1998
Gerrish P J; Lenski R E
The fate of competing beneficial mutations in an asexual population Journal Article
Genetica, 102-103 , pp. 127-44, 1998, ISBN: 978-94-010-6193-3.
Abstract | Links | BibTeX | Altmetric | Tags: Theory and Simulations
@article{article,
title = {The fate of competing beneficial mutations in an asexual population},
author = {Philip J. Gerrish and Richard E. Lenski},
url = {https://link.springer.com/article/10.1023%2FA%3A1017067816551},
doi = {10.1023/A:1017067816551},
isbn = {978-94-010-6193-3},
year = {1998},
date = {1998-01-01},
urldate = {1998-01-01},
journal = {Genetica},
volume = {102-103},
pages = {127-44},
abstract = {In sexual populations, beneficial mutations that occur in different lineages may be recombined into a single lineage. In asexual populations, however, clones that carry such alternative beneficial mutations compete with one another and, thereby, interfere with the expected progression of a given mutation to fixation. From theoretical exploration of such ‘clonal interference’, we have derived (1) a fixation probability for beneficial mutations, (2) an expected substitution rate, (3) an expected coefficient of selection for realized substitutions, (4) an expected rate of fitness increase, (5) the probability that a beneficial mutation transiently achieves polymorphic frequency (≥ 1%), and (6) the probability that a beneficial mutation transiently achieves majority status. Based on (2) and (3), we were able to estimate the beneficial mutation rate and the distribution of mutational effects from changes in mean fitness in an evolving \textit{E. coli} population.},
keywords = {Theory and Simulations},
pubstate = {published},
tppubtype = {article}
}
In sexual populations, beneficial mutations that occur in different lineages may be recombined into a single lineage. In asexual populations, however, clones that carry such alternative beneficial mutations compete with one another and, thereby, interfere with the expected progression of a given mutation to fixation. From theoretical exploration of such ‘clonal interference’, we have derived (1) a fixation probability for beneficial mutations, (2) an expected substitution rate, (3) an expected coefficient of selection for realized substitutions, (4) an expected rate of fitness increase, (5) the probability that a beneficial mutation transiently achieves polymorphic frequency (≥ 1%), and (6) the probability that a beneficial mutation transiently achieves majority status. Based on (2) and (3), we were able to estimate the beneficial mutation rate and the distribution of mutational effects from changes in mean fitness in an evolving E. coli population.
Elena S F; Ekunwe L; Hajela N; Oden S A; Lenski R E
Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Journal Article
Genetica, 102-103 (1-6), pp. 349–58, 1998, ISSN: 0016-6707.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Elena1998,
title = {Distribution of fitness effects caused by random insertion mutations in \textit{Escherichia coli}.},
author = {Santiago F. Elena and Lynette Ekunwe and Neerja Hajela and Shenandoah A. Oden and Richard E. Lenski},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9720287},
doi = {10.1023/a:1017031008316},
issn = {0016-6707},
year = {1998},
date = {1998-01-01},
urldate = {1998-01-01},
journal = {Genetica},
volume = {102-103},
number = {1-6},
pages = {349--58},
abstract = {Very little is known about the distribution of mutational effects on organismal fitness, despite the fundamental importance of this information for the study of evolution. This lack of information reflects the fact that it is generally difficult to quantify the dynamic effects of mutation and natural selection using only static distributions of allele frequencies. In this study, we took a direct approach to measuring the effects of mutations on fitness. We used transposon-mutagenesis to create 226 mutant clones of \textit{Escherichia coli}. Each mutant clone carried a single random insertion of a derivative of Tn\textit{10}. All 226 mutants were independently derived from the same progenitor clone, which was obtained from a population that had evolved in a constant laboratory environment for 10,000 generations. We then performed competition experiments to measure the effect of each mutation on fitness relative to a common competitor. At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect. The mutations reduced fitness by about 3%, on average, but the distribution of fitness effects was highly skewed and had a long, flat tail. A compound distribution, which includes both gamma and uniform components, provided an excellent fit to the observed fitness values.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Very little is known about the distribution of mutational effects on organismal fitness, despite the fundamental importance of this information for the study of evolution. This lack of information reflects the fact that it is generally difficult to quantify the dynamic effects of mutation and natural selection using only static distributions of allele frequencies. In this study, we took a direct approach to measuring the effects of mutations on fitness. We used transposon-mutagenesis to create 226 mutant clones of Escherichia coli. Each mutant clone carried a single random insertion of a derivative of Tn10. All 226 mutants were independently derived from the same progenitor clone, which was obtained from a population that had evolved in a constant laboratory environment for 10,000 generations. We then performed competition experiments to measure the effect of each mutation on fitness relative to a common competitor. At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect. The mutations reduced fitness by about 3%, on average, but the distribution of fitness effects was highly skewed and had a long, flat tail. A compound distribution, which includes both gamma and uniform components, provided an excellent fit to the observed fitness values.
1997
Elena S F; Lenski R E
Test of synergistic interactions among deleterious mutations in bacteria Journal Article
Nature, 390 (6658), pp. 395–398, 1997, ISSN: 0028-0836.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Elena1997b,
title = {Test of synergistic interactions among deleterious mutations in bacteria},
author = {Santiago F. Elena and Richard E. Lenski},
url = {http://www.nature.com/articles/37108},
doi = {10.1038/37108},
issn = {0028-0836},
year = {1997},
date = {1997-11-01},
urldate = {1997-11-01},
journal = {Nature},
volume = {390},
number = {6658},
pages = {395--398},
abstract = {Identifying the forces responsible for the origin and maintenance of sexuality remains one of the greatest unsolved problems in biology. The mutational deterministic hypothesis postulates that sex is an adaptation that allows deleterious mutations to be purged from the genome; it requires synergistic interactions, which means that two mutations would be more harmful together than expected from their separate effects. We generated 225 genotypes of \textit{Escherichia coli} carrying one, two or three successive mutations and measured their fitness relative to an unmutated competitor. The relationship between mutation number and average fitness is nearly log- linear. We also constructed 27 recombinant genotypes having pairs of mutations whose separate and combined effects on fitness were determined. Several pairs exhibit significant interactions for fitness, but they are antagonistic as often as they are synergistic. These results do not support the mutational deterministic hypothesis for the evolution of sex.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Identifying the forces responsible for the origin and maintenance of sexuality remains one of the greatest unsolved problems in biology. The mutational deterministic hypothesis postulates that sex is an adaptation that allows deleterious mutations to be purged from the genome; it requires synergistic interactions, which means that two mutations would be more harmful together than expected from their separate effects. We generated 225 genotypes of Escherichia coli carrying one, two or three successive mutations and measured their fitness relative to an unmutated competitor. The relationship between mutation number and average fitness is nearly log- linear. We also constructed 27 recombinant genotypes having pairs of mutations whose separate and combined effects on fitness were determined. Several pairs exhibit significant interactions for fitness, but they are antagonistic as often as they are synergistic. These results do not support the mutational deterministic hypothesis for the evolution of sex.
