenski and Dominique Schneider},
url = {https://onlinelibrary.wiley.com/doi/10.1002/bies.20629},
doi = {10.1002/bies.20629},
issn = {02659247},
year = {2007},
date = {2007-08-09},
urldate = {2007-08-09},
journal = {BioEssays},
volume = {29},
number = {9},
pages = {846-860},
abstract = {Evolution has shaped all living organisms on Earth, although many details of this process are shrouded in time. However, it is possible to see, with one's own eyes, evolution as it happens by performing experiments in defined laboratory conditions with microbes that have suitably fast generations. The longest-running microbial evolution experiment was started in 1988, at which time twelve populations were founded by the same strain of \textit{Escherichia coli}. Since then, the populations have been serially propagated and have evolved for tens of thousands of generations in the same environment. The populations show numerous parallel phenotypic changes, and such parallelism is a hallmark of adaptive evolution. Many genetic targets of natural selection have been identified, revealing a high level of genetic parallelism as well. Beneficial mutations affect all levels of gene regulation in the cells including individual genes and operons all the way to global regulatory networks. Of particular interest, two highly interconnected networks - governing DNA superhelicity and the stringent response - have been demonstrated to be deeply involved in the phenotypic and genetic adaptation of these experimental populations.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
Evolution has shaped all living organisms on Earth, although many details of this process are shrouded in time. However, it is possible to see, with one's own eyes, evolution as it happens by performing experiments in defined laboratory conditions with microbes that have suitably fast generations. The longest-running microbial evolution experiment was started in 1988, at which time twelve populations were founded by the same strain of Escherichia coli. Since then, the populations have been serially propagated and have evolved for tens of thousands of generations in the same environment. The populations show numerous parallel phenotypic changes, and such parallelism is a hallmark of adaptive evolution. Many genetic targets of natural selection have been identified, revealing a high level of genetic parallelism as well. Beneficial mutations affect all levels of gene regulation in the cells including individual genes and operons all the way to global regulatory networks. Of particular interest, two highly interconnected networks - governing DNA superhelicity and the stringent response - have been demonstrated to be deeply involved in the phenotypic and genetic adaptation of these experimental populations.
2004
Schneider D; Lenski R E
Dynamics of insertion sequence elements during experimental evolution of bacteria Journal Article
Research in Microbiology, 155 (5), pp. 319–327, 2004, ISSN: 09232508.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{Schneider2004,
title = {Dynamics of insertion sequence elements during experimental evolution of bacteria},
author = {Dominique Schneider and Richard E. Lenski},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0923250804000671},
doi = {10.1016/j.resmic.2003.12.008},
issn = {09232508},
year = {2004},
date = {2004-06-01},
urldate = {2004-06-01},
journal = {Research in Microbiology},
volume = {155},
number = {5},
pages = {319--327},
abstract = {We review the intersection between two areas of microbial evolution that were research foci of Michel Blot. One focus is the behavior of insertion sequence (IS) elements, including their role in promoting the evolutionary adaptation of their hosts. The other focus is experimental evolution, an approach that allows the dynamics of genomic and phenotypic change to be observed in the laboratory. This review shows that IS elements are useful as markers for detecting genomic change over experimental time scales and, moreover, that IS elements generate some of the beneficial mutations that increase organismal fitness. },
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
We review the intersection between two areas of microbial evolution that were research foci of Michel Blot. One focus is the behavior of insertion sequence (IS) elements, including their role in promoting the evolutionary adaptation of their hosts. The other focus is experimental evolution, an approach that allows the dynamics of genomic and phenotypic change to be observed in the laboratory. This review shows that IS elements are useful as markers for detecting genomic change over experimental time scales and, moreover, that IS elements generate some of the beneficial mutations that increase organismal fitness.
Lenski R E
Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. Incollection
Plant Breeding Reviews, pp. 225 – 265, 2004.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@incollection{Lenski2004,
title = {Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium \textit{Escherichia coli}.},
author = {Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1002/9780470650288.ch8},
doi = {http://dx.doi.org/10.1002/9780470650288.ch8},
year = {2004},
date = {2004-01-01},
urldate = {2004-01-01},
booktitle = {Plant Breeding Reviews},
pages = {225 -- 265},
edition = {24},
chapter = {8},
abstract = {This paper reviews another long-term selection experiment, one that is both shorter and longer than the 100 years of selection for oil and protein content in maize that is the main focus of this volume. In 1988, 12 populations of the bacterium \textit{Escherichia coli} were founded from the same strain, and these have been propagated in a simple, defined laboratory environment ever since. Each day, the populations are diluted in fresh medium, undergo about 6.6 generations of binary fission before they exhaust the limiting resource, and then must wait until their “springtime” appears again the next day.
