2002
Cooper V S
Long-term experimental evolution in Escherichia coli. X. Quantifying the fundamental and realized niche. Journal Article
BMC Evolutionary Biology, 9 , pp. 1–9, 2002.
Abstract | Links | BibTeX | Altmetric | Tags: Correlated Responses
@article{Cooper2002,
title = {Long-term experimental evolution in \textit{Escherichia coli}. X. Quantifying the fundamental and realized niche.},
author = {Vaughn S. Cooper},
url = {https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-2-12},
doi = {https://doi.org/10.1186/1471-2148-2-12},
year = {2002},
date = {2002-01-01},
urldate = {2002-01-01},
journal = {BMC Evolutionary Biology},
volume = {9},
pages = {1--9},
abstract = {Background
Twelve populations of the bacterium, \textit{Escherichia coli}, adapted to a simple, glucose-limited, laboratory environment over 10,000 generations. As a consequence, these populations tended to lose functionality on alternative resources. I examined whether these populations in turn became inferior competitors in four alternative environments. These experiments are among the first to quantify and compare dimensions of the fundamental and realized niches.
Results
Three clones were isolated from each of the twelve populations after 10,000 generations of evolution. Direct competition between these clones and the ancestor in the selective environment revealed average fitness improvements of ~50%. When grown in the wells of Biolog plates, however, evolved clones grew 25% worse on average than the ancestor on a variety of different carbon sources. Next, I competed each evolved population versus the ancestor in four foreign environments (10-fold higher and lower glucose concentration, added bile salts, and dilute LB media). Surprisingly, nearly all populations were more fit than the ancestor in each foreign environment, though the margin of improvement was least in the most different environment. Most populations also evolved increased sensitivity to novobiocin.
Conclusions
Reduced functionality on numerous carbon sources suggested that the fundamental niche of twelve \textit{E. coli} populations had narrowed after adapting to a specific laboratory environment. However, in spite of these results, the same populations were competitively superior in four novel environments. These findings suggest that adaptation to certain dimensions of the environment may compensate for other functional losses and apparently enhance the realized niche.},
keywords = {Correlated Responses},
pubstate = {published},
tppubtype = {article}
}
Background
Twelve populations of the bacterium, Escherichia coli, adapted to a simple, glucose-limited, laboratory environment over 10,000 generations. As a consequence, these populations tended to lose functionality on alternative resources. I examined whether these populations in turn became inferior competitors in four alternative environments. These experiments are among the first to quantify and compare dimensions of the fundamental and realized niches.
Results
Three clones were isolated from each of the twelve populations after 10,000 generations of evolution. Direct competition between these clones and the ancestor in the selective environment revealed average fitness improvements of ~50%. When grown in the wells of Biolog plates, however, evolved clones grew 25% worse on average than the ancestor on a variety of different carbon sources. Next, I competed each evolved population versus the ancestor in four foreign environments (10-fold higher and lower glucose concentration, added bile salts, and dilute LB media). Surprisingly, nearly all populations were more fit than the ancestor in each foreign environment, though the margin of improvement was least in the most different environment. Most populations also evolved increased sensitivity to novobiocin.
Conclusions
Reduced functionality on numerous carbon sources suggested that the fundamental niche of twelve E. coli populations had narrowed after adapting to a specific laboratory environment. However, in spite of these results, the same populations were competitively superior in four novel environments. These findings suggest that adaptation to certain dimensions of the environment may compensate for other functional losses and apparently enhance the realized niche.
Twelve populations of the bacterium, Escherichia coli, adapted to a simple, glucose-limited, laboratory environment over 10,000 generations. As a consequence, these populations tended to lose functionality on alternative resources. I examined whether these populations in turn became inferior competitors in four alternative environments. These experiments are among the first to quantify and compare dimensions of the fundamental and realized niches.
Results
Three clones were isolated from each of the twelve populations after 10,000 generations of evolution. Direct competition between these clones and the ancestor in the selective environment revealed average fitness improvements of ~50%. When grown in the wells of Biolog plates, however, evolved clones grew 25% worse on average than the ancestor on a variety of different carbon sources. Next, I competed each evolved population versus the ancestor in four foreign environments (10-fold higher and lower glucose concentration, added bile salts, and dilute LB media). Surprisingly, nearly all populations were more fit than the ancestor in each foreign environment, though the margin of improvement was least in the most different environment. Most populations also evolved increased sensitivity to novobiocin.
Conclusions
Reduced functionality on numerous carbon sources suggested that the fundamental niche of twelve E. coli populations had narrowed after adapting to a specific laboratory environment. However, in spite of these results, the same populations were competitively superior in four novel environments. These findings suggest that adaptation to certain dimensions of the environment may compensate for other functional losses and apparently enhance the realized niche.