Elena S F; Lenski R E
Long-term experimental evolution in Escherichia coli. VII. Mechanisms maintaining genetic variability within populations. Journal Article
Evolution, 51 (4), pp. 1058–1067, 1997, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Demography and Ecology, Fitness Trajectories, Mutation Rates, Theory and Simulations
@article{Elena1997,
title = {Long-term experimental evolution in \textit{Escherichia coli}. VII. Mechanisms maintaining genetic variability within populations.},
author = {Santiago F. Elena and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1997.tb03953.x},
doi = {10.1111/j.1558-5646.1997.tb03953.x},
issn = {0014-3820},
year = {1997},
date = {1997-08-01},
urldate = {1997-08-01},
journal = {Evolution},
volume = {51},
number = {4},
pages = {1058--1067},
abstract = {Six replicate populations of the bacterium \textit{Escherichia coli} were propagated for more than 10,000 generations in a defined environment. We sought to quantify the variation among clones within these populations with respect to their relative fitness, and to evaluate the roles of three distinct population genetic processes in maintaining this variation. On average, a pair of clones from the same population differed from one another in their relative fitness by approximately 4%. This within-population variation was small compared with the average fitness gain relative to the common ancestor, but it was statistically significant. According to one hypothesis. The variation in fitness is transient and reflects the ongoing substitution of beneficial alleles. We used Fisher's fundamental theorem to compare the observed rate of each population's change in mean fitness with the extent of variation for fitness within that population, but we failed to discern any correspondence between these quantities. A second hypothesis supposes that the variation in fitness is maintained by recurrent deleterious mutations that give rise to a mutation-selection balance. To test this hypothesis, we made use of the fact that two of the six replicate populations had evolved mutator phenotypes, which gave them a genomic mutation rate approximately 100-fold higher than that of the other populations. There was a marginally significant correlation between a population's mutation rate and the extent of its within-population variance for fitness, but this correlation was driven by only one population (whereas two of the populations had elevated mutation rates). Under a third hypothesis, this variation is maintained by frequency-dependent selection, whereby genotypes have an advantage when they are rare relative to when they are common. In all six populations, clones were more fit, on average, when they were rare than when they were common, although the magnitude of the advantage when rare was usually small (~1% in five populations and ~45% in the other). These three hypotheses are not mutually exclusive, but frequency-dependent selection appears to be the primary force maintaining the fitness variation within these experimental populations.},
keywords = {Demography and Ecology, Fitness Trajectories, Mutation Rates, Theory and Simulations},
pubstate = {published},
tppubtype = {article}
}
Six replicate populations of the bacterium Escherichia coli were propagated for more than 10,000 generations in a defined environment. We sought to quantify the variation among clones within these populations with respect to their relative fitness, and to evaluate the roles of three distinct population genetic processes in maintaining this variation. On average, a pair of clones from the same population differed from one another in their relative fitness by approximately 4%. This within-population variation was small compared with the average fitness gain relative to the common ancestor, but it was statistically significant. According to one hypothesis. The variation in fitness is transient and reflects the ongoing substitution of beneficial alleles. We used Fisher's fundamental theorem to compare the observed rate of each population's change in mean fitness with the extent of variation for fitness within that population, but we failed to discern any correspondence between these quantities. A second hypothesis supposes that the variation in fitness is maintained by recurrent deleterious mutations that give rise to a mutation-selection balance. To test this hypothesis, we made use of the fact that two of the six replicate populations had evolved mutator phenotypes, which gave them a genomic mutation rate approximately 100-fold higher than that of the other populations. There was a marginally significant correlation between a population's mutation rate and the extent of its within-population variance for fitness, but this correlation was driven by only one population (whereas two of the populations had elevated mutation rates). Under a third hypothesis, this variation is maintained by frequency-dependent selection, whereby genotypes have an advantage when they are rare relative to when they are common. In all six populations, clones were more fit, on average, when they were rare than when they were common, although the magnitude of the advantage when rare was usually small (~1% in five populations and ~45% in the other). These three hypotheses are not mutually exclusive, but frequency-dependent selection appears to be the primary force maintaining the fitness variation within these experimental populations.
Sniegowski P D; Gerrish P J; Lenski R E
Evolution of high mutation rates in experimental populations of E. coli Journal Article
Nature, 387 (6634), pp. 703–705, 1997, ISSN: 0028-0836.
Abstract | Links | BibTeX | Altmetric | Tags: Genotypes and Phenotypes, Mutation Rates
@article{Sniegowski1997,
title = {Evolution of high mutation rates in experimental populations of \textit{E. coli}},
author = {Paul D. Sniegowski and Philip J. Gerrish and Richard E. Lenski},
url = {http://www.nature.com/articles/42701},
doi = {10.1038/42701},
issn = {0028-0836},
year = {1997},
date = {1997-06-01},
urldate = {1997-06-01},
journal = {Nature},
volume = {387},
number = {6634},
pages = {703--705},
abstract = {Most mutations are likely to be deleterious, and so the spontaneous mutation rate is generally held at a very low value. Nonetheless, evolutionary theory predicts that high mutation rates can evolve under certain circumstances. Empirical observations have previously been limited to short-term studies of the fates of mutator strains deliberately introduced into laboratory populations of \textit{Escherichia coli}, and to the effects of intense selective events on mutator frequencies in \textit{E. coli}. Here we report the rise of spontaneously originated mutators in populations of \textit{E. coli} undergoing long-term adaptation to a new environment. Our results corroborate computer simulations of mutator evolution in adapting clonal populations, and may help to explain observations that associate high mutation rates with emerging pathogens and with certain cancers.},
keywords = {Genotypes and Phenotypes, Mutation Rates},
pubstate = {published},
tppubtype = {article}
}
Most mutations are likely to be deleterious, and so the spontaneous mutation rate is generally held at a very low value. Nonetheless, evolutionary theory predicts that high mutation rates can evolve under certain circumstances. Empirical observations have previously been limited to short-term studies of the fates of mutator strains deliberately introduced into laboratory populations of Escherichia coli, and to the effects of intense selective events on mutator frequencies in E. coli. Here we report the rise of spontaneously originated mutators in populations of E. coli undergoing long-term adaptation to a new environment. Our results corroborate computer simulations of mutator evolution in adapting clonal populations, and may help to explain observations that associate high mutation rates with emerging pathogens and with certain cancers.