This review summarizes some interesting changes and dynamics, both phenotypic and genomic, that occurred in these populations through generation 20,000. For an annual plant 20,000 generations would of course require some 20,000 years; for humans 20,000 generations would span 400,000 years, assuming an average generation of 20 years. This ability to observe evolution in action over many generations is an obvious benefit of studying bacteria. In fact, the experiment recently passed 30,000 generations, but the bacteria evolve faster than we can study them, and generation 20,000 represents the last milestone at which we systematically studied the populations. Rather than taking the same measurements at intervals, we have repeatedly pushed our analyses in new directions. Thus, some changes were analyzed through 2,000 generations, others through 10,000 generations, and still other changes through 20,000 generations. Another wonderful feature of bacteria for evolutionary research is that we can store entire populations frozen, and resurrect them whenever we wish, such that we can gather more data about earlier generations if we later find other aspects of the evolving bacteria that we want to measure and study.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {incollection}
}
This paper reviews another long-term selection experiment, one that is both shorter and longer than the 100 years of selection for oil and protein content in maize that is the main focus of this volume. In 1988, 12 populations of the bacterium Escherichia coli were founded from the same strain, and these have been propagated in a simple, defined laboratory environment ever since. Each day, the populations are diluted in fresh medium, undergo about 6.6 generations of binary fission before they exhaust the limiting resource, and then must wait until their “springtime” appears again the next day.
This review summarizes some interesting changes and dynamics, both phenotypic and genomic, that occurred in these populations through generation 20,000. For an annual plant 20,000 generations would of course require some 20,000 years; for humans 20,000 generations would span 400,000 years, assuming an average generation of 20 years. This ability to observe evolution in action over many generations is an obvious benefit of studying bacteria. In fact, the experiment recently passed 30,000 generations, but the bacteria evolve faster than we can study them, and generation 20,000 represents the last milestone at which we systematically studied the populations. Rather than taking the same measurements at intervals, we have repeatedly pushed our analyses in new directions. Thus, some changes were analyzed through 2,000 generations, others through 10,000 generations, and still other changes through 20,000 generations. Another wonderful feature of bacteria for evolutionary research is that we can store entire populations frozen, and resurrect them whenever we wish, such that we can gather more data about earlier generations if we later find other aspects of the evolving bacteria that we want to measure and study.
This review summarizes some interesting changes and dynamics, both phenotypic and genomic, that occurred in these populations through generation 20,000. For an annual plant 20,000 generations would of course require some 20,000 years; for humans 20,000 generations would span 400,000 years, assuming an average generation of 20 years. This ability to observe evolution in action over many generations is an obvious benefit of studying bacteria. In fact, the experiment recently passed 30,000 generations, but the bacteria evolve faster than we can study them, and generation 20,000 represents the last milestone at which we systematically studied the populations. Rather than taking the same measurements at intervals, we have repeatedly pushed our analyses in new directions. Thus, some changes were analyzed through 2,000 generations, others through 10,000 generations, and still other changes through 20,000 generations. Another wonderful feature of bacteria for evolutionary research is that we can store entire populations frozen, and resurrect them whenever we wish, such that we can gather more data about earlier generations if we later find other aspects of the evolving bacteria that we want to measure and study.
2003
Elena S F; Lenski R E
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation Journal Article
Nature Reviews Genetics, 4 (6), pp. 457–469, 2003, ISSN: 1471-0056.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{Elena2003,
title = {Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation},
author = {Santiago F. Elena and Richard E. Lenski},
url = {http://www.nature.com/articles/nrg1088},
doi = {10.1038/nrg1088},
issn = {1471-0056},
year = {2003},
date = {2003-06-01},
urldate = {2003-06-01},
journal = {Nature Reviews Genetics},
volume = {4},
number = {6},
pages = {457--469},
abstract = {Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.