2001
Cullum A J; Bennett A F; Lenski R E
Evolutionary adaptation to temperature. IX. Preadaptation to novel stressful environments of Escherichia coli adapted to high temperature Journal Article
Evolution, 55 (11), pp. 2194–2202, 2001, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Cullum2001,
title = {Evolutionary adaptation to temperature. IX. Preadaptation to novel stressful environments of \textit{Escherichia coli} adapted to high temperature},
author = {Alistair J. Cullum and Albert F. Bennett and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2001.tb00735.x},
doi = {10.1111/j.0014-3820.2001.tb00735.x},
issn = {0014-3820},
year = {2001},
date = {2001-11-01},
urldate = {2001-11-01},
journal = {Evolution},
volume = {55},
number = {11},
pages = {2194--2202},
abstract = {Stressful environments may be considered as those that reduce fitness, sometimes due in part to the increased metabolic expenditure required to sustain life. Direct adaptation to a stressor is expected to increase fitness and reduce maintenance metabolism, with the latter leading to increased biomass production. In this study, we test the general hypothesis that such adaptation to one stressor can preadapt organisms to novel stressful environments. Six lines of \textit{Escherichia coli} propagated for 2000 generations at 41-42°C (42 group), a stressful temperature, were compared to six control lines propagated for 2000 generations at 37°C (37 group) and to the common ancestor of both groups. We assayed biovolume yield (a measure of growth efficiency) and competitive fitness in the 42 group's selective high temperature environment as well as five novel stressful environments - acid, alkali, ethanol, high osmolarity and peroxide. As previously reported, at high temperature the 42 group had both higher yield and fitness than the 37 group and ancestor. In the novel environments, the 42 group generally produced yields higher than the 37 group (and marginally higher than the ancestor), but we found no differences in competitive fitness among the 37 and 42 groups and the ancestor. We also found that the performance of lines within groups was not correlated across stressful environments for either yield or relative fitness. Because previous adaptation to one stressor did not improve our measure of Darwinian fitness in novel stressful environments, we conclude that the 42 group shows no useful pre-adaptation, or cross-tolerance, to these types of environments.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Stressful environments may be considered as those that reduce fitness, sometimes due in part to the increased metabolic expenditure required to sustain life. Direct adaptation to a stressor is expected to increase fitness and reduce maintenance metabolism, with the latter leading to increased biomass production. In this study, we test the general hypothesis that such adaptation to one stressor can preadapt organisms to novel stressful environments. Six lines of Escherichia coli propagated for 2000 generations at 41-42°C (42 group), a stressful temperature, were compared to six control lines propagated for 2000 generations at 37°C (37 group) and to the common ancestor of both groups. We assayed biovolume yield (a measure of growth efficiency) and competitive fitness in the 42 group's selective high temperature environment as well as five novel stressful environments - acid, alkali, ethanol, high osmolarity and peroxide. As previously reported, at high temperature the 42 group had both higher yield and fitness than the 37 group and ancestor. In the novel environments, the 42 group generally produced yields higher than the 37 group (and marginally higher than the ancestor), but we found no differences in competitive fitness among the 37 and 42 groups and the ancestor. We also found that the performance of lines within groups was not correlated across stressful environments for either yield or relative fitness. Because previous adaptation to one stressor did not improve our measure of Darwinian fitness in novel stressful environments, we conclude that the 42 group shows no useful pre-adaptation, or cross-tolerance, to these types of environments.
Elena S F; Lenski R E
Epistasis between new mutations and genetic background and a test of genetic canalization Journal Article
Evolution, 55 (9), pp. 1746–1752, 2001, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Historical Contingency
@article{Elena2001,
title = {Epistasis between new mutations and genetic background and a test of genetic canalization},
author = {Santiago F. Elena and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2001.tb00824.x},
doi = {10.1111/j.0014-3820.2001.tb00824.x},
issn = {0014-3820},
year = {2001},
date = {2001-09-01},
urldate = {2001-09-01},
journal = {Evolution},
volume = {55},
number = {9},
pages = {1746--1752},
abstract = {The importance for fitness of epistatic interactions among mutations is poorly known, yet epistasis can exert important effects on the dynamics of evolving populations. We showed previously that epistatic interactions are common between pairs of random insertion mutations in the bacterium \textit{Escherichia coli}. In this paper, we examine interactions between these mutations and other mutations by transducing each of twelve insertion mutations into two genetic backgrounds, one ancestral and the other having evolved in, and adapted to, a defined laboratory environment for 10,000 generations. To assess the effect of the mutation on fitness, we allowed each mutant to compete against its unmutated counterpart in that same environment. Overall, there was a strong positive correlation between the mutational effects on the two genetic backgrounds. Nonetheless, three of the twelve mutations had significantly different effects on the two backgrounds, indicating epistasis. There was no significant tendency for the mutations to be less harmful on the derived background. Thus, there is no evidence supporting the hypothesis that the derived bacteria had adapted, in part, by becoming buffered against the harmful effects of mutations.},
keywords = {Historical Contingency},
pubstate = {published},
tppubtype = {article}
}
The importance for fitness of epistatic interactions among mutations is poorly known, yet epistasis can exert important effects on the dynamics of evolving populations. We showed previously that epistatic interactions are common between pairs of random insertion mutations in the bacterium Escherichia coli. In this paper, we examine interactions between these mutations and other mutations by transducing each of twelve insertion mutations into two genetic backgrounds, one ancestral and the other having evolved in, and adapted to, a defined laboratory environment for 10,000 generations. To assess the effect of the mutation on fitness, we allowed each mutant to compete against its unmutated counterpart in that same environment. Overall, there was a strong positive correlation between the mutational effects on the two genetic backgrounds. Nonetheless, three of the twelve mutations had significantly different effects on the two backgrounds, indicating epistasis. There was no significant tendency for the mutations to be less harmful on the derived background. Thus, there is no evidence supporting the hypothesis that the derived bacteria had adapted, in part, by becoming buffered against the harmful effects of mutations.
Remold S K; Lenski R E
Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli Journal Article
Proceedings of the National Academy of Sciences of the United States of America, 98 (20), pp. 11388–11393, 2001, ISSN: 0027-8424.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Remold2001,
title = {Contribution of individual random mutations to genotype-by-environment interactions in \textit{Escherichia coli}},
author = {Susanna K. Remold and Richard E. Lenski},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.201140198},
doi = {10.1073/pnas.201140198},
issn = {0027-8424},
year = {2001},
date = {2001-09-01},
urldate = {2001-09-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {98},
number = {20},
pages = {11388--11393},
abstract = {Numerous studies have shown genotype-by-environment (GxE) interactions for traits related to organismal fitness. However, the genetic architecture of the interaction is usually unknown because these studies used genotypes that differ from one another by many unknown mutations. These mutations were also present as standing variation in populations and hence had been subject to prior selection. Based on such studies, it is therefore impossible to say what fraction of new, random mutations contributes to GxE interactions. In this study, we measured the fitness in four environments of 26 genotypes of \textit{Escherichia coli}, each containing a single random insertion mutation. Fitness was measured relative to their common progenitor, which had evolved on glucose at 37°C for the preceding 10,000 generations. The four assay environments differed in limiting resource and temperature (glucose, 28°C; maltose, 28°C; glucose, 37°C; and maltose, 37°C). A highly significant interaction between mutation and resource was found. In contrast, there was no interaction involving temperature. The resource interaction reflected much higher among mutation variation for fitness in maltose than in glucose. At least 11 mutations (42%) contributed to this GxE interaction through their differential fitness effects across resources. Beneficial mutations are generally thought to be rare but, surprisingly, at least three mutations (12%) significantly improved fitness in maltose, a resource novel to the progenitor. More generally, our findings demonstrate that GxE interactions can be quite common, even for genotypes that differ by only one mutation and in environments differing by only a single factor.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Numerous studies have shown genotype-by-environment (GxE) interactions for traits related to organismal fitness. However, the genetic architecture of the interaction is usually unknown because these studies used genotypes that differ from one another by many unknown mutations. These mutations were also present as standing variation in populations and hence had been subject to prior selection. Based on such studies, it is therefore impossible to say what fraction of new, random mutations contributes to GxE interactions. In this study, we measured the fitness in four environments of 26 genotypes of Escherichia coli, each containing a single random insertion mutation. Fitness was measured relative to their common progenitor, which had evolved on glucose at 37°C for the preceding 10,000 generations. The four assay environments differed in limiting resource and temperature (glucose, 28°C; maltose, 28°C; glucose, 37°C; and maltose, 37°C). A highly significant interaction between mutation and resource was found. In contrast, there was no interaction involving temperature. The resource interaction reflected much higher among mutation variation for fitness in maltose than in glucose. At least 11 mutations (42%) contributed to this GxE interaction through their differential fitness effects across resources. Beneficial mutations are generally thought to be rare but, surprisingly, at least three mutations (12%) significantly improved fitness in maltose, a resource novel to the progenitor. More generally, our findings demonstrate that GxE interactions can be quite common, even for genotypes that differ by only one mutation and in environments differing by only a single factor.