Bennett A F; Lenski R E
Evolutionary adaptation to temperature. VI. Phenotypic acclimation and its evolution in Escherichia coli Journal Article
Evolution, 51 (1), pp. 36–44, 1997, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Bennett1997,
title = {Evolutionary adaptation to temperature. VI. Phenotypic acclimation and its evolution in \textit{Escherichia coli}},
author = {Albert F. Bennett and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1997.tb02386.x},
doi = {10.1111/j.1558-5646.1997.tb02386.x},
issn = {0014-3820},
year = {1997},
date = {1997-02-01},
urldate = {1997-02-01},
journal = {Evolution},
volume = {51},
number = {1},
pages = {36--44},
abstract = {Acclimation refers to reversible, nongenetic changes in phenotype that are induced by specific environmental conditions. Acclimation is generally assumed to improve function in the environment that induces it (the beneficial acclimation hypothesis). In this study, we experimentally tested this assumption by measuring relative fitness of the bacterium \textit{Escherichia coli} acclimated to different thermal environments. The beneficial acclimation hypothesis predicts that bacteria acclimated to the temperature of competition should have greater fitness than do bacteria acclimated to any other temperature. The benefit predicted by the hypothesis was found in only seven of 12 comparisons; in the other comparisons, either no statistically demonstrable benefit was observed or a detrimental effect of acclimation was demonstrated. For example, in a lineage evolutionarily adapted to 37°C, bacteria acclimated to 37°C have a higher fitness at 32°C than do bacteria acclimated to 32°C, a result exactly contrary to prediction; acclimation to 27°C or 40°C prior to competition at those temperatures confers no benefit over 37°C acclimated forms. Consequently, the beneficial acclimation hypothesis must be rejected as a general prediction of the inevitable result of phenotypic adjustments associated with new environments. However, the hypothesis is supported in many instances when the acclimation and competition temperatures coincide with the historical temperature at which the bacterial populations have evolved. For example, when the evolutionary temperature of the population was 37°C, bacteria acclimated to 37°C had superior fitness at 37°C to those acclimated to 32°C; similarly, bacteria evolutionarily adapted to 32°C had a higher fitness during competition at 32°C than they did when acclimated to 37°C. The more surprising results are that when the bacteria are acclimated to their historical evolutionary temperature, they are frequently competitively superior even at other temperatures. For example, bacteria that have evolved at either 20°C or 32°C and are acclimated to their respective evolutionary temperatures have a greater fitness at 37°C than when they are acclimated to 37°C. Thus, acclimation to evolutionary temperature may, as a correlated consequence, enhance performance not only in the evolutionary environment, but also in a variety of other thermal environments.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Acclimation refers to reversible, nongenetic changes in phenotype that are induced by specific environmental conditions. Acclimation is generally assumed to improve function in the environment that induces it (the beneficial acclimation hypothesis). In this study, we experimentally tested this assumption by measuring relative fitness of the bacterium Escherichia coli acclimated to different thermal environments. The beneficial acclimation hypothesis predicts that bacteria acclimated to the temperature of competition should have greater fitness than do bacteria acclimated to any other temperature. The benefit predicted by the hypothesis was found in only seven of 12 comparisons; in the other comparisons, either no statistically demonstrable benefit was observed or a detrimental effect of acclimation was demonstrated. For example, in a lineage evolutionarily adapted to 37°C, bacteria acclimated to 37°C have a higher fitness at 32°C than do bacteria acclimated to 32°C, a result exactly contrary to prediction; acclimation to 27°C or 40°C prior to competition at those temperatures confers no benefit over 37°C acclimated forms. Consequently, the beneficial acclimation hypothesis must be rejected as a general prediction of the inevitable result of phenotypic adjustments associated with new environments. However, the hypothesis is supported in many instances when the acclimation and competition temperatures coincide with the historical temperature at which the bacterial populations have evolved. For example, when the evolutionary temperature of the population was 37°C, bacteria acclimated to 37°C had superior fitness at 37°C to those acclimated to 32°C; similarly, bacteria evolutionarily adapted to 32°C had a higher fitness during competition at 32°C than they did when acclimated to 37°C. The more surprising results are that when the bacteria are acclimated to their historical evolutionary temperature, they are frequently competitively superior even at other temperatures. For example, bacteria that have evolved at either 20°C or 32°C and are acclimated to their respective evolutionary temperatures have a greater fitness at 37°C than when they are acclimated to 37°C. Thus, acclimation to evolutionary temperature may, as a correlated consequence, enhance performance not only in the evolutionary environment, but also in a variety of other thermal environments.
Souza V; Turner P E; Lenski R E
Long-term experimental evolution in Escherichia coli. V. Effects of recombination with immigrant genotypes on the rate of bacterial evolution Journal Article
Journal of Evolutionary Biology, 10 (5), pp. 743, 1997, ISSN: 1010061X.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Souza1997,
title = {Long-term experimental evolution in \textit{Escherichia coli}. V. Effects of recombination with immigrant genotypes on the rate of bacterial evolution},
author = {Valeria Souza and Paul E. Turner and Richard E. Lenski},
url = {https://turnerlab.yale.edu/sites/default/files/souza_etal_1997.pdf
https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1420-9101.1997.10050743.x},
doi = {https://doi.org/10.1046/j.1420-9101.1997.10050743.x},
issn = {1010061X},
year = {1997},
date = {1997-01-01},
urldate = {1997-01-01},
journal = {Journal of Evolutionary Biology},
volume = {10},
number = {5},
pages = {743},
abstract = {This study builds upon an earlier experiment that examined the dynamics of mean fitness in evolving populations of \textit{Escherichia coli} in which mutations were the sole source of genetic variation. During thousands of generations in a constant environment, the rate of improvement in mean fitness of these asexual populations slowed considerably from an initially rapid pace. In this study, we sought to determine whether sexual recombination with novel genotypes would reaccelerate the rate of adaption in these populations. To that end, treatment populations were propagated for an additional 1000 generations in the same environment as their ancestors, but they were periodically allowed to mate with an immigrant pool of genetically distinct Hfr (high frequency recombination) donors. These donors could transfer genes to the resident populations by conjugation, but the donors themselves could not grow in the experimental environment. Control populations were propagated under identical conditions, but in the absence of sexual recombination with the donors. All twelve control populations retained the ancestral alleles at every locus that was scored. In contrast, the sexual recombination treatment yielded dramatic increases in genetic variation. Thus, there was a profound effect of recombination on the rate of genetic change. However, the increased genetic variation in the treatment populations had no significant effect on the rate of adaptive evolution, as measured by changes in mean fitness relative to a common competitor. We then considered three hypotheses that might reconcile these two outcomes: recombination pressure, hitchhiking of recombinant genotypes in association with beneficial mutations, and complex selection dynamics whereby certain genotypes may have a selective advantage only within a particular milieu of competitors. The estimated recombination rate was too low to explain the observed rate of genetic change, either alone or in combination with hitchhiking effects. However, we documented complex ecological interactions among some recombinant genotypes, suggesting that our method for estimating fitness relative to a common competitor might have underestimated the rate of adaptive evolution in the treatment populations.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
This study builds upon an earlier experiment that examined the dynamics of mean fitness in evolving populations of Escherichia coli in which mutations were the sole source of genetic variation. During thousands of generations in a constant environment, the rate of improvement in mean fitness of these asexual populations slowed considerably from an initially rapid pace. In this study, we sought to determine whether sexual recombination with novel genotypes would reaccelerate the rate of adaption in these populations. To that end, treatment populations were propagated for an additional 1000 generations in the same environment as their ancestors, but they were periodically allowed to mate with an immigrant pool of genetically distinct Hfr (high frequency recombination) donors. These donors could transfer genes to the resident populations by conjugation, but the donors themselves could not grow in the experimental environment. Control populations were propagated under identical conditions, but in the absence of sexual recombination with the donors. All twelve control populations retained the ancestral alleles at every locus that was scored. In contrast, the sexual recombination treatment yielded dramatic increases in genetic variation. Thus, there was a profound effect of recombination on the rate of genetic change. However, the increased genetic variation in the treatment populations had no significant effect on the rate of adaptive evolution, as measured by changes in mean fitness relative to a common competitor. We then considered three hypotheses that might reconcile these two outcomes: recombination pressure, hitchhiking of recombinant genotypes in association with beneficial mutations, and complex selection dynamics whereby certain genotypes may have a selective advantage only within a particular milieu of competitors. The estimated recombination rate was too low to explain the observed rate of genetic change, either alone or in combination with hitchhiking effects. However, we documented complex ecological interactions among some recombinant genotypes, suggesting that our method for estimating fitness relative to a common competitor might have underestimated the rate of adaptive evolution in the treatment populations.
