Research Topics
Genomes and Genes | Richard LenskiSummaryAffiliation: Michigan State University Country: USA Publications
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Publications
Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coliMark T Stanek
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824 4320, USA
BMC Evol Biol 9:302. 2009..We sought to find and characterize one of the beneficial mutations responsible for the adaptation and other phenotypic changes, including increased cell size, in one of these populations...- Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure foldingClaus O Wilke
Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
BMC Evol Biol 3:3. 2003..However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed... - Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptationJ Arjan G M de Visser
Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
BMC Evol Biol 2:19. 2002..Alternatively, this deceleration might be caused by non-transitive competitive interactions, in particular such that the measured advantage of later genotypes relative to earlier ones would be greater if they competed directly... - Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populationsTim F Cooper
Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
BMC Evol Biol 10:11. 2010..To date, the influence of environmental variability on evolutionary dynamics has received relatively little experimental study... - Analysis of epistatic interactions and fitness landscapes using a new geometric approachNiko Beerenwinkel
Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
BMC Evol Biol 7:60. 2007..In this paper, we propose and employ a new mathematical approach that allows a more complete description of multi-way interactions and provides new insights into the structure of fitness landscapes... - Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environmentSean C Sleight
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
BMC Evol Biol 6:104. 2006..This study examines whether these evolved lines changed in their ability to tolerate the stresses of prolonged freezing and repeated freeze-thaw cycles during adaptation to a benign environment... - Balancing robustness and evolvabilityRichard E Lenski
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
PLoS Biol 4:e428. 2006 - Chance and necessity in the evolution of a bacterial pathogenRichard E Lenski
BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
Nat Genet 43:1174-6. 2011..By sequencing 112 Burkholderia dolosa genomes from an outbreak among patients with cystic fibrosis, a new study documents evolution in action and identifies a set of genes that contributed to the pathogen's adaptation... - The ecology, genetics and evolution of bacteria in an experimental settingRichard Lenski
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing 48824, USA
Curr Biol 13:R466-7. 2003b>Richard Lenski is the John Hannah Distinguished Professor of Microbial Ecology at Michigan State University... - The evolutionary origin of complex featuresRichard E Lenski
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
Nature 423:139-44. 2003..In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection... - Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generationsRichard E Lenski
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
J Mol Evol 56:498-508. 2003..However, this limited variation also provides a useful baseline for research aimed at finding the beneficial substitutions in these populations... - Chemical warfare from an ecological perspectiveRichard E Lenski
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
Proc Natl Acad Sci U S A 99:556-8. 2002 - The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coliElizabeth A Ostrowski
Department of Zoology, Michigan State University, East Lansing, MI 48824, USA
Proc Biol Sci 275:277-84. 2008..Substitutions in the same locus clustered together phenotypically, indicating concordance between molecular and phenotypic measures of divergence... - Genetic basis of evolutionary adaptation by Escherichia coli to stressful cycles of freezing, thawing and growthSean C Sleight
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
Genetics 180:431-43. 2008..The evolved insertions reduce uspB transcription and increase both FT survival and recovery, but the physiological mechanism for this fitness improvement remains unknown... - Ecological specialization and adaptive decay in digital organismsElizabeth A Ostrowski
Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
Am Nat 169:E1-20. 2007..Occasionally, unused functions were not lost and even increased in performance. Here we find that understanding how the functions were integrated into the genome was crucial to predictions of their maintenance... - Genome evolution and adaptation in a long-term experiment with Escherichia coliJeffrey E Barrick
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
Nature 461:1243-7. 2009..In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable... - Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapesJeff Clune
Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
PLoS Comput Biol 4:e1000187. 2008..This finding has important implications for applied evolutionary research in both biological and computational realms... - Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defectsJeffrey E Barrick
Department of Microbiology and Molecular Genetics, Michigan State University, USA
Mol Biol Evol 27:1338-47. 2010.... - Evolutionary adaptation to freeze-thaw-growth cycles in Escherichia coliSean C Sleight
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
Physiol Biochem Zool 80:370-85. 2007..Future work will seek to identify the mutations responsible for evolutionary adaptation to the FTG environment and use them to explore the physiological mechanisms that allow increased survival and more rapid recovery... - Parallel changes in gene expression after 20,000 generations of evolution in EscherichiacoliTim F Cooper
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
Proc Natl Acad Sci U S A 100:1072-7. 2003..Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations... - Evolutionary dynamics, epistatic interactions, and biological informationChristopher C Strelioff
Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
J Theor Biol 266:584-94. 2010..As modular interactions are inherently epistatic, we demonstrate that our refined approximation provides insight into the underlying structure of these non-trivial fitness landscapes... - Pleiotropic effects of beneficial mutations in Escherichia coliElizabeth A Ostrowski
Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing 48824, USA
Evolution 59:2343-52. 2005.... - Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sexTim F Cooper
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
Proc Biol Sci 272:311-7. 2005..These results suggest that, on average, deleterious mutations act multiplicatively with each other but in synergy with infection in determining fitness... - Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coliZachary D Blount
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
Proc Natl Acad Sci U S A 105:7899-906. 2008..More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection... - Sexual reproduction reshapes the genetic architecture of digital organismsDusan Misevic
Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