Cooper V S; Schneider D; Blot M; Lenski R E
Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B Journal Article
Journal of Bacteriology, 183 (9), pp. 2834-2841, 2001, ISSN: 0021-9193.
Abstract | Links | BibTeX | Altmetric | Tags: Correlated Responses, Genotypes and Phenotypes
@article{nokey,
title = {Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of \textit{Escherichia coli} B},
author = {Vaughn S. Cooper and Dominique Schneider and Michel Blot and Richard E. Lenski},
url = {https://journals.asm.org/doi/full/10.1128/JB.183.9.2834-2841.2001},
doi = {10.1128/JB.183.9.2834-2841.2001},
issn = {0021-9193},
year = {2001},
date = {2001-05-01},
urldate = {2001-05-01},
journal = {Journal of Bacteriology},
volume = {183},
number = {9},
pages = {2834-2841},
abstract = {Twelve populations of \textit{Escherichia coli} B all lost d -ribose catabolic function during 2,000 generations of evolution in glucose minimal medium. We sought to identify the population genetic processes and molecular genetic events that caused these rapid and parallel losses. Seven independent Rbs ^{−} mutants were isolated, and their competitive fitnesses were measured relative to that of their Rbs ^{+} progenitor. These Rbs ^{−} mutants were all about 1 to 2% more fit than the progenitor. A fluctuation test revealed an unusually high rate, about 5 × 10 ^{−5} per cell generation, of mutation from Rbs ^{+} to Rbs ^{−}, which contributed to rapid fixation. At the molecular level, the loss of ribose catabolic function involved the deletion of part or all of the ribose operon (\textit{rbs} genes). The physical extent of the deletion varied between mutants, but each deletion was associated with an IS\textit{150} element located immediately upstream of the \textit{rbs} operon. The deletions apparently involved transposition into various locations within the \textit{rbs} operon; recombination between the new IS\textit{150} copy and the one upstream of the \textit{rbs} operon then led to the deletion of the intervening sequence. To confirm that the beneficial fitness effect was caused by deletion of the \textit{rbs} operon (and not some undetected mutation elsewhere), we used P1 transduction to restore the functional \textit{rbs} operon to two Rbs^{−} mutants, and we constructed another Rbs^{−} strain by gene replacement with a deletion not involving IS\textit{150}. All three of these new constructs confirmed that Rbs^{−} mutants have a competitive advantage relative to their Rbs^{+} counterparts in glucose minimal medium. The rapid and parallel evolutionary losses of ribose catabolic function thus involved both (i) an unusually high mutation rate, such that Rbs^{−} mutants appeared repeatedly in all populations, and (ii) a selective advantage in glucose minimal medium that drove these mutants to fixation.},
keywords = {Correlated Responses, Genotypes and Phenotypes},
pubstate = {published},
tppubtype = {article}
}
Twelve populations of Escherichia coli B all lost d -ribose catabolic function during 2,000 generations of evolution in glucose minimal medium. We sought to identify the population genetic processes and molecular genetic events that caused these rapid and parallel losses. Seven independent Rbs − mutants were isolated, and their competitive fitnesses were measured relative to that of their Rbs + progenitor. These Rbs − mutants were all about 1 to 2% more fit than the progenitor. A fluctuation test revealed an unusually high rate, about 5 × 10 −5 per cell generation, of mutation from Rbs + to Rbs −, which contributed to rapid fixation. At the molecular level, the loss of ribose catabolic function involved the deletion of part or all of the ribose operon (rbs genes). The physical extent of the deletion varied between mutants, but each deletion was associated with an IS150 element located immediately upstream of the rbs operon. The deletions apparently involved transposition into various locations within the rbs operon; recombination between the new IS150 copy and the one upstream of the rbs operon then led to the deletion of the intervening sequence. To confirm that the beneficial fitness effect was caused by deletion of the rbs operon (and not some undetected mutation elsewhere), we used P1 transduction to restore the functional rbs operon to two Rbs− mutants, and we constructed another Rbs− strain by gene replacement with a deletion not involving IS150. All three of these new constructs confirmed that Rbs− mutants have a competitive advantage relative to their Rbs+ counterparts in glucose minimal medium. The rapid and parallel evolutionary losses of ribose catabolic function thus involved both (i) an unusually high mutation rate, such that Rbs− mutants appeared repeatedly in all populations, and (ii) a selective advantage in glucose minimal medium that drove these mutants to fixation.
Cooper V S; Bennett A F; Lenski R E
Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment Journal Article
Evolution, 55 , pp. 889 - 896, 2001.