Bennett A F; Lenski R E
Phenotypic and evolutionary adaptation of a model bacterial system to stressful thermal environments Book Chapter
Bijlsma, R.; Loeschcke, V. (Ed.): Environmental Stress, Adaptation and Evolution, pp. 135–154, Birkhäuser Basel, Basel, 1997, ISBN: 978-3-0348-8882-0.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@inbook{Bennett1997b,
title = {Phenotypic and evolutionary adaptation of a model bacterial system to stressful thermal environments},
author = {Albert F. Bennett and Richard E. Lenski},
editor = {R. Bijlsma and V. Loeschcke},
url = {https://doi.org/10.1007/978-3-0348-8882-0_8
http://link.springer.com/10.1007/978-3-0348-8882-0_8},
doi = {10.1007/978-3-0348-8882-0_8},
isbn = {978-3-0348-8882-0},
year = {1997},
date = {1997-01-01},
urldate = {1997-01-01},
booktitle = {Environmental Stress, Adaptation and Evolution},
pages = {135--154},
publisher = {Birkhäuser Basel},
address = {Basel},
abstract = {We studied both phenotypic and evolutionary adaptation to various thermal environments using the bacterium \textit{Escherichia coli} as an experimental model system. We determined that 42°C was stressful to a bacterial clone adapted to 37°C, based on reductions in both absolute and competitive fitness, as well as induction of a heat stress response. This clone was also used to found replicated populations that were propagated for thousands of generations under several different thermal regimes, including 42°C. Evolutionary adaptation of the populations to 42°C resulted in an increase in both absolute and relative fitness at that temperature, measured respectively as an increase in the number of descendants (and their biovolume) and in competitive ability relative to the ancestral clone. The replicated experimental lineages achieved their evolutionary improvement by several distinct pathways, which produced differential preadaptation to a non-stressful nutrient environment. Adaptation to this stressful temperature entailed neither a change in the ancestral thermal niche nor any pronounced tradeoffs in fitness within the thermal niche, contrary to \textit{a priori} predictions. This study system has several important advantages for evaluating hypotheses concerning the effects of stress on phenotypic and evolutionary adaptation, including the ability to obtain lineages that have evolved in controlled and defined environments, to make direct measurements of fitness and to quantify the degree of stress imposed by different environments.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {inbook}
}
We studied both phenotypic and evolutionary adaptation to various thermal environments using the bacterium Escherichia coli as an experimental model system. We determined that 42°C was stressful to a bacterial clone adapted to 37°C, based on reductions in both absolute and competitive fitness, as well as induction of a heat stress response. This clone was also used to found replicated populations that were propagated for thousands of generations under several different thermal regimes, including 42°C. Evolutionary adaptation of the populations to 42°C resulted in an increase in both absolute and relative fitness at that temperature, measured respectively as an increase in the number of descendants (and their biovolume) and in competitive ability relative to the ancestral clone. The replicated experimental lineages achieved their evolutionary improvement by several distinct pathways, which produced differential preadaptation to a non-stressful nutrient environment. Adaptation to this stressful temperature entailed neither a change in the ancestral thermal niche nor any pronounced tradeoffs in fitness within the thermal niche, contrary to a priori predictions. This study system has several important advantages for evaluating hypotheses concerning the effects of stress on phenotypic and evolutionary adaptation, including the ability to obtain lineages that have evolved in controlled and defined environments, to make direct measurements of fitness and to quantify the degree of stress imposed by different environments.
1996
Coyne J A; Charlesworth B; Elena S F; Cooper V S; Lenski R E
Mechanisms of Punctuated Evolution Journal Article
Science, 274 (5293), pp. 1748–1750, 1996, ISSN: 0036-8075.
Abstract | Links | BibTeX | Altmetric | Tags:
@article{Coyne1996,
title = {Mechanisms of Punctuated Evolution},
author = {Jerry A. Coyne and B. Charlesworth and Santiago F. Elena and Vaughn S. Cooper and Richard E. Lenski},
url = {https://www.sciencemag.org/lookup/doi/10.1126/science.274.5293.1748},
doi = {10.1126/science.274.5293.1748},
issn = {0036-8075},
year = {1996},
date = {1996-12-01},
urldate = {1996-12-01},
journal = {Science},
volume = {274},
number = {5293},
pages = {1748--1750},
abstract = {In their report, "Punctuated evolution caused by selection of rare beneficial mutations," Santiago F. Elena \textit{et al.} describe (1) punctuated changes in a morphological character (cell size) in a population of \textit{Escherichia coli} kept in batch culture with daily transfer for 3000 generations. They state that their observations might explain some aspects of punctuated evolutionary change, a phenomenon often said to be in consistent with classical neo-Darwinism (2). The controversy about punctuated equilibrium involves two questions: (i) How ubiquitous is the pattern of "jerky" evolution in nature? and (ii) Do novel evolutionary processes cause this pattern? Elena \textit{et al.} answer the second question by proposing that stasis in the fossil record arises (as it does in their bacteria) from an absence of genetic variation, while rapid changes in the record reflect the spread of new beneficial mutations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In their report, "Punctuated evolution caused by selection of rare beneficial mutations," Santiago F. Elena et al. describe (1) punctuated changes in a morphological character (cell size) in a population of Escherichia coli kept in batch culture with daily transfer for 3000 generations. They state that their observations might explain some aspects of punctuated evolutionary change, a phenomenon often said to be in consistent with classical neo-Darwinism (2). The controversy about punctuated equilibrium involves two questions: (i) How ubiquitous is the pattern of "jerky" evolution in nature? and (ii) Do novel evolutionary processes cause this pattern? Elena et al. answer the second question by proposing that stasis in the fossil record arises (as it does in their bacteria) from an absence of genetic variation, while rapid changes in the record reflect the spread of new beneficial mutations.
