Richard Lenski

Summary

Affiliation: Michigan State University
Country: USA

Publications

  1. pmc Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli
    Mark T Stanek
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824 4320, USA
    BMC Evol Biol 9:302. 2009
  2. pmc Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding
    Claus O Wilke
    Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Evol Biol 3:3. 2003
  3. pmc Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation
    J Arjan G M de Visser
    Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
    BMC Evol Biol 2:19. 2002
  4. pmc Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations
    Tim F Cooper
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    BMC Evol Biol 10:11. 2010
  5. pmc Analysis of epistatic interactions and fitness landscapes using a new geometric approach
    Niko Beerenwinkel
    Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
    BMC Evol Biol 7:60. 2007
  6. pmc Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environment
    Sean C Sleight
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    BMC Evol Biol 6:104. 2006
  7. pmc Balancing robustness and evolvability
    Richard E Lenski
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
    PLoS Biol 4:e428. 2006
  8. doi request reprint Chance and necessity in the evolution of a bacterial pathogen
    Richard E Lenski
    BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, USA
    Nat Genet 43:1174-6. 2011
  9. ncbi request reprint The ecology, genetics and evolution of bacteria in an experimental setting
    Richard Lenski
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing 48824, USA
    Curr Biol 13:R466-7. 2003
  10. ncbi request reprint The evolutionary origin of complex features
    Richard E Lenski
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    Nature 423:139-44. 2003

Detail Information

Publications46

  1. pmc Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli
    Mark 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...
  2. pmc Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding
    Claus 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...
  3. pmc Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation
    J 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...
  4. pmc Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations
    Tim 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...
  5. pmc Analysis of epistatic interactions and fitness landscapes using a new geometric approach
    Niko 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...
  6. pmc Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environment
    Sean 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...
  7. pmc Balancing robustness and evolvability
    Richard E Lenski
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
    PLoS Biol 4:e428. 2006
  8. doi request reprint Chance and necessity in the evolution of a bacterial pathogen
    Richard E Lenski
    BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, 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...
  9. ncbi request reprint The ecology, genetics and evolution of bacteria in an experimental setting
    Richard Lenski
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing 48824, USA
    Curr Biol 13:R466-7. 2003
    b>Richard Lenski is the John Hannah Distinguished Professor of Microbial Ecology at Michigan State University...
  10. ncbi request reprint The evolutionary origin of complex features
    Richard 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...
  11. ncbi request reprint Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations
    Richard 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...
  12. pmc Chemical warfare from an ecological perspective
    Richard 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
  13. pmc The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli
    Elizabeth 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...
  14. pmc Genetic basis of evolutionary adaptation by Escherichia coli to stressful cycles of freezing, thawing and growth
    Sean 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...
  15. ncbi request reprint Ecological specialization and adaptive decay in digital organisms
    Elizabeth 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...
  16. doi request reprint Genome evolution and adaptation in a long-term experiment with Escherichia coli
    Jeffrey 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...
  17. pmc Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes
    Jeff 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...
  18. pmc Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects
    Jeffrey E Barrick
    Department of Microbiology and Molecular Genetics, Michigan State University, USA
    Mol Biol Evol 27:1338-47. 2010
    ....
  19. ncbi request reprint Evolutionary adaptation to freeze-thaw-growth cycles in Escherichia coli
    Sean 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...
  20. pmc Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli
    Tim 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...
  21. doi request reprint Evolutionary dynamics, epistatic interactions, and biological information
    Christopher 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...
  22. ncbi request reprint Pleiotropic effects of beneficial mutations in Escherichia coli
    Elizabeth A Ostrowski
    Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing 48824, USA
    Evolution 59:2343-52. 2005
    ....
  23. pmc Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex
    Tim 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...
  24. pmc Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
    Zachary 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...
  25. pmc Sexual reproduction reshapes the genetic architecture of digital organisms
    Dusan 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...
  26. ncbi request reprint Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism
    Daniel 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...
  27. doi request reprint Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms
    Gabriel 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...
  28. doi request reprint Experiments with digital organisms on the origin and maintenance of sex in changing environments
    Dusan 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...
  29. ncbi request reprint Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli
    Susanna K Remold
    Center for Microbial Ecology, Michigan State University, East Lansing, 48824, USA
    Nat Genet 36:423-6. 2004
    ....
  30. pmc Experimental evolution of a microbial predator's ability to find prey
    Kristina 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...
  31. pmc Tests of parallel molecular evolution in a long-term experiment with Escherichia coli
    Robert 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...
  32. pmc Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection
    Estelle 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...
  33. ncbi request reprint Adaptive radiation from resource competition in digital organisms
    Stephanie 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...
  34. ncbi request reprint Dynamics of insertion sequence elements during experimental evolution of bacteria
    Dominique 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...
  35. ncbi request reprint Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli
    Maja 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...
  36. ncbi request reprint Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates
    Santiago 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...
  37. pmc Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli
    Tim 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...
  38. pmc Cryptic population dynamics: rapid evolution masks trophic interactions
    Takehito 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...
  39. ncbi request reprint Evolution of global regulatory networks during a long-term experiment with Escherichia coli
    Nadège Philippe
    Laboratoire Adaptation et Pathogénie des Micro Organismes, CNRS UMR5163, Universite Joseph Fourier, Grenoble, France
    Bioessays 29:846-60. 2007
    ....
  40. pmc An experimental test of evolutionary trade-offs during temperature adaptation
    Albert 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
    ....
  41. ncbi request reprint Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature
    Michelle 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...
  42. pmc Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli
    Ludovic 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...
  43. ncbi request reprint Effects of population size and mutation rate on the evolution of mutational robustness
    Santiago 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...
  44. ncbi request reprint Ecological variables affecting predatory success in Myxococcus xanthus
    Kristina 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...
  45. pmc Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environment
    Gregory 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...
  46. ncbi request reprint Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
    Santiago 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
    ....