scholarly journals Reinterpreting Long-Term Evolution Experiments: Is Delayed Adaptation an Example of Historical Contingency or a Consequence of Intermittent Selection?

2016 ◽  
Vol 198 (7) ◽  
pp. 1009-1012 ◽  
Author(s):  
John R. Roth ◽  
Sophie Maisnier-Patin
Keyword(s):  
Escherichia Coli ◽  
Rapid Evolution ◽  
Long Term Evolution ◽  
Historical Contingency ◽  
Short Pulses ◽  
Content Type ◽  
Link Type ◽  
Term Evolution ◽  
Selection For

Van Hofwegen et al. demonstrated thatEscherichia colirapidly evolves the ability to use citrate when long selective periods are provided (D. J. Van Hofwegen, C. J. Hovde, and S. A. Minnich, J Bacteriol 198:1022–1034, 2016,http://dx.doi.org/10.1128/JB.00831-15). This contrasts with the extreme delay (15 years of daily transfers) seen in the long-term evolution experiments of Lenski and coworkers. Their idea of “historical contingency” may require reinterpretation. Rapid evolution seems to involve selection for duplications of the wholecitlocus that are too unstable to contribute when selection is provided in short pulses.

scholarly journals Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli

2020 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Nkrumah A. Grant
Keyword(s):  
Escherichia Coli ◽  
Point Mutations ◽  
Long Term Evolution ◽  
Dna Topology ◽  
Mutation Rates ◽  
Rate Variation ◽  
Historical Contingency ◽  
Term Evolution ◽  
Evolution Experiment

ABSTRACTAll organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB— loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.

scholarly journals Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli

2020 ◽  
Vol 12 (9) ◽  
pp. 1591-1603 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Nkrumah A Grant
Keyword(s):  
Escherichia Coli ◽  
Point Mutations ◽  
Long Term Evolution ◽  
Dna Topology ◽  
Mutation Rates ◽  
Rate Variation ◽  
Historical Contingency ◽  
Term Evolution ◽  
Evolution Experiment

Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. 2017. The dynamics of molecular evolution over 60,000 generations. Nature 551(7678):45–50.), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB—loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.

Selection against hypermutability in Escherichia coli during long term evolution

1984 ◽  
Vol 198 (1) ◽  
pp. 177-178 ◽  
Author(s):  
Wolfgang Tröbner ◽  
Reinhard Piechocki
Keyword(s):  
Escherichia Coli ◽  
Long Term Evolution ◽  
Term Evolution

scholarly journals Growth and business cycle in Argentina. A long-run approach, 1870–2015

2020 ◽  
Vol 28 (84) ◽  
pp. 197-220
Author(s):  
María Dolores Gadea ◽  
Isabel Sanz-Villarroya
Keyword(s):  
Long Term Evolution ◽  
Growth Potential ◽  
Short Term ◽  
Content Type ◽  
Developed Economies ◽  
Term Evolution ◽  
Long Run ◽  
High Volatility ◽  
The Moment

Purpose The purpose of this study is to focus deeply on the short term to explain the relative long-term evolution of the Argentinian economy in the long and the short term. Design/methodology/approach The study of the long-term evolution of the Argentine economy and identifying the moment in which it began to lose ground compared to other developed economies, such as Australia and Canada, constitutes the central axis of the historiography of this country. However, an additional problem presented by the Argentine economy is its high volatility. For this reason, the long term should be influenced by the short term, an issue that requires a more detailed study of the cyclical behavior and a deep analysis of the relationship between the long and the short term. Findings The results obtained point to a cyclical development that influences the long-term evolution and, therefore, explains Argentina’s convergence process with Australia and Canada. Frequent deep busts and short booms characterize the Argentine cycle, offsetting its long-term growth potential. Originality/value Although the long term has been profusely studied in Argentina, the short term has not been analyzed to the same extent, which is surprising given the extreme volatility of this economy (Prebisch, 1950). The studies performed on economic cycles have always been partial, disconnected from the long term and carried out without much technical rigor.