Turner P E; Souza V; Lenski R E
Tests of Ecological Mechanisms Promoting the Stable Coexistence of Two Bacterial Genotypes Journal Article
Ecology, 77 (7), pp. 2119–2129, 1996, ISSN: 00129658.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Turner1996,
title = {Tests of Ecological Mechanisms Promoting the Stable Coexistence of Two Bacterial Genotypes},
author = {Paul E. Turner and Valeria Souza and Richard E. Lenski},
url = {http://doi.wiley.com/10.2307/2265706},
doi = {10.2307/2265706},
issn = {00129658},
year = {1996},
date = {1996-10-01},
urldate = {1996-10-01},
journal = {Ecology},
volume = {77},
number = {7},
pages = {2119--2129},
abstract = {A series of competition experiments with two genotypes of \textit{Escherichia coli} showed that each genotype was favored when it was the minority, allowing their coexistence in a stable polymorphism. In these experiments, glucose was the sole source of carbon provided, and its concentration was limiting to population density. Thus, the stable polymorphism did not conform to a simple model of competitive exclusion. In similar experiments also with glucose as the sole resource, we considered two hypotheses that might explain the observed coexistence: (1) a strictly demographic trade—off, such that one genotype is competitively superior when glucose is abundant whereas the other genotype is the better competitor for sparse glucose; and (2) a cross—feeding interaction, whereby the superior competitor for glucose excretes a metabolite that acts as a second resource for which the other genotype is the better competitor. Although there was a demographic tradeoff, the advantage to the superior competitor at high glucose concentrations was too large (given the initial concentration of glucose used in these experiments) to allow the second genotype to invade when rare at the observed rate. Therefore, the second genotype must have had some other advantage that allowed it to readily invade a population of the superior competitor for glucose. Indeed, the second genotype could increase in abundance after glucose was depleted, but only in the presence of the superior competitor for glucose, thus implicating a cross—feeding interaction. These results confirmed earlier studies showing that populations of \textit{E. coli} can maintain ecologically relevant genetic diversity even in a simple environment.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
A series of competition experiments with two genotypes of Escherichia coli showed that each genotype was favored when it was the minority, allowing their coexistence in a stable polymorphism. In these experiments, glucose was the sole source of carbon provided, and its concentration was limiting to population density. Thus, the stable polymorphism did not conform to a simple model of competitive exclusion. In similar experiments also with glucose as the sole resource, we considered two hypotheses that might explain the observed coexistence: (1) a strictly demographic trade—off, such that one genotype is competitively superior when glucose is abundant whereas the other genotype is the better competitor for sparse glucose; and (2) a cross—feeding interaction, whereby the superior competitor for glucose excretes a metabolite that acts as a second resource for which the other genotype is the better competitor. Although there was a demographic tradeoff, the advantage to the superior competitor at high glucose concentrations was too large (given the initial concentration of glucose used in these experiments) to allow the second genotype to invade when rare at the observed rate. Therefore, the second genotype must have had some other advantage that allowed it to readily invade a population of the superior competitor for glucose. Indeed, the second genotype could increase in abundance after glucose was depleted, but only in the presence of the superior competitor for glucose, thus implicating a cross—feeding interaction. These results confirmed earlier studies showing that populations of E. coli can maintain ecologically relevant genetic diversity even in a simple environment.
Mongold J A; Lenski R E
Experimental rejection of a nonadaptive explanation for increased cell size in Escherichia coli Journal Article
Journal of Bacteriology, 178 (17), pp. 5333–5334, 1996, ISSN: 0021-9193.
Abstract | Links | BibTeX | Altmetric | Tags: Cell Morphology
@article{Mongold1996,
title = {Experimental rejection of a nonadaptive explanation for increased cell size in \textit{Escherichia coli}},
author = {Judith A. Mongold and Richard E. Lenski},
url = {https://journals.asm.org/doi/10.1128/jb.178.17.5333-5334.1996},
doi = {10.1128/jb.178.17.5333-5334.1996},
issn = {0021-9193},
year = {1996},
date = {1996-09-01},
urldate = {1996-09-01},
journal = {Journal of Bacteriology},
volume = {178},
number = {17},
pages = {5333--5334},
abstract = {Populations of \textit{Escherichia coli} that have been serially propagated for thousands of generations in glucose minimal medium show heritable increases in both cell size and growth rate. We sought to test the hypothesis that the increased cell size of the derived genotypes could be explained solely by their faster growth. The regression of cell size on growth rate differed significantly between populations having ancestral and derived genotypes, with the latter producing larger cells over almost the entire range of growth rates. Thus, the physiological coupling between cell size and growth rate has been evolutionarily altered.},
keywords = {Cell Morphology},
pubstate = {published},
tppubtype = {article}
}
Populations of Escherichia coli that have been serially propagated for thousands of generations in glucose minimal medium show heritable increases in both cell size and growth rate. We sought to test the hypothesis that the increased cell size of the derived genotypes could be explained solely by their faster growth. The regression of cell size on growth rate differed significantly between populations having ancestral and derived genotypes, with the latter producing larger cells over almost the entire range of growth rates. Thus, the physiological coupling between cell size and growth rate has been evolutionarily altered.
Elena S F; Cooper V S; Lenski R E
Punctuated Evolution Caused by Selection of Rare Beneficial Mutations Journal Article
Science, 272 (5269), pp. 1802–1804, 1996, ISSN: 0036-8075.
Abstract | Links | BibTeX | Altmetric | Tags: Cell Morphology
@article{Elena1996,
title = {Punctuated Evolution Caused by Selection of Rare Beneficial Mutations},
author = {Santiago F. Elena and Vaughn S. Cooper and Richard E. Lenski},
url = {https://www.sciencemag.org/lookup/doi/10.1126/science.272.5269.1802},
doi = {10.1126/science.272.5269.1802},
issn = {0036-8075},
year = {1996},
date = {1996-06-01},
urldate = {1996-06-01},
journal = {Science},
volume = {272},
number = {5269},
pages = {1802--1804},
abstract = {For more than two decades there has been intense debate over the hypothesis that most morphological evolution occurs during relatively brief episodes of rapid change that punctuate much longer periods of stasis. A clear and unambiguous case of punctuated evolution is presented for cell size in a population of \textit{Escherichia coli} evolving for 3000 generations in a constant environment. The punctuation is caused by natural selection as rare, beneficial mutations sweep successively through the population. This experiment shows that the most elementary processes in population genetics can give rise to punctuated evolutionary dynamics.},
keywords = {Cell Morphology},
pubstate = {published},
tppubtype = {article}
}
For more than two decades there has been intense debate over the hypothesis that most morphological evolution occurs during relatively brief episodes of rapid change that punctuate much longer periods of stasis. A clear and unambiguous case of punctuated evolution is presented for cell size in a population of Escherichia coli evolving for 3000 generations in a constant environment. The punctuation is caused by natural selection as rare, beneficial mutations sweep successively through the population. This experiment shows that the most elementary processes in population genetics can give rise to punctuated evolutionary dynamics.
Travisano M; Lenski R E
Long-Term Experimental Evolution in Escherichia coli. IV. Targets of Selection and the Specificity of Adaptation Journal Article
Genetics, 143 (1), pp. 15–26, 1996, ISSN: 1943-2631.
Abstract | Links | BibTeX | Altmetric | Tags: Correlated Responses, Genotypes and Phenotypes, Parallelism and Divergence
@article{Travisano1996,
title = {Long-Term Experimental Evolution in \textit{Escherichia coli}. IV. Targets of Selection and the Specificity of Adaptation},
author = {Michael Travisano and Richard E. Lenski},
url = {https://academic.oup.com/genetics/article/143/1/15/6016887},
doi = {10.1093/genetics/143.1.15},
issn = {1943-2631},
year = {1996},
date = {1996-05-01},
urldate = {1996-05-01},
journal = {Genetics},
volume = {143},
number = {1},
pages = {15--26},
abstract = {This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of \textit{Escherichia coli} that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.},
keywords = {Correlated Responses, Genotypes and Phenotypes, Parallelism and Divergence},
pubstate = {published},
tppubtype = {article}
}
This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.