Abstract | Links | BibTeX | Altmetric | Tags: Correlated Responses
@article{articleb,
title = {Evolution of thermal dependence of growth rate of \textit{Escherichia coli} populations during 20,000 generations in a constant environment},
author = {Vaughn S. Cooper and Albert F. Bennett and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2001.tb00606.x},
doi = {10.1111/j.0014-3820.2001.tb00606.x},
year = {2001},
date = {2001-01-01},
urldate = {2001-01-01},
journal = {Evolution},
volume = {55},
pages = {889 - 896},
abstract = {Twelve experimental populations of the bacterium \textit{Escherichia coli} evolved for 20,000 generations in a defined medium at 37°C. We measured their maximum growth rates across a broad range of temperatures and at several evolutionary time points to quantify the extent to which they became thermal specialists with diminished performance at other temperatures. We also sought to determine whether antagonistic pleiotropy (genetic trade-offs) or mutation accumulation (drift decay) was primarily responsible for any thermal specialization. Populations showed consistent improvement in growth rate at moderate temperatures (27-39°C), but tended to have decreased growth rate at both low (20°C) and high (41-42°C) temperatures. Most loss occurred early in the experiment, when adaptation was most rapid. This dynamic is predicted by antagonistic pleiotropy but not by mutation accumulation. Several populations evolved high mutation rates due to defects in their DNA repair, but they did not subsequently undergo a greater decrease in growth rate at thermal extremes than populations that retained low mutation rates, contrary to the acceleration of decay predicted by mutation accumulation. Antagonistic pleiotropy therefore is more likely to be responsible for the evolution of thermal specialization observed in maximum growth rate.},
keywords = {Correlated Responses},
pubstate = {published},
tppubtype = {article}
}
Twelve experimental populations of the bacterium Escherichia coli evolved for 20,000 generations in a defined medium at 37°C. We measured their maximum growth rates across a broad range of temperatures and at several evolutionary time points to quantify the extent to which they became thermal specialists with diminished performance at other temperatures. We also sought to determine whether antagonistic pleiotropy (genetic trade-offs) or mutation accumulation (drift decay) was primarily responsible for any thermal specialization. Populations showed consistent improvement in growth rate at moderate temperatures (27-39°C), but tended to have decreased growth rate at both low (20°C) and high (41-42°C) temperatures. Most loss occurred early in the experiment, when adaptation was most rapid. This dynamic is predicted by antagonistic pleiotropy but not by mutation accumulation. Several populations evolved high mutation rates due to defects in their DNA repair, but they did not subsequently undergo a greater decrease in growth rate at thermal extremes than populations that retained low mutation rates, contrary to the acceleration of decay predicted by mutation accumulation. Antagonistic pleiotropy therefore is more likely to be responsible for the evolution of thermal specialization observed in maximum growth rate.
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.
2000
Schneider D; Duperchy E; Coursange E; Lenski R E; Blot M
Long-Term Experimental Evolution in Escherichia coli. IX. Characterization of Insertion Sequence-Mediated Mutations and Rearrangements Journal Article
Genetics, 156 (2), pp. 477–488, 2000, ISSN: 1943-2631.
Abstract | Links | BibTeX | Altmetric | Tags: Genome Evolution, Genotypes and Phenotypes
@article{Schneider2000,
title = {Long-Term Experimental Evolution in \textit{Escherichia coli}. IX. Characterization of Insertion Sequence-Mediated Mutations and Rearrangements},
author = {Dominique Schneider and Esther Duperchy and Evelyne Coursange and Richard E. Lenski and Michel Blot},
url = {https://academic.oup.com/genetics/article/156/2/477/6051340},
doi = {10.1093/genetics/156.2.477},
issn = {1943-2631},
year = {2000},
date = {2000-10-01},
urldate = {2000-10-01},
journal = {Genetics},
volume = {156},
number = {2},
pages = {477--488},
abstract = {As part of a long-term evolution experiment, two populations of \textit{Escherichia coli} B adapted to a glucose minimal medium for 10,000 generations. In both populations, multiple IS-associated mutations arose that then went to fixation. We identify the affected genetic loci and characterize the molecular events that produced nine of these mutations. All nine were IS-mediated events, including simple insertions as well as recombination between homologous elements that generated inversions and deletions. Sequencing DNA adjacent to the insertions indicates that the affected genes are involved in central metabolism (knockouts of \textit{pykF} and \textit{nadR}), cell wall synthesis (adjacent to the promoter of \textit{pbpA-rodA}), and ill-defined functions (knockouts of \textit{hokB-sokB} and \textit{yfcU}). These genes are candidates for manipulation and competition experiments to determine whether the mutations were beneficial or merely hitchhiked to fixation.},
keywords = {Genome Evolution, Genotypes and Phenotypes},
pubstate = {published},
tppubtype = {article}
}
As part of a long-term evolution experiment, two populations of Escherichia coli B adapted to a glucose minimal medium for 10,000 generations. In both populations, multiple IS-associated mutations arose that then went to fixation. We identify the affected genetic loci and characterize the molecular events that produced nine of these mutations. All nine were IS-mediated events, including simple insertions as well as recombination between homologous elements that generated inversions and deletions. Sequencing DNA adjacent to the insertions indicates that the affected genes are involved in central metabolism (knockouts of pykF and nadR), cell wall synthesis (adjacent to the promoter of pbpA-rodA), and ill-defined functions (knockouts of hokB-sokB and yfcU). These genes are candidates for manipulation and competition experiments to determine whether the mutations were beneficial or merely hitchhiked to fixation.
Cooper V S; Lenski R E
The population genetics of ecological specialization in evolving Escherichia coli populations Journal Article
Nature, 407 (6805), pp. 736–739, 2000, ISSN: 0028-0836.
Abstract | Links | BibTeX | Altmetric | Tags: Correlated Responses, Fitness Trajectories, Mutation Rates
@article{Schneider2000b,
title = {The population genetics of ecological specialization in evolving \textit{Escherichia coli} populations},
author = {Vaughn S. Cooper and Richard E. Lenski},
url = {http://www.nature.com/articles/35037572},
doi = {10.1038/35037572},
issn = {0028-0836},
year = {2000},
date = {2000-10-01},
urldate = {2000-10-01},
journal = {Nature},
volume = {407},
number = {6805},
pages = {736--739},
abstract = {When organisms adapt genetically to one environment, they may lose fitness in other environments. Two distinct population genetic processes can produce ecological specialization—mutation accumulation and antagonistic pleiotropy. In mutation accumulation, mutations become fixed by genetic drift in genes that are not maintained by selection; adaptation to one environment and loss of adaptation to another are caused by different mutations. Antagonistic pleiotropy arises from trade-offs, such that the same mutations that are beneficial in one environment are detrimental in another. In general, it is difficult to distinguish between these processes. We analysed the decay of unused catabolic functions in 12 lines of \textit{Escherichia coli} propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.},
keywords = {Correlated Responses, Fitness Trajectories, Mutation Rates},
pubstate = {published},
tppubtype = {article}
}
When organisms adapt genetically to one environment, they may lose fitness in other environments. Two distinct population genetic processes can produce ecological specialization—mutation accumulation and antagonistic pleiotropy. In mutation accumulation, mutations become fixed by genetic drift in genes that are not maintained by selection; adaptation to one environment and loss of adaptation to another are caused by different mutations. Antagonistic pleiotropy arises from trade-offs, such that the same mutations that are beneficial in one environment are detrimental in another. In general, it is difficult to distinguish between these processes. We analysed the decay of unused catabolic functions in 12 lines of Escherichia coli propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.