scholarly journals Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

2011 ◽  
Vol 1 (3) ◽  
pp. 183-186 ◽  
Author(s):  
Sébastien Wielgoss ◽  
Jeffrey E. Barrick ◽  
Olivier Tenaillon ◽  
Stéphane Cruveiller ◽  
Béatrice Chane-Woon-Ming ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Mutation Rate ◽  
Long Term Evolution ◽  
Synonymous Substitutions ◽  
Term Evolution ◽  
Evolution Experiment

scholarly journals Escherichia coli EDL933 Requires Gluconeogenic Nutrients To Successfully Colonize the Intestines of Streptomycin-Treated Mice Precolonized with E. coli Nissle 1917

2015 ◽  
Vol 83 (5) ◽  
pp. 1983-1991 ◽  
Author(s):  
Silvia A. C. Schinner ◽  
Matthew E. Mokszycki ◽  
Jimmy Adediran ◽  
Mary Leatham-Jensen ◽  
Tyrrell Conway ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Probiotic Strain ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Mouse Intestine ◽  
K 12 ◽  
Rule Out

Escherichia coliMG1655, a K-12 strain, uses glycolytic nutrients exclusively to colonize the intestines of streptomycin-treated mice when it is the onlyE. colistrain present or when it is confronted withE. coliEDL933, an O157:H7 strain. In contrast,E. coliEDL933 uses glycolytic nutrients exclusively when it is the onlyE. colistrain in the intestine but switches in part to gluconeogenic nutrients when it colonizes mice precolonized withE. coliMG1655 (R. L. Miranda et al., Infect Immun 72:1666–1676, 2004,http://dx.doi.org/10.1128/IAI.72.3.1666-1676.2004). Recently, J. W. Njoroge et al. (mBio 3:e00280-12, 2012,http://dx.doi.org/10.1128/mBio.00280-12) reported thatE. coli86-24, an O157:H7 strain, activates the expression of virulence genes under gluconeogenic conditions, suggesting that colonization of the intestine with a probioticE. colistrain that outcompetes O157:H7 strains for gluconeogenic nutrients could render them nonpathogenic. Here we report thatE. coliNissle 1917, a probiotic strain, uses both glycolytic and gluconeogenic nutrients to colonize the mouse intestine between 1 and 5 days postfeeding, appears to stop using gluconeogenic nutrients thereafter in a large, long-term colonization niche, but continues to use them in a smaller niche to compete with invadingE. coliEDL933. Evidence is also presented suggesting that invadingE. coliEDL933 uses both glycolytic and gluconeogenic nutrients and needs the ability to perform gluconeogenesis in order to colonize mice precolonized withE. coliNissle 1917. The data presented here therefore rule out the possibility thatE. coliNissle 1917 can starve the O157:H7E. colistrain EDL933 of gluconeogenic nutrients, even thoughE. coliNissle 1917 uses such nutrients to compete withE. coliEDL933 in the mouse intestine.

scholarly journals Universal constraints on protein evolution in the long-term evolution experiment with Escherichia coli

2021 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Escherichia Coli ◽  
Protein Evolution ◽  
Long Term Evolution ◽  
Protein Abundance ◽  
Nonsynonymous Mutation ◽  
Protein Protein Interaction ◽  
Term Evolution ◽  
Mutation Density ◽  
Evolution Experiment

Abstract Although it is well known that abundant proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that abundant proteins evolve slowly in the hypermutator populations of Lenski’s long-term evolution experiment with Escherichia coli (LTEE). Specifically, the density of all observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, significantly anti-correlates with mRNA abundance, protein abundance, and degree of protein-protein interaction. The same pattern holds for nonsynonymous mutation density. However, synonymous mutation density, measured across the LTEE hypermutator populations, positively correlates with protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why abundant proteins evolve slowly.

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