Bennett A F; Lenski R E
Evolutionary Adaptation to Temperature. V. Adaptive Mechanisms and Correlated Responses in Experimental Lines of Escherichia coli Journal Article
Evolution, 50 (2), pp. 493–503, 1996, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Bennett1996,
title = {Evolutionary Adaptation to Temperature. V. Adaptive Mechanisms and Correlated Responses in Experimental Lines of \textit{Escherichia coli}},
author = {Albert F. Bennett and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1996.tb03862.x},
doi = {10.1111/j.1558-5646.1996.tb03862.x},
issn = {0014-3820},
year = {1996},
date = {1996-04-01},
urldate = {1996-04-01},
journal = {Evolution},
volume = {50},
number = {2},
pages = {493--503},
abstract = {We previously demonstrated temperature-specific genetic adaptation in experimental lines of \textit{Escherichia coli}. Six initially identical populations were propagated for 2000 generations under each of five regimes: constant 20°C, 32°C, 37°C, and 42°C, and a daily switch between 32°C and 42°C. Glucose was the sole carbon source in all cases. Here, we examine the physiological bases of adaptation to determine whether the same mechanisms evolved among the replicate lines within each thermal regime and across different regimes. Specifically, we investigate whether changes in glucose transport may account for the temperature-specific adaptation. We compared each line's direct response of fitness to glucose with its correlated response to maltose; glucose and maltose enter the cell by different pathways, but their catabolism is identical. Except for lines maintained at the ancestral temperature (37°C), almost all derived lines had significantly different fitnesses (relative to their common ancestor) in glucose and maltose, supporting the hypothesis that adaptation involved changes in glucose transport. An alternative explanation, that maltose transport decayed by genetic drift, appears unlikely for reasons that are discussed. Although most lines showed evidence of temperature-specific adaptation in glucose transport, several different mechanisms may underlie these improvements, as indicated by heterogeneity in correlated responses (across temperatures and substrates) among replicate lines adapted to the same regime. This heterogeneity provides a latent pool of genetic variation for responding to environmental change.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
We previously demonstrated temperature-specific genetic adaptation in experimental lines of Escherichia coli. Six initially identical populations were propagated for 2000 generations under each of five regimes: constant 20°C, 32°C, 37°C, and 42°C, and a daily switch between 32°C and 42°C. Glucose was the sole carbon source in all cases. Here, we examine the physiological bases of adaptation to determine whether the same mechanisms evolved among the replicate lines within each thermal regime and across different regimes. Specifically, we investigate whether changes in glucose transport may account for the temperature-specific adaptation. We compared each line's direct response of fitness to glucose with its correlated response to maltose; glucose and maltose enter the cell by different pathways, but their catabolism is identical. Except for lines maintained at the ancestral temperature (37°C), almost all derived lines had significantly different fitnesses (relative to their common ancestor) in glucose and maltose, supporting the hypothesis that adaptation involved changes in glucose transport. An alternative explanation, that maltose transport decayed by genetic drift, appears unlikely for reasons that are discussed. Although most lines showed evidence of temperature-specific adaptation in glucose transport, several different mechanisms may underlie these improvements, as indicated by heterogeneity in correlated responses (across temperatures and substrates) among replicate lines adapted to the same regime. This heterogeneity provides a latent pool of genetic variation for responding to environmental change.
Mongold J A; Bennett A F; Lenski R E
Evolutionary Adaptation to Temperature. VI. Phenotypic Acclimation and Its Evolution in Escherichia coli Journal Article
Evolution, 50 (1), pp. 35–43, 1996, ISSN: 0014-3820.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@article{Mongold1996b,
title = {Evolutionary Adaptation to Temperature. VI. Phenotypic Acclimation and Its Evolution in \textit{Escherichia coli}},
author = {Judith A. Mongold and Albert F. Bennett and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1996.tb04470.x},
doi = {10.1111/j.1558-5646.1996.tb04470.x},
issn = {0014-3820},
year = {1996},
date = {1996-02-01},
urldate = {1996-02-01},
journal = {Evolution},
volume = {50},
number = {1},
pages = {35--43},
abstract = {Following an environmental change, the course of a population's adaptive evolution may be influenced by environmental factors, such as the degree of marginality of the new environment relative to the organism's potential range, and by genetic factors, including constraints that may have arisen during its past history. Experimental populations of bacteria were used to address these issues in the context of evolutionary adaptation to the thermal environment. Six replicate lines of \textit{Escherichia coli} (20°C group), founded from a common ancestor, were propagated for 2000 generations at 20°C, a novel temperature that is very near the lower thermal limit at which it can maintain a stable population size in a daily serial transfer (100-fold dilution) regime. Four additional groups (32/20, 37/20, 42/20, and 32-42/20°C groups) of six lines, each with 2000 generation selection histories at different temperatures (32, 37, 42, and daily alternation of 32 and 42°C), were moved to the same 20°C environment and propagated in parallel to ascertain whether selection histories influence the adaptive response in this novel environment. Adaptation was measured by improvement in fitness relative to the common ancestor in direct competition experiments conducted at 20°C. All five groups showed improvement in relative fitness in this environment; the mean fitness of the 20°C group after 2000 generations increased by about 8%. Selection history had no discernible effect on the rate or final magnitude of the fitness responses of the four groups with different histories after 2000 generations. The correlated fitness responses of the 20°C group were measured across the entire thermal niche. There were significant tradeoffs in fitness at higher temperatures; for example, at 40°C the average fitness of the 20°C group was reduced by almost 20% relative to the common ancestor. We also observed a downward shift of 1-2°C in both the upper and lower thermal niche limits for the 20°C selected group. These observations are contrasted with previous observations of a markedly greater rate of adaptation to growth near the upper thermal limit (42°C) and a lack of trade-off in fitness at lower temperatures for lines adapted to that high temperature. The evolutionary implications of this asymmetry are discussed.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {article}
}
Following an environmental change, the course of a population's adaptive evolution may be influenced by environmental factors, such as the degree of marginality of the new environment relative to the organism's potential range, and by genetic factors, including constraints that may have arisen during its past history. Experimental populations of bacteria were used to address these issues in the context of evolutionary adaptation to the thermal environment. Six replicate lines of Escherichia coli (20°C group), founded from a common ancestor, were propagated for 2000 generations at 20°C, a novel temperature that is very near the lower thermal limit at which it can maintain a stable population size in a daily serial transfer (100-fold dilution) regime. Four additional groups (32/20, 37/20, 42/20, and 32-42/20°C groups) of six lines, each with 2000 generation selection histories at different temperatures (32, 37, 42, and daily alternation of 32 and 42°C), were moved to the same 20°C environment and propagated in parallel to ascertain whether selection histories influence the adaptive response in this novel environment. Adaptation was measured by improvement in fitness relative to the common ancestor in direct competition experiments conducted at 20°C. All five groups showed improvement in relative fitness in this environment; the mean fitness of the 20°C group after 2000 generations increased by about 8%. Selection history had no discernible effect on the rate or final magnitude of the fitness responses of the four groups with different histories after 2000 generations. The correlated fitness responses of the 20°C group were measured across the entire thermal niche. There were significant tradeoffs in fitness at higher temperatures; for example, at 40°C the average fitness of the 20°C group was reduced by almost 20% relative to the common ancestor. We also observed a downward shift of 1-2°C in both the upper and lower thermal niche limits for the 20°C selected group. These observations are contrasted with previous observations of a markedly greater rate of adaptation to growth near the upper thermal limit (42°C) and a lack of trade-off in fitness at lower temperatures for lines adapted to that high temperature. The evolutionary implications of this asymmetry are discussed.
