Charles Ofria

Summary

Affiliation: Michigan State University
Country: USA

Publications

  1. ncbi request reprint Selective pressures on genomes in molecular evolution
    Charles Ofria
    Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    J Theor Biol 222:477-83. 2003
  2. ncbi request reprint Avida: a software platform for research in computational evolutionary biology
    Charles Ofria
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    Artif Life 10:191-229. 2004
  3. 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
  4. pmc The effect of natural selection on the performance of maximum parsimony
    Dehua Hang
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    BMC Evol Biol 7:94. 2007
  5. 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
  6. 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
  7. doi request reprint On the gradual evolution of complexity and the sudden emergence of complex features
    Charles Ofria
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    Artif Life 14:255-63. 2008
  8. doi request reprint Ontogeny tends to recapitulate phylogeny in digital organisms
    Jeff Clune
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    Am Nat 180:E54-63. 2012
  9. 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
  10. 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

Detail Information

Publications20

  1. ncbi request reprint Selective pressures on genomes in molecular evolution
    Charles Ofria
    Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    J Theor Biol 222:477-83. 2003
    ..This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms...
  2. ncbi request reprint Avida: a software platform for research in computational evolutionary biology
    Charles Ofria
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    Artif Life 10:191-229. 2004
    ..We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed...
  3. 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...
  4. pmc The effect of natural selection on the performance of maximum parsimony
    Dehua Hang
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    BMC Evol Biol 7:94. 2007
    ..To gain insight into these issues, we study how well maximum parsimony performs with data generated by Avida, a digital life platform where populations of digital organisms evolve subject to natural selective pressures...
  5. 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...
  6. 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...
  7. doi request reprint On the gradual evolution of complexity and the sudden emergence of complex features
    Charles Ofria
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    Artif Life 14:255-63. 2008
    ..Thus, while total genomic information increases incrementally, traits that require much more information can still arise during the evolutionary process...
  8. doi request reprint Ontogeny tends to recapitulate phylogeny in digital organisms
    Jeff Clune
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    Am Nat 180:E54-63. 2012
    ..This additional effect provides evidence that selection against developmental disruption also contributed to the conservation of early stages in development...
  9. 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...
  10. 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...
  11. pmc Experiments on the role of deleterious mutations as stepping stones in adaptive evolution
    Arthur W Covert
    Program in Ecology, Evolutionary Biology and Behavior, Department of Computer Science and Engineering, and BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824
    Proc Natl Acad Sci U S A 110:E3171-8. 2013
    ..Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions...
  12. pmc Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory
    Jeff Clune
    Department of Philosophy, Michigan State University, East Lansing, MI 48824, USA
    Proc Biol Sci 278:666-74. 2011
    ..Our work also emphasizes that the concept of targeting accuracy must include both the presence of an altruist gene and the level of altruism it produces...
  13. 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...
  14. 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
  15. ncbi request reprint The evolutionary origin of somatic cells under the dirty work hypothesis
    Heather J Goldsby
    BEACON Center for Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America Department of Biology, University of Washington, Seattle, Washington, United States of America
    PLoS Biol 12:e1001858. 2014
    ....
  16. doi request reprint Runaway sexual selection leads to good genes
    Christopher H Chandler
    BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
    Evolution 67:110-9. 2013
    ..Instead, a pleiotropic genetic architecture underlies both displays and viability. Runaway sexual selection and good genes benefits should thus be viewed as interacting mechanisms that reinforce one another...
  17. 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...
  18. 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...
  19. ncbi request reprint Perspective: Evolution and detection of genetic robustness
    J Arjan G M de Visser
    Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
    Evolution 57:1959-72. 2003
    ....
  20. ncbi request reprint Using Avida to test the effects of natural selection on phylogenetic reconstruction methods
    George I Hagstrom
    California Institute of Technology, Pasadena, CA 91125, USA
    Artif Life 10:157-66. 2004
    ..We find that if the organisms undergo natural selection between branch points, the methods will be successful even on very large time scales. However, these algorithms often falter when selection is absent...