1997
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.
1996
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
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; 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.
1994
Lenski R E; Travisano M
Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Journal Article
Proceedings of the National Academy of Sciences of the United States of America, 91 (15), pp. 6808–6814, 1994, ISSN: 0027-8424.
Abstract | Links | BibTeX | Altmetric | Tags: Cell Morphology, Fitness Trajectories, Parallelism and Divergence
@article{Lenski1994,
title = {Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations.},
author = {Richard E. Lenski and Michael Travisano},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.91.15.6808},
doi = {10.1073/pnas.91.15.6808},
issn = {0027-8424},
year = {1994},
date = {1994-07-01},
urldate = {1994-07-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {91},
number = {15},
pages = {6808--6814},
abstract = {We followed evolutionary change in 12 populations of \textit{Escherichia coli} propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.},
keywords = {Cell Morphology, Fitness Trajectories, Parallelism and Divergence},
pubstate = {published},
tppubtype = {article}
}
We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.
1991
Lenski R E; Rose M R; Simpson S C; Tadler S C
Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations Journal Article
Am. Nat., 138 (6), pp. 1315–1341, 1991.
Abstract | Links | BibTeX | Altmetric | Tags: Fitness Trajectories, Parallelism and Divergence
@article{Lenski1991,
title = {Long-term experimental evolution in \textit{Escherichia coli}. I. Adaptation and divergence during 2,000 generations},
author = {Richard E. Lenski and M R. Rose and S C. Simpson and S C. Tadler},
url = {https://www.jstor.org/stable/2462549},
doi = {https://doi.org/10.1086/285289},
year = {1991},
date = {1991-01-01},
urldate = {1991-01-01},
journal = {Am. Nat.},
volume = {138},
number = {6},
pages = {1315--1341},
publisher = {JSTOR},
abstract = {We assess the degree to which adaptation to a uniform environment among independently evolving asexual populations is associated with increasing divergence of those populations. In addition, we are concerned with the pattern of adaptation itself, particularly whether the rate of increase in mean fitness tends to decline with the number of generations of selection in a constant environment. The correspondence between the rate of increase in mean fitness and the within-population genetic variance of fitness, as expected from Fisher's fundamental theorem, is also addressed. Twelve \textit{Escherichia coli} populations were founded from a single clonal ancestor and allowed to evolve for 2,000 generations. Mean fitness increased by about 37%. However, the rate of increase in mean fitness was slower in later generations. There was no statistically significant within-population genetic variance of fitness, but there was significant between-population variance. Although the estimated genetic variation in fitness within populations was not statistically significant, it was consistent in magnitude with theoretical expectations. Similarly, the variance of mean fitness between populations was consistent with a model that incorporated stochastic variation in the timing and order of substitutions at a finite number of nonepistatic loci, coupled with substitutional delays and interference between substitutions arising from clonality. These results, taken as a whole, are consistent with theoretical expectations that do not invoke divergence due to multiple fitness peaks in a Wrightian evolutionary landscape.},
keywords = {Fitness Trajectories, Parallelism and Divergence},
pubstate = {published},
tppubtype = {article}
}
We assess the degree to which adaptation to a uniform environment among independently evolving asexual populations is associated with increasing divergence of those populations. In addition, we are concerned with the pattern of adaptation itself, particularly whether the rate of increase in mean fitness tends to decline with the number of generations of selection in a constant environment. The correspondence between the rate of increase in mean fitness and the within-population genetic variance of fitness, as expected from Fisher's fundamental theorem, is also addressed. Twelve Escherichia coli populations were founded from a single clonal ancestor and allowed to evolve for 2,000 generations. Mean fitness increased by about 37%. However, the rate of increase in mean fitness was slower in later generations. There was no statistically significant within-population genetic variance of fitness, but there was significant between-population variance. Although the estimated genetic variation in fitness within populations was not statistically significant, it was consistent in magnitude with theoretical expectations. Similarly, the variance of mean fitness between populations was consistent with a model that incorporated stochastic variation in the timing and order of substitutions at a finite number of nonepistatic loci, coupled with substitutional delays and interference between substitutions arising from clonality. These results, taken as a whole, are consistent with theoretical expectations that do not invoke divergence due to multiple fitness peaks in a Wrightian evolutionary landscape.