Mongold J A; Bennett A F; Lenski R E
Experimental investigations of evolutionary adaptation to temperature. Incollection
Bennet, Albert F.; Johnston, I. A. (Ed.): Animals and Temperature: Phenotypic and Evolutionary Adaptation, pp. 239 – 264, Cambridge University Press, Cambridge, 1996, ISBN: 9780511721854.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments
@incollection{Mongold1996c,
title = {Experimental investigations of evolutionary adaptation to temperature.},
author = {Judith A. Mongold and Albert F. Bennett and Richard E. Lenski},
editor = {Albert F. Bennet and I. A. Johnston},
url = {https://www.cambridge.org/core/books/animals-and-temperature/EAC172DF2783C04EDEA19E84D40E0A6A
https://www.cambridge.org/core/books/abs/animals-and-temperature/experimental-investigations-of-evolutionary-adaptation-to-temperature/E2D8AD8E2D50A525012CD0A6A22A507E},
doi = {https://doi.org/10.1017/CBO9780511721854},
isbn = {9780511721854},
year = {1996},
date = {1996-01-01},
urldate = {1996-01-01},
booktitle = {Animals and Temperature: Phenotypic and Evolutionary Adaptation},
pages = {239 -- 264},
publisher = {Cambridge University Press},
address = {Cambridge},
abstract = {Organismal biologists employ two principal methods in their investigation of the natural world: comparison and experiment. The latter is most familiar in the context of laboratory investigations of functional mechanisms. Experiment is the classic application of the scientific method, including such elements as rigorous and replicated design, controlled manipulation of a single variable of interest and the incorporation of a control group into the study. While experimental science has been crucial to our understanding of how organisms work, to date it has had relatively less application in studying how those organisms came to be the way they are, i.e. in studies of the evolution of organismal characters. In such evolutionary studies, comparative investigations have been by far the dominant methodological tradition.
In the study of evolutionary adaptation to temperature, for example, virtually all our knowledge is derived from comparative studies of different populations, species, or other taxa inhabiting different thermal environments (for reviews, see Precht \textit{et al.}, 1973; Prosser, 1973; Hochachka & Somero, 1984; Cossins & Bowler, 1987). The comparative approach involves the measurement of a character and its correlation with environmental temperature. If the character (e.g. a rate process) is thermally dependent, then it is measured either over a similar range of temperatures or at a single temperature common to the different groups examined. The pattern of character on environmental temperature is then analysed and interpreted, most frequently in an adaptive context (Prosser, 1986; Cossins & Bowler, 1987; Bennett, 1996), and compared with the pattern found for other biological systems inhabiting similar thermal environments.},
keywords = {Descendant Experiments},
pubstate = {published},
tppubtype = {incollection}
}
Organismal biologists employ two principal methods in their investigation of the natural world: comparison and experiment. The latter is most familiar in the context of laboratory investigations of functional mechanisms. Experiment is the classic application of the scientific method, including such elements as rigorous and replicated design, controlled manipulation of a single variable of interest and the incorporation of a control group into the study. While experimental science has been crucial to our understanding of how organisms work, to date it has had relatively less application in studying how those organisms came to be the way they are, i.e. in studies of the evolution of organismal characters. In such evolutionary studies, comparative investigations have been by far the dominant methodological tradition.
In the study of evolutionary adaptation to temperature, for example, virtually all our knowledge is derived from comparative studies of different populations, species, or other taxa inhabiting different thermal environments (for reviews, see Precht et al., 1973; Prosser, 1973; Hochachka & Somero, 1984; Cossins & Bowler, 1987). The comparative approach involves the measurement of a character and its correlation with environmental temperature. If the character (e.g. a rate process) is thermally dependent, then it is measured either over a similar range of temperatures or at a single temperature common to the different groups examined. The pattern of character on environmental temperature is then analysed and interpreted, most frequently in an adaptive context (Prosser, 1986; Cossins & Bowler, 1987; Bennett, 1996), and compared with the pattern found for other biological systems inhabiting similar thermal environments.
In the study of evolutionary adaptation to temperature, for example, virtually all our knowledge is derived from comparative studies of different populations, species, or other taxa inhabiting different thermal environments (for reviews, see Precht et al., 1973; Prosser, 1973; Hochachka & Somero, 1984; Cossins & Bowler, 1987). The comparative approach involves the measurement of a character and its correlation with environmental temperature. If the character (e.g. a rate process) is thermally dependent, then it is measured either over a similar range of temperatures or at a single temperature common to the different groups examined. The pattern of character on environmental temperature is then analysed and interpreted, most frequently in an adaptive context (Prosser, 1986; Cossins & Bowler, 1987; Bennett, 1996), and compared with the pattern found for other biological systems inhabiting similar thermal environments.
Kibota T T; Lynch M
Estimate of the genomic mutation rate deleterious to overall fitness in E. coli Journal Article
Nature, 381 (6584), pp. 694–696, 1996.
Abstract | Links | BibTeX | Altmetric | Tags: Descendant Experiments, Fitness Trajectories, Mutation Rates
@article{kibota1996,
title = {Estimate of the genomic mutation rate deleterious to overall fitness in \textit{E. coli}},
author = {Travis T. Kibota and Michael Lynch},
doi = {10.1038/381694a0},
year = {1996},
date = {1996-01-01},
urldate = {1996-01-01},
journal = {Nature},
volume = {381},
number = {6584},
pages = {694--696},
abstract = {Mutations are a double-edged sword: they are the ultimate source of genetic variation upon which evolution depends, yet most mutations affecting fitness (viability and reproductive success) appear to be harmful. Deleterious mutations of small effect can escape natural selection, and should accumulate in small population. Reduced fitness from deleterious-mutation accumulation may be important in the evolution of sex, mate choice, and diploid life-cycles, and in the extinction of small populations. Few empirical data exist, however. Minimum estimates of the genomic deleterious-mutation rate for viability in \textit{Drosophila melanogaster} are surprisingly high, leading to the conjecture that the rate for total fitness could exceed 1.0 mutation per individual per generation. Here we use \textit{Escherichia coli} to provide an estimate of the genomic deleterious-mutation rate for total fitness in a microbe. We estimate that the per-microbe rate of deleterious mutations is in excess of 0.0002.},
keywords = {Descendant Experiments, Fitness Trajectories, Mutation Rates},
pubstate = {published},
tppubtype = {article}
}
Mutations are a double-edged sword: they are the ultimate source of genetic variation upon which evolution depends, yet most mutations affecting fitness (viability and reproductive success) appear to be harmful. Deleterious mutations of small effect can escape natural selection, and should accumulate in small population. Reduced fitness from deleterious-mutation accumulation may be important in the evolution of sex, mate choice, and diploid life-cycles, and in the extinction of small populations. Few empirical data exist, however. Minimum estimates of the genomic deleterious-mutation rate for viability in Drosophila melanogaster are surprisingly high, leading to the conjecture that the rate for total fitness could exceed 1.0 mutation per individual per generation. Here we use Escherichia coli to provide an estimate of the genomic deleterious-mutation rate for total fitness in a microbe. We estimate that the per-microbe rate of deleterious mutations is in excess of 0.0002.
1995
Travisano M; Mongold J A; Bennett A F; Lenski R E
Experimental Tests of the Roles of Adaptation, Chance, and History Journal Article
Science, 267 (January), 1995.
