Research Topics
| Charles OfriaSummaryAffiliation: Michigan State University Country: USA Publications
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Detail Information
Publications
Selective pressures on genomes in molecular evolutionCharles 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...- Avida: a software platform for research in computational evolutionary biologyCharles 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... - 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... - The effect of natural selection on the performance of maximum parsimonyDehua 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... - On the gradual evolution of complexity and the sudden emergence of complex featuresCharles 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... - 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... - 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... - 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... - 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... - 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... - 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 - Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theoryJeff 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... - 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... - 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... - Perspective: Evolution and detection of genetic robustnessJ Arjan G M de Visser
Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
Evolution 57:1959-72. 2003.... - Using Avida to test the effects of natural selection on phylogenetic reconstruction methodsGeorge 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...