Proc Biol Sci 273:457-64. 2006..Our results show that sexual reproduction profoundly influences the evolution of the genetic architecture... - Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphismDaniel E Rozen
Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
J Mol Evol 61:171-80. 2005..Based on their phylogenetic history and independent evolutionary trajectories, S and L fulfill Cohan's criteria for being different asexual species... - Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organismsGabriel Yedid
Department of Zoology, Michigan State University, East Lansing, MI 48824, USA
Am Nat 173:E139-54. 2009..Adaptation to conditions during an extended disturbance may hinder subsequent recovery... - Experiments with digital organisms on the origin and maintenance of sex in changing environmentsDusan Misevic
Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824, USA
J Hered 101:S46-54. 2010..Our study provides some limited support for the importance of changing environments to the evolution of sex, while also reinforcing the difficulty of evolving and maintaining sexual reproduction... - Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coliSusanna K Remold
Center for Microbial Ecology, Michigan State University, East Lansing, 48824, USA
Nat Genet 36:423-6. 2004.... - Experimental evolution of a microbial predator's ability to find preyKristina L Hillesland
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
Proc Biol Sci 276:459-67. 2009..More generally, these results demonstrate that predators evolve behaviours that reflect at least some of the opportunities and limitations imposed by the distribution and abundance of their prey... - Tests of parallel molecular evolution in a long-term experiment with Escherichia coliRobert Woods
Department of Zoology, Michigan State University, East Lansing, MI 48824, USA
Proc Natl Acad Sci U S A 103:9107-12. 2006..Tests of four different statistical aspects of the pattern of molecular evolution all indicate that adaptation by natural selection drove the parallel changes in these candidate genes... - Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selectionEstelle Crozat
Laboratoire Adaptation et Pathogenie des Microorganismes, Universite Joseph Fourier, Institut Jean Roget, CNRS UMR 5163, F 38041 Grenoble, France
Genetics 169:523-32. 2005..These findings define a new class of fitness-enhancing mutations and indicate that the control of DNA supercoiling can be a key target of selection in evolving bacterial populations... - Adaptive radiation from resource competition in digital organismsStephanie S Chow
Digital Life Laboratory 136-93, California Institute of Technology, Pasadena, CA 91125, USA
Science 305:84-6. 2004..A diverse pool of limiting resources is sufficient to cause adaptive radiation, which is manifest by the origin and maintenance of phenotypically and phylogenetically distinct groups of organisms... - Dynamics of insertion sequence elements during experimental evolution of bacteriaDominique Schneider
Laboratoire Adaptation et Pathogenie des Microorganismes, CNRS UMR5163, Universite Joseph Fourier, 38041 Grenoble Cedex 9, France
Res Microbiol 155:319-27. 2004..This review shows that IS elements are useful as markers for detecting genomic change over experimental time scales and, moreover, that IS elements generate some of the beneficial mutations that increase organismal fitness... - Experimental tests for an evolutionary trade-off between growth rate and yield in E. coliMaja Novak
Institute of Integrative Biology, Eldgenossische Technische Hochschule Zurich, 8092 Zurich, Switzerland
Am Nat 168:242-51. 2006..The observation of a trade-off within, but not between, populations suggests that the populations evolved different genetic solutions for growth in the selective environment, which in turn led to different physiological constraints... - Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation ratesSantiago F Elena
Inst for Molecular and Cellular Plant Biology, CSIC UPV, Valencia, Spain
Int Microbiol 8:271-8. 2005..coli B, and an estimate of 200 generations per year, it was estimated that B and K-12 diverged several hundred thousand years ago, while O157:H7 split off from their common ancestor about 1.5-2 million years ago... - Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coliTim F Cooper
Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
PLoS Genet 4:e35. 2008..More generally, we demonstrate that expression profiles can be profitably used to investigate epistatic interactions... - Cryptic population dynamics: rapid evolution masks trophic interactionsTakehito Yoshida
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
PLoS Biol 5:e235. 2007..Modeling suggests that rapid evolution may also confound experimental approaches to measuring interaction strength, but it identifies certain experimental designs as being more robust against potential confounding by rapid evolution... - Evolution of global regulatory networks during a long-term experiment with Escherichia coliNadège Philippe
Laboratoire Adaptation et Pathogénie des Micro Organismes, CNRS UMR5163, Universite Joseph Fourier, Grenoble, France
Bioessays 29:846-60. 2007.... - An experimental test of evolutionary trade-offs during temperature adaptationAlbert F Bennett
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
Proc Natl Acad Sci U S A 104:8649-54. 2007.... - Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperatureMichelle M Riehle
Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, California 92697 2525, USA
Physiol Genomics 14:47-58. 2003..Thus evolution at high temperature led to significant changes at the molecular level in heat-inducible gene expression and at the organismal level in inducible thermotolerance and fitness... - Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coliLudovic Pelosi
Laboratoire Adaptation et Pathogenie des Microorganismes, Universite Joseph Fourier, Grenoble, France
Genetics 173:1851-69. 2006..Functional and evolutionary analyses of these mutations revealed parallel phenotypic decreases in the maltose regulon expression and a high level of polymorphism at this locus in the evolved populations... - Effects of population size and mutation rate on the evolution of mutational robustnessSantiago F Elena
Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, 46022 Valencia, Spain
Evolution 61:666-74. 2007..These results are independent of whether genomes were constrained to their original length or allowed to change in size... - Ecological variables affecting predatory success in Myxococcus xanthusKristina L Hillesland
Department of Civil and Environmental Engineering, University of Washington, 167 Wilcox, Box 352700, Seattle, WA 98195, USA
Microb Ecol 53:571-8. 2007..xanthus quickly kills most nearby E. coli or M. luteus regardless of the surface. However, the ability of M. xanthus to search out patches of these prey is affected by surface hardness, the density of prey patches, and the prey species... - Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environmentGregory J Velicer
Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37, D 72076 Tubingen, Germany
J Bacteriol 184:2719-27. 2002..Moreover, an amino acid substitution in an evolved genotype was located in a region predicted by genetic complementation analysis to bear an adaptive mutation... - Evolution experiments with microorganisms: the dynamics and genetic bases of adaptationSantiago F Elena
Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas, 46022 Valencia, Spain
Nat Rev Genet 4:457-69. 2003....