Moore F B G; Rozen D E; Lenski R E
Pervasive compensatory adaptation in Escherichia coli Journal Article
Proceedings of the Royal Society of London. Series B: Biological Sciences, 267 (1442), pp. 515–522, 2000, ISSN: 0962-8452.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Moore2000,
title = {Pervasive compensatory adaptation in \textit{Escherichia coli}},
author = {Francisco B. G. Moore and Daniel E. Rozen and Richard E. Lenski},
url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2000.1030},
doi = {10.1098/rspb.2000.1030},
issn = {0962-8452},
year = {2000},
date = {2000-03-01},
urldate = {2000-03-01},
journal = {Proceedings of the Royal Society of London. Series B: Biological Sciences},
volume = {267},
number = {1442},
pages = {515--522},
abstract = {To investigate compensatory adaptation (CA), we used genotypes of \textit{Escherichia coli} which were identical except for one or two deleterious mutations. We compared CA for (i) deleterious mutations with large versus small effects, (ii) genotypes carrying one versus two mutations, and (iii) pairs of deleterious mutations which interact in a multiplicative versus synergistic fashion. In all, we studied 14 different genotypes, plus a control strain which was not mutated. Most genotypes showed CA during 200 generations of experimental evolution, where we define CA as a fitness increase which is disproportionately large relative to that in evolving control lines, coupled with retention of the original deleterious mutation(s). We observed greater CA for mutations of large effect than for those of small effect, which can be explained by the greater benefit to recovery in severely handicapped genotypes given the dynamics of selection. The rates of CA were similar for double and single mutants whose initial fitnesses were approximately equal. CA was faster for synergistic than for multiplicative pairs, presumably because the marginal gain which results from CA for one of the component mutations is greater in that case. The most surprising result in our view, is that compensation should be so readily achieved in an organism which is haploid and has little genetic redundancy. This finding suggests a degree of versatility in the \textit{E. coli} genome which demands further study from both genetic and physiological perspectives.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
To investigate compensatory adaptation (CA), we used genotypes of Escherichia coli which were identical except for one or two deleterious mutations. We compared CA for (i) deleterious mutations with large versus small effects, (ii) genotypes carrying one versus two mutations, and (iii) pairs of deleterious mutations which interact in a multiplicative versus synergistic fashion. In all, we studied 14 different genotypes, plus a control strain which was not mutated. Most genotypes showed CA during 200 generations of experimental evolution, where we define CA as a fitness increase which is disproportionately large relative to that in evolving control lines, coupled with retention of the original deleterious mutation(s). We observed greater CA for mutations of large effect than for those of small effect, which can be explained by the greater benefit to recovery in severely handicapped genotypes given the dynamics of selection. The rates of CA were similar for double and single mutants whose initial fitnesses were approximately equal. CA was faster for synergistic than for multiplicative pairs, presumably because the marginal gain which results from CA for one of the component mutations is greater in that case. The most surprising result in our view, is that compensation should be so readily achieved in an organism which is haploid and has little genetic redundancy. This finding suggests a degree of versatility in the E. coli genome which demands further study from both genetic and physiological perspectives.
Rozen D E; Lenski R E
Long-term experimental evolution in Escherichia coli. VIII. Dynamics of a balanced polymorphism Journal Article
American Naturalist, 155 (1), pp. 24–35, 2000, ISSN: 00030147.
Abstract | Links | BibTeX | Altmetric | Tags: Demography and Ecology
@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}
}
We describe the short- and long-term dynamics of a phenotypic polymorphism that arose in a population of Escherichia coli while it was serially propagated for almost 20,000 generations in a glucose-limited minimal medium. The two types, designated L and 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 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, L and S diverged in important ecological properties. With clones isolated at 18,000 generations, L has a maximal growth rate in fresh medium that is ~20% higher than that of S. However, experiments with conditioned media demonstrate that L and S secrete one or more metabolites that promote the growth of S but not of L. The death rate of L during stationary phase also increases when S is abundant, which suggests that S may either secrete a metabolite that is toxic to L or remove some factor that enables the survival of 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 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.
Lenski R E; Mongold J A
Cell Size, Shape, and Fitness in Evolving Populations of Bacteria Book Chapter
Scaling in Biology, Oxford University Press, Inc., USA, 2000, ISBN: 019513141X.
Abstract | BibTeX | Tags: Cell Morphology, Correlated Responses, Demography and Ecology
@inbook{10.5555/345504.345526,
title = {Cell Size, Shape, and Fitness in Evolving Populations of Bacteria},
author = {Richard E. Lenski and Judith A. Mongold},
isbn = {019513141X},
year = {2000},
date = {2000-01-01},
urldate = {2000-01-01},
booktitle = {Scaling in Biology},
publisher = {Oxford University Press, Inc.},
address = {USA},
abstract = {There is a long and substantial history of studying allometric scaling relationships in animals and plants, which is well represented by other chapters in this volume. These studies have relevance for many fields, from cardiovascular physiology to community ecology. From the perspective of evolutionary biology, scaling relationships are important because they provide an empirical focus for investigating the tensions between structural constraints, on the one hand, and natural selection, on the other, as they vie to shape—quite literally—organisms and life histories. Despite the breadth of research on allometric scaling, those organisms at the microscopic end of the scale, especially bacteria, have been largely ignored.},
keywords = {Cell Morphology, Correlated Responses, Demography and Ecology},
pubstate = {published},
tppubtype = {inbook}
}
There is a long and substantial history of studying allometric scaling relationships in animals and plants, which is well represented by other chapters in this volume. These studies have relevance for many fields, from cardiovascular physiology to community ecology. From the perspective of evolutionary biology, scaling relationships are important because they provide an empirical focus for investigating the tensions between structural constraints, on the one hand, and natural selection, on the other, as they vie to shape—quite literally—organisms and life histories. Despite the breadth of research on allometric scaling, those organisms at the microscopic end of the scale, especially bacteria, have been largely ignored.
