title: Evolutionary Design of Gene Networks: Forced Evolution by Genomic Parasites.
abstract: The co-evolution of species with their genomic parasites (transposons) is thought to be one of the primary ways of rewiring gene regulatory networks (GRNs). We develop a framework for conducting evolutionary computations (EC) using the transposon mechanism. We find that the selective pressure of transposons can speed evolutionary searches for solutions and lead to outgrowth of GRNs (through co-option of new genes to acquire insensitivity to the attacking transposons). We test the approach by finding GRNs which can solve a fundamental problem in developmental biology: how GRNs in early embryo development can robustly read maternal signaling gradients, despite continued attacks on the genome by transposons. We observed co-evolutionary oscillations in the abundance of particular GRNs and their transposons, reminiscent of predator-prey or host-parasite dynamics.
authors.affiliation: Computer Science and CEWIT, SUNY Stony Brook, 1500 Stony Brook Road, Stony Brook, NY 11794, USA The Sechenov Institute of Evolutionary Physiology & Biochemistry, Thorez Pr. 44, St.-Petersburg, 2194223, Russia Alexander.Spirov@sunysb.edu.
authors.forename: A V
authors.initials: AV
authors.lastname: Spirov
authors.affiliation: The Sechenov Institute of Evolutionary Physiology & Biochemistry, Thorez Pr. 44, St.-Petersburg, 2194223, Russia Zagriychuk.Elisaveta@yandex.ru.
authors.forename: E A
authors.initials: EA
authors.lastname: Zagriychuk
authors.affiliation: Mathematics Department, British Columbia Institute of Technology, 3700 Willingdon Avenue, Burnaby, B.C., Canada, V5G 3H2 David_Holloway@bcit.ca.
authors.forename: D M
authors.initials: DM
authors.lastname: Holloway
keywords: Evolution in silico; artificial transposons; co-evolution; gene co-option; gene networks; genetic algorithms