Abstract | Links | BibTeX | Altmetric | Tags: Cell Morphology, Correlated Responses, Descendant Experiments, Fitness Trajectories, Historical Contingency, Methods and Miscellaneous, Parallelism and Divergence
@article{Travisano1995,
title = {Experimental Tests of the Roles of Adaptation, Chance, and History},
author = {Michael Travisano and Judith A. Mongold and Albert F. Bennett and Richard E. Lenski},
url = {https://www.science.org/lookup/doi/10.1126/science.7809610},
doi = {https://doi.org/10.1126/science.7809610},
year = {1995},
date = {1995-01-01},
urldate = {1995-01-01},
journal = {Science},
volume = {267},
number = {January},
abstract = {The contributions of adaptation, chance, and history to the evolution of fitness and cell size were measured in two separate experiments using bacteria. In both experiments, populations propagated in identical environments achieved similar fitnesses, regardless of prior history or subsequent chance events. In contrast, the evolution of cell size, a trait weakly correlated with fitness, was more strongly influenced by history and chance.},
keywords = {Cell Morphology, Correlated Responses, Descendant Experiments, Fitness Trajectories, Historical Contingency, Methods and Miscellaneous, Parallelism and Divergence},
pubstate = {published},
tppubtype = {article}
}
The contributions of adaptation, chance, and history to the evolution of fitness and cell size were measured in two separate experiments using bacteria. In both experiments, populations propagated in identical environments achieved similar fitnesses, regardless of prior history or subsequent chance events. In contrast, the evolution of cell size, a trait weakly correlated with fitness, was more strongly influenced by history and chance.
Johnson P A; Lenski R E; Hoppensteadt F C
Theoretical Analysis of Divergence in Mean Fitness between Initially Identical Populations Journal Article
Proceedings of the Royal Society, London, pp. 125–130, 1995.
Abstract | Links | BibTeX | Altmetric | Tags: Fitness Trajectories, Parallelism and Divergence, Theory and Simulations
@article{Johnson1995,
title = {Theoretical Analysis of Divergence in Mean Fitness between Initially Identical Populations},
author = {Paul A. Johnson and Richard E. Lenski and Frank C. Hoppensteadt},
url = {https://royalsocietypublishing.org/doi/10.1098/rspb.1995.0019},
doi = {10.1098/rspb.1995.0019},
year = {1995},
date = {1995-01-01},
urldate = {1995-01-01},
journal = {Proceedings of the Royal Society, London},
pages = {125--130},
abstract = {Initially identical populations in identical environments may subsequently diverge from one another not only via the effects of genetic drift on neutral alleles, but also by selection on beneficial alleles that arise stochastically by mutation. In the simple case of one locus with two alleles in a haploid organism, a full range of combinations of population sizes, selection pressures, mutation rates and fixation probabilities reveals two qualitatively distinct dynamics of divergence among such initially identical populations. We define a non-dimensional parameter \textit{k} that describes conditions for the occurrence of these different dynamics. One dynamic (\textit{k} > 1) occurs when beneficial mutations are sufficiently common that substitutions within the populations are essentially simultaneous; the other dynamic (\textit{k} < 1) occurs when beneficial mutations are so rare that substitutions are likely to occur as isolated events. If there are more than two alleles, or multiple loci, divergence among the populations can be sustained indefinitely if \textit{k} < 1. The parameter \textit{k} pertains to the nature of biological evolution and its tendency to be gradual or punctuated.},
keywords = {Fitness Trajectories, Parallelism and Divergence, Theory and Simulations},
pubstate = {published},
tppubtype = {article}
}
Initially identical populations in identical environments may subsequently diverge from one another not only via the effects of genetic drift on neutral alleles, but also by selection on beneficial alleles that arise stochastically by mutation. In the simple case of one locus with two alleles in a haploid organism, a full range of combinations of population sizes, selection pressures, mutation rates and fixation probabilities reveals two qualitatively distinct dynamics of divergence among such initially identical populations. We define a non-dimensional parameter k that describes conditions for the occurrence of these different dynamics. One dynamic (k > 1) occurs when beneficial mutations are sufficiently common that substitutions within the populations are essentially simultaneous; the other dynamic (k < 1) occurs when beneficial mutations are so rare that substitutions are likely to occur as isolated events. If there are more than two alleles, or multiple loci, divergence among the populations can be sustained indefinitely if k < 1. The parameter k pertains to the nature of biological evolution and its tendency to be gradual or punctuated.
Travisano M; Vasi F K; Lenski R E
Long-Term Experimental Evolution in Escherichia coli. III. Variation Among Replicate Populations in Correlated Responses to Novel Environments Journal Article
Evolution, 49 (1), pp. 189–200, 1995.
Abstract | Links | BibTeX | Altmetric | Tags: Correlated Responses, Genotypes and Phenotypes, Parallelism and Divergence
@article{Travisano1995b,
title = {Long-Term Experimental Evolution in \textit{Escherichia coli}. III. Variation Among Replicate Populations in Correlated Responses to Novel Environments},
author = {Michael Travisano and Farida K. Vasi and Richard E. Lenski},
url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1995.tb05970.x},
doi = {https://doi.org/10.1111/j.1558-5646.1995.tb05970.x},
year = {1995},
date = {1995-01-01},
urldate = {1995-01-01},
journal = {Evolution},
volume = {49},
number = {1},
pages = {189--200},
abstract = {Twelve populations of \textit{Escherichia coli} were founded from a single clone and propagated for 2000 gen- erations in identical glucose-limited environments. During this time, the mean fitnesses of the evolving populations relative to their common ancestor improved greatly, but their fitnesses relative to one another diverged only slightly. Although the populations showed similar fitness increases, they may have done so by different underlying adaptations, or they may have diverged in other respects by random genetic drift. Therefore, we examined the relative fitnesses of independently derived genotypes in two other sugars, maltose and lactose, to determine whether they were ho- mogeneous or heterogeneous in these environments. The genetic variation among the derived lines in fitness on maltose and lactose was more than 100-times greater than their variation in fitness on glucose. Moreover, the glucose-adapted genotypes, on average, showed significant adaptation to lactose, but not to maltose. That pathways for use of maltose and glucose are virtually identical in \textit{E. coli}, except for their distinct mechanisms of uptake, suggests that the derived genotypes have adapted primarily by improved glucose transport. From consideration of the number of generations of divergence, the mutation rate in \textit{E. coli}, and the proportion of its genome required for growth on maltose (but not glucose), we hypothesize that pleiotropy involving the selected alleles, rather than random genetic drift of alleles at other loci, was the major cause of the variation among the derived genotypes in fitness on these other sugars.},
keywords = {Correlated Responses, Genotypes and Phenotypes, Parallelism and Divergence},
pubstate = {published},
tppubtype = {article}
}
Twelve populations of Escherichia coli were founded from a single clone and propagated for 2000 gen- erations in identical glucose-limited environments. During this time, the mean fitnesses of the evolving populations relative to their common ancestor improved greatly, but their fitnesses relative to one another diverged only slightly. Although the populations showed similar fitness increases, they may have done so by different underlying adaptations, or they may have diverged in other respects by random genetic drift. Therefore, we examined the relative fitnesses of independently derived genotypes in two other sugars, maltose and lactose, to determine whether they were ho- mogeneous or heterogeneous in these environments. The genetic variation among the derived lines in fitness on maltose and lactose was more than 100-times greater than their variation in fitness on glucose. Moreover, the glucose-adapted genotypes, on average, showed significant adaptation to lactose, but not to maltose. That pathways for use of maltose and glucose are virtually identical in E. coli, except for their distinct mechanisms of uptake, suggests that the derived genotypes have adapted primarily by improved glucose transport. From consideration of the number of generations of divergence, the mutation rate in E. coli, and the proportion of its genome required for growth on maltose (but not glucose), we hypothesize that pleiotropy involving the selected alleles, rather than random genetic drift of alleles at other loci, was the major cause of the variation among the derived genotypes in fitness on these other sugars.