1999
Vulic M; Lenski R E; Radman M
Mutation, recombination, and incipient speciation of bacteria in the laboratory Journal Article
Proceedings of the National Academy of Sciences of the United States of America, 96 (13), pp. 7348–7351, 1999, ISSN: 0027-8424.
Abstract | Links | BibTeX | Altmetric | Tags: Genome Evolution, Mutation Rates
@article{Vulic1999,
title = {Mutation, recombination, and incipient speciation of bacteria in the laboratory},
author = {M. Vulic and Richard E. Lenski and Miroslav Radman},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.96.13.7348},
doi = {10.1073/pnas.96.13.7348},
issn = {0027-8424},
year = {1999},
date = {1999-06-01},
urldate = {1999-06-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {96},
number = {13},
pages = {7348--7351},
abstract = {Mutations in the DNA mismatch repair system increase mutation and recombination. They may thereby promote the genetic divergence that underlies speciation, after which the reacquisition of a functional repair system may sustain that divergence by creating a barrier to recombination. We tested several lines of \textit{Escherichia coli}, derived from a common ancestor and evolved for 20,000 generations, for their recombination ability. Some lines, but not others, had become mismatch repair-defective mutators during experimental evolution, providing different opportunities for DNA sequence divergence. We knocked out the repair system in lines that had retained this function, and we restored function to those lines that had become defective. We then estimated recombination rates in various crosses between these repair- deficient and -proficient strains. The effect of the mismatch repair system on recombination was greatest in those lines that had evolved nonfunctional repair, indicating they had undergone more sequence divergence and, consequently, were more sensitive to the recombination-inhibiting effect of a functional repair system. These results demonstrate the establishment of an incipient genetic barrier between formerly identical lines, and they support a model in which the mismatch repair system can influence speciation dynamics through its simultaneous effects on mutation and recombination.},
keywords = {Genome Evolution, Mutation Rates},
pubstate = {published},
tppubtype = {article}
}
Mutations in the DNA mismatch repair system increase mutation and recombination. They may thereby promote the genetic divergence that underlies speciation, after which the reacquisition of a functional repair system may sustain that divergence by creating a barrier to recombination. We tested several lines of Escherichia coli, derived from a common ancestor and evolved for 20,000 generations, for their recombination ability. Some lines, but not others, had become mismatch repair-defective mutators during experimental evolution, providing different opportunities for DNA sequence divergence. We knocked out the repair system in lines that had retained this function, and we restored function to those lines that had become defective. We then estimated recombination rates in various crosses between these repair- deficient and -proficient strains. The effect of the mismatch repair system on recombination was greatest in those lines that had evolved nonfunctional repair, indicating they had undergone more sequence divergence and, consequently, were more sensitive to the recombination-inhibiting effect of a functional repair system. These results demonstrate the establishment of an incipient genetic barrier between formerly identical lines, and they support a model in which the mismatch repair system can influence speciation dynamics through its simultaneous effects on mutation and recombination.
Vasi F K; Lenski R E
Ecological strategies and fitness tradeoffs in Escherichia coli mutants adapted to prolonged starvation Journal Article
Journal of Genetics, 78 (1), pp. 43–49, 1999, ISSN: 0022-1333.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Vasi1999,
title = {Ecological strategies and fitness tradeoffs in \textit{Escherichia coli} mutants adapted to prolonged starvation},
author = {Farida K. Vasi and Richard E. Lenski},
url = {http://link.springer.com/10.1007/BF02994702},
doi = {10.1007/BF02994702},
issn = {0022-1333},
year = {1999},
date = {1999-04-01},
urldate = {1999-04-01},
journal = {Journal of Genetics},
volume = {78},
number = {1},
pages = {43--49},
abstract = {Many bacteria in nature are nutritionally deprived, and there has been heightened interest during the past decade in the properties of these bacteria. We subjected five populations of \textit{Escherichia coli} to prolonged starvation in a minimal salts medium, during which time the density of viable cells declined by several orders of magnitude. From each one, we isolated a surviving clone that showed some heritable difference in colony morphology. We then characterized these mutants in two ecologically relevant respects. First, we determined the nature of their selective advantage, if any, during prolonged starvation. (i) Three of the five mutants had significantly lower net death rate when progenitor and mutant clones were starved separately. (ii) Three mutants showed a significant reduction in death rate in mixed culture that was frequency dependent and manifest when the mutant clone was initially rare. This pattern suggests that these mutants fed on some byproduct of progenitor cells (living or dead). (iii) Two mutants caused the death rate of their progenitors to increase significantly relative to the rate measured in the absence of the mutant. This pattern suggests that these mutants had become allelopathic to their progenitors. Thus, three distinct ecological adaptations to prolonged starvation are evident. No advantage was detected for one mutant, whereas two mutants exhibited multiple advantages. Second, we asked whether the starvation-selected mutants were as fit in growth-supporting conditions as their progenitors. All five mutants were inferior to their progenitor during competition in fresh medium. Evidently, there is an evolutionary tradeoff between performance under growth and starvation conditions. },
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Many bacteria in nature are nutritionally deprived, and there has been heightened interest during the past decade in the properties of these bacteria. We subjected five populations of Escherichia coli to prolonged starvation in a minimal salts medium, during which time the density of viable cells declined by several orders of magnitude. From each one, we isolated a surviving clone that showed some heritable difference in colony morphology. We then characterized these mutants in two ecologically relevant respects. First, we determined the nature of their selective advantage, if any, during prolonged starvation. (i) Three of the five mutants had significantly lower net death rate when progenitor and mutant clones were starved separately. (ii) Three mutants showed a significant reduction in death rate in mixed culture that was frequency dependent and manifest when the mutant clone was initially rare. This pattern suggests that these mutants fed on some byproduct of progenitor cells (living or dead). (iii) Two mutants caused the death rate of their progenitors to increase significantly relative to the rate measured in the absence of the mutant. This pattern suggests that these mutants had become allelopathic to their progenitors. Thus, three distinct ecological adaptations to prolonged starvation are evident. No advantage was detected for one mutant, whereas two mutants exhibited multiple advantages. Second, we asked whether the starvation-selected mutants were as fit in growth-supporting conditions as their progenitors. All five mutants were inferior to their progenitor during competition in fresh medium. Evidently, there is an evolutionary tradeoff between performance under growth and starvation conditions.
