Virtual retroviruses in grid walkers: Effects on genome organization

Retroviruses are believed to been important in the evolution of genome organization in biological organisms. This study investigates the impact of virtual retroviruses on the genome organization of an artificial organism using the simulation environment developed in. The artificial organisms, grid walkers, were designed to be a model of biological organisms. They have a complex fitness landscape with many local optima connected by neutral networks, a variable-sized self-organized epistatic genome with analogs to biological exons and introns, and a visible phenotype. This study examines the impact of retroviral insertions on genome organization with two different types of crossover. The choice of crossover type is shown to have a large impact. With one type of crossover, retroviral insertions cause the genome to grow rapidly and become fragmented; with the other, they cause it to grow slowly and to have long exons that cover more of the genome. We also tested the impact of changing the source of the retroviruses from a retroviral bank to within the organism´s genome. This change also had a different impact on genome organization depending on which type of crossover was used. With one type of crossover, it caused greater fragmentation; with the other it had little effect.