2002
Lenski R E
Experimental evolution: a long-term study with E. coli. Miscellaneous
2002, ISBN: 9780195122008.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@misc{Lenski2002,
title = {Experimental evolution: a long-term study with \textit{E. coli}.},
author = {Richard E. Lenski},
editor = {M. Pagel and S. Frank and C. Godfray and B. K. Hall and K. Hawkes and D. M. Hillis and A. Kodric-Brown and R. E. Lenski and A. Pomiankowski},
url = {https://www.oxfordreference.com/view/10.1093/acref/9780195122008.001.0001/acref-9780195122008-e-137?rskey=hBoe2z&result=128},
doi = {10.1093/acref/9780195122008.001.0001},
isbn = {9780195122008},
year = {2002},
date = {2002-01-01},
urldate = {2002-01-01},
booktitle = {Encyclopedia of Evolution},
pages = {342--344},
publisher = {Oxford University Press},
address = {New York},
abstract = {The paleontologist Stephen Jay Gould envisioned a thought experiment of “replaying life’s tape” to explore the predictability, or repeatability, of evolution. Gould (1989) argued that evolution is not repeatable: “Any replay of the tape would lead evolution down a pathway radically different from the road actually taken ... no finale can be specified at the start, and none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages.” No one can replay evolution on the vast scale imagined by Gould. But on a much smaller scale, the following experiment examines the same issue by monitoring multiple populations, all founded all founded from the same ancestor, as they evolve in identical environments for thousands of generations.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {misc}
}
The paleontologist Stephen Jay Gould envisioned a thought experiment of “replaying life’s tape” to explore the predictability, or repeatability, of evolution. Gould (1989) argued that evolution is not repeatable: “Any replay of the tape would lead evolution down a pathway radically different from the road actually taken ... no finale can be specified at the start, and none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages.” No one can replay evolution on the vast scale imagined by Gould. But on a much smaller scale, the following experiment examines the same issue by monitoring multiple populations, all founded all founded from the same ancestor, as they evolve in identical environments for thousands of generations.
2001
Lenski R E
Chapter 2, pp. 25-45, 2001.
Abstract | Links | BibTeX | Tags: Review Articles
@inbook{articlec,
title = {Testing Antonovics' five tenets of ecological genetics: Experiments with bacteria at the interface of ecology and genetics},
author = {Richard E. Lenski},
url = {http://myxo.css.msu.edu/lenski/pdf/2001,%20EcoAchievementChallenge,%20Lenski.pdf
},
year = {2001},
date = {2001-01-01},
urldate = {2001-01-01},
journal = {Ecology: Achievement and Challenge},
pages = {25-45},
chapter = {2},
abstract = {When I began graduate school in 1977, I thought that ecology and genetics were completely distinct fields of study. I imagined that I could study ecological patterns and processes in blissful ignorance of genetics and without worrying that evolution would directly impinge on my research. This naïve view was soon dispelled by Janis Antonovics, who taught a wonderful course at Duke University in North Carolina on Ecological Genetics, which I took in 1979. In many treatments of population genetics, natural selection is largely devoid of its ecological context and appears only as an abstract coefficient, \textit{S}, that operates on gene frequencies, \textit{p} and \textit{q}. But Antonovics' course placed selection squarely in its ecological context. Moreover, his course examined the ecological consequences of changing gene frequencies, this emphasizing the feedback of evolutionary change on ecology. },
keywords = {Review Articles},
pubstate = {published},
tppubtype = {inbook}
}
When I began graduate school in 1977, I thought that ecology and genetics were completely distinct fields of study. I imagined that I could study ecological patterns and processes in blissful ignorance of genetics and without worrying that evolution would directly impinge on my research. This naïve view was soon dispelled by Janis Antonovics, who taught a wonderful course at Duke University in North Carolina on Ecological Genetics, which I took in 1979. In many treatments of population genetics, natural selection is largely devoid of its ecological context and appears only as an abstract coefficient, S, that operates on gene frequencies, p and q. But Antonovics' course placed selection squarely in its ecological context. Moreover, his course examined the ecological consequences of changing gene frequencies, this emphasizing the feedback of evolutionary change on ecology.
1998
Lenski R E; Mongold J A; Sniegowski P D; Travisano M; Vasi F K; Gerrish P J; Schmidt T M
Evolution of competitive fitness in experimental populations of E. coli: What makes one genotype a better competitor than another? Journal Article
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 73 (1), pp. 35–47, 1998, ISSN: 00036072.
Abstract | Links | BibTeX | Altmetric | Tags: Review Articles
@article{Lenski1998,
title = {Evolution of competitive fitness in experimental populations of \textit{E. coli}: What makes one genotype a better competitor than another?},
author = {Richard E. Lenski and Judith A. Mongold and Paul D. Sniegowski and Michael Travisano and Farida K. Vasi and Philip J. Gerrish and Thomas M. Schmidt},
url = {https://link.springer.com/article/10.1023%2FA%3A1000675521611},
doi = {10.1023/A:1000675521611},
issn = {00036072},
year = {1998},
date = {1998-01-01},
urldate = {1998-01-01},
journal = {Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology},
volume = {73},
number = {1},
pages = {35--47},
abstract = {An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of \textit{Escherichia coli} and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve \textit{E. coli} populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10,000 generations, the average fitness of the derived genotypes had increased by ~ 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some, but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate, for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.},
keywords = {Review Articles},
pubstate = {published},
tppubtype = {article}
}
An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10,000 generations, the average fitness of the derived genotypes had increased by ~ 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some, but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate, for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.