Mongold J A; Bennett A F; Lenski R E
Evolutionary adaptation to temperature. VII. Extension of the upper thermal limit of Escherichia coli Journal Article
Evolution, 53 (2), pp. 386–394, 1999, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Mongold1999,
title = {Evolutionary adaptation to temperature. VII. Extension of the upper thermal limit of \textit{Escherichia coli}},
author = {Judith A. Mongold and Albert F. Bennett and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1999.tb03774.x},
doi = {10.1111/j.1558-5646.1999.tb03774.x},
issn = {0014-3820},
year = {1999},
date = {1999-04-01},
urldate = {1999-04-01},
journal = {Evolution},
volume = {53},
number = {2},
pages = {386--394},
abstract = {What factors influence the ability of populations to adapt to extreme environments that lie outside their current tolerance limits? We investigated this question by exposing experimental populations of the bacterium \textit{Escherichia coli} to lethally high temperatures. We asked: (1) whether we could obtain thermotolerant mutants with an extended upper thermal limit by this selective screen; (2) whether the propensity to obtain thermotolerant mutants depended on the prior selective history of the progenitor genotypes; and (3) how the fitness properties of these mutants compared to those of their progenitors within the ancestral thermal niche. Specifically, we subjected 15 independent populations founded from each of six progenitors to 44°C; all of the progenitors had upper thermal limits between about 40°C and 42°C. Two of the progenitors were from populations that had previously adapted to 32°C, two were from populations adapted to 37°C, and two were from populations adapted to 41-42°C. All 90 populations were screened for mutants that could survive and grow at 44°C. We obtained three thermotolerant mutants, all derived from progenitors previously adapted to 41-42°C. In an earlier study, we serendipitously found one other thermotolerant mutant derived from a population that had previously adapted to 32°C. Thus, prior selection at an elevated but nonlethal temperature may predispose organisms to evolve more extreme thermotolerance, but this is not an absolute requirement. It is evidently possible to obtain mutants that tolerate more extreme temperatures, so why did they not become prevalent during prior selection at 41-42°C, near the upper limit of the thermal niche? To address this question, we measured the fitness of the thermotolerant mutants at high temperatures just within the ancestral niche. None of the four thermotolerant mutants had an advantage relative to their progenitor even very near the upper limit of the thermal niche; in fact, all of the mutants showed a noticeable loss of fitness around 41°C. Thus, the genetic adaptations that improve competitive fitness at high but nonlethal temperatures are distinct from those that permit tolerance of otherwise lethal temperatures.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
What factors influence the ability of populations to adapt to extreme environments that lie outside their current tolerance limits? We investigated this question by exposing experimental populations of the bacterium Escherichia coli to lethally high temperatures. We asked: (1) whether we could obtain thermotolerant mutants with an extended upper thermal limit by this selective screen; (2) whether the propensity to obtain thermotolerant mutants depended on the prior selective history of the progenitor genotypes; and (3) how the fitness properties of these mutants compared to those of their progenitors within the ancestral thermal niche. Specifically, we subjected 15 independent populations founded from each of six progenitors to 44°C; all of the progenitors had upper thermal limits between about 40°C and 42°C. Two of the progenitors were from populations that had previously adapted to 32°C, two were from populations adapted to 37°C, and two were from populations adapted to 41-42°C. All 90 populations were screened for mutants that could survive and grow at 44°C. We obtained three thermotolerant mutants, all derived from progenitors previously adapted to 41-42°C. In an earlier study, we serendipitously found one other thermotolerant mutant derived from a population that had previously adapted to 32°C. Thus, prior selection at an elevated but nonlethal temperature may predispose organisms to evolve more extreme thermotolerance, but this is not an absolute requirement. It is evidently possible to obtain mutants that tolerate more extreme temperatures, so why did they not become prevalent during prior selection at 41-42°C, near the upper limit of the thermal niche? To address this question, we measured the fitness of the thermotolerant mutants at high temperatures just within the ancestral niche. None of the four thermotolerant mutants had an advantage relative to their progenitor even very near the upper limit of the thermal niche; in fact, all of the mutants showed a noticeable loss of fitness around 41°C. Thus, the genetic adaptations that improve competitive fitness at high but nonlethal temperatures are distinct from those that permit tolerance of otherwise lethal temperatures.
Bennett A F; Lenski R E
Experimental Evolution and Its Role in Evolutionary Physiology Journal Article
American Zoologist, 39 (2), pp. 346–362, 1999, ISSN: 0003-1569.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{10.1093/icb/39.2.346,
title = {Experimental Evolution and Its Role in Evolutionary Physiology},
author = {Albert F. Bennett and Richard E. Lenski},
url = {https://doi.org/10.1093/icb/39.2.346
https://academic.oup.com/icb/article-lookup/doi/10.1093/icb/39.2.346},
doi = {10.1093/icb/39.2.346},
issn = {0003-1569},
year = {1999},
date = {1999-04-01},
urldate = {1999-04-01},
journal = {American Zoologist},
volume = {39},
number = {2},
pages = {346--362},
abstract = {Four general approaches to the study of evolutionary physiology—phylogenetically-based comparisons, genetic analyses and manipulations, phenotypic plasticity and manipulation, and selection studies—are outlined and discussed. We provide an example of the latter, the application of laboratory selection experiments to the study of a general issue in environmental adaptation, differences in adaptive patterns of generalists and specialists. A clone of the bacterium \textit{Escherichia coli} that had evolved in a constant environment of 37°C was replicated into 6 populations and allowed to reproduce for 2,000 generations in a variable thermal environment alternating between 32 and 42°C. As predicted by theory, fitness and efficiency of resource use increased in this new environment, as did stress resistance. Contrary to predictions, however, fitness and efficiency in the constant ancestral environment of 37°C did not decrease, nor did thermal niche breadth or phenotypic plasticity increase. Selection experiments can thus provide a valuable approach to testing hypotheses and assumptions about the evolution of functional characters.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Four general approaches to the study of evolutionary physiology—phylogenetically-based comparisons, genetic analyses and manipulations, phenotypic plasticity and manipulation, and selection studies—are outlined and discussed. We provide an example of the latter, the application of laboratory selection experiments to the study of a general issue in environmental adaptation, differences in adaptive patterns of generalists and specialists. A clone of the bacterium Escherichia coli that had evolved in a constant environment of 37°C was replicated into 6 populations and allowed to reproduce for 2,000 generations in a variable thermal environment alternating between 32 and 42°C. As predicted by theory, fitness and efficiency of resource use increased in this new environment, as did stress resistance. Contrary to predictions, however, fitness and efficiency in the constant ancestral environment of 37°C did not decrease, nor did thermal niche breadth or phenotypic plasticity increase. Selection experiments can thus provide a valuable approach to testing hypotheses and assumptions about the evolution of functional characters.
