Simulation of the impact of retroviruses on genome organization of an artificial organism

  • Authors:

  • Daniel Ashlock;Wendy Ashlock

  • Affiliations:

  • Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada;Department of Computer Science and Engineering, York University in Toronto, Ontario, Canada

  • Venue:
  • CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
  • Year:
  • 2009

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Abstract

Retroviruses are RNA viruses whose RNA can be transformed into DNA and inserted in the genome of a host cell. This study prototypes a simulation environment in which a simple artificial organism with a variable-size genome evolves with and without retroviruses. The simulated organisms are called grid walkers. They are evolved to efficiently occupy space on a two-dimensional grid. Grid walkers develop a self-organized genome structure with analogs to biological introns and exons. The introduction of retroviruses is found to cause several significant changes: the rate of genome growth is increased, the number of exons is increased, mean exon size is decreased, and fitness is retarded. The grid walkers are found to evolve heritable fitness in preference to high fitness ("survival of the flattest"), a process that is enhanced when retroviruses are present.