de Visser J A G M; Zeyl C W; Gerrish P J; Blanchard J L; Lenski R E
Diminishing returns from mutation supply rate in asexual populations. Journal Article
Science, 283 , pp. 404-406, 1999, ISSN: 00368075.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments, Fitness Trajectories, Mutation Rates
@article{nokey,
title = {Diminishing returns from mutation supply rate in asexual populations.},
author = {J. Arjan G. M. {de Visser} and C. W. Zeyl and Philip J. Gerrish and Jeffrey L. Blanchard and Richard E. Lenski},
url = {https://www.science.org/lookup/doi/10.1126/science.283.5400.404},
doi = {10.1126/science.283.5400.404},
issn = {00368075},
year = {1999},
date = {1999-01-15},
urldate = {1999-01-15},
journal = {Science},
volume = {283},
pages = {404-406},
abstract = {Mutator genotypes with increased mutation rates may be especially important in microbial evolution if genetic adaptation is generally limited by the supply of mutations. In experimental populations of the bacterium \textit{Escherichia coli}, the rate of evolutionary adaptation was proportional to the mutation supply rate only in particular circumstances of small or initially well-adapted populations. These experiments also demonstrate a "speed limit" on adaptive evolution in asexual populations, one that is independent of the mutation supply rate.},
keywords = {Descendant Experiments, Fitness Trajectories, Mutation Rates},
pubstate = {published},
tppubtype = {article}
}
Mutator genotypes with increased mutation rates may be especially important in microbial evolution if genetic adaptation is generally limited by the supply of mutations. In experimental populations of the bacterium Escherichia coli, the rate of evolutionary adaptation was proportional to the mutation supply rate only in particular circumstances of small or initially well-adapted populations. These experiments also demonstrate a "speed limit" on adaptive evolution in asexual populations, one that is independent of the mutation supply rate.
Papadopoulos D; Schneider D; Meier-Eiss J; Arber W; Lenski R E; Blot M
Genomic evolution during a 10,000-generation experiment with bacteria Journal Article
Proceedings of the National Academy of Sciences of the United States of America, 96 (7), pp. 3807–3812, 1999, ISSN: 0027-8424.
Abstract | Links | BibTeX | Altmetric | Tags: Genome Evolution, Mutation Rates
@article{Papadopoulos3807,
title = {Genomic evolution during a 10,000-generation experiment with bacteria},
author = {Dimitri Papadopoulos and Dominique Schneider and Jessica Meier-Eiss and Werner Arber and Richard E. Lenski and Michel Blot},
url = {https://www.pnas.org/content/96/7/3807},
doi = {10.1073/pnas.96.7.3807},
issn = {0027-8424},
year = {1999},
date = {1999-01-01},
urldate = {1999-01-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {96},
number = {7},
pages = {3807--3812},
publisher = {National Academy of Sciences},
abstract = {Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of \textit{Escherichia coli} evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief. },
keywords = {Genome Evolution, Mutation Rates},
pubstate = {published},
tppubtype = {article}
}
Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.
1998
Turner P E; Cooper V S; Lenski R E
Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids. Journal Article
Evolution, 52 (2), pp. 315–329, 1998, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Turner1998,
title = {Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids.},
author = {Paul E. Turner and Vaughn S. Cooper and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1998.tb01634.x},
doi = {10.1111/j.1558-5646.1998.tb01634.x},
issn = {0014-3820},
year = {1998},
date = {1998-04-01},
urldate = {1998-04-01},
journal = {Evolution},
volume = {52},
number = {2},
pages = {315--329},
abstract = {It has been hypothesized that there is a fundamental conflict between horizontal (infectious) and vertical (intergenerational) modes of parasite transmission. Activities of a parasite that increase its rate of infectious transmission are presumed to reduce its host's fitness. This reduction in host fitness impedes vertical transmission of the parasite and causes a tradeoff between horizontal and vertical transmission. Given this tradeoff, and assuming no multiple infections (no within-host competition among parasites), a simple model predicts that the density of uninfected hosts in the environment should determine the optimum balance between modes of parasite transmission. When susceptible hosts are abundant, selection should favor increased rates of horizontal transfer, even at the expense of reduced vertical transmission. Conversely, when hosts are rare, selection should favor increased vertical transmission even at the expense of lower horizontal transfer. We tested the tradeoff hypothesis and these evolutionary predictions using conjugative plasmids and the bacteria that they infect. Plasmids were allowed to evolve for 500 generations in environments with different densities of susceptible hosts. The plasmid's rate of horizontal transfer by conjugation increased at the expense of host fitness, indicating a tradeoff between horizontal and vertical transmission. Also, reductions in conjugation rate repeatedly coincided with the loss of a particular plasmid-encoded antibiotic resistance gene. However, susceptible host density had no significant effect on the evolution of horizontal versus vertical modes of plasmid transmission. We consider several possible explanations for the failure to observe such an effect.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
It has been hypothesized that there is a fundamental conflict between horizontal (infectious) and vertical (intergenerational) modes of parasite transmission. Activities of a parasite that increase its rate of infectious transmission are presumed to reduce its host's fitness. This reduction in host fitness impedes vertical transmission of the parasite and causes a tradeoff between horizontal and vertical transmission. Given this tradeoff, and assuming no multiple infections (no within-host competition among parasites), a simple model predicts that the density of uninfected hosts in the environment should determine the optimum balance between modes of parasite transmission. When susceptible hosts are abundant, selection should favor increased rates of horizontal transfer, even at the expense of reduced vertical transmission. Conversely, when hosts are rare, selection should favor increased vertical transmission even at the expense of lower horizontal transfer. We tested the tradeoff hypothesis and these evolutionary predictions using conjugative plasmids and the bacteria that they infect. Plasmids were allowed to evolve for 500 generations in environments with different densities of susceptible hosts. The plasmid's rate of horizontal transfer by conjugation increased at the expense of host fitness, indicating a tradeoff between horizontal and vertical transmission. Also, reductions in conjugation rate repeatedly coincided with the loss of a particular plasmid-encoded antibiotic resistance gene. However, susceptible host density had no significant effect on the evolution of horizontal versus vertical modes of plasmid transmission. We consider several possible explanations for the failure to observe such an effect.
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.