The Effects of Gene Recruitment on the Evolvability and Robustness of Pattern-Forming Gene Networks

Gene recruitment or co-option is defined as the placement of a new gene under a foreign regulatory system. Such re-arrangement of pre-existing regulatory networks can lead to an increase in genomic complexity. This reorganization is recognized as a major driving force in evolution. We simulated the evolution of gene networks by means of the Genetic Algorithms (GA) technique. We used standard GA methods of point mutation and multi-point crossover, as well as our own operators for introducing or withdrawing new genes on the network. The starting point for our computer evolutionary experiments was a 4-gene dynamic model representing the real genetic network controlling segmentation in the fruit fly Drosophila. Model output was fit to experimentally observed gene expression patterns in the early fly embryo. We compared this to output for networks with more and less genes, and with variation in maternal regulatory input. We found that the mutation operator, together with the gene introduction procedure, was sufficient for recruiting new genes into pre-existing networks. Reinforcement of the evolutionary search by crossover operators facilitates this recruitment, but is not necessary. Gene recruitment causes outgrowth of an evolving network, resulting in redundancy, in the sense that the number of genes goes up, as well as the regulatory interactions on the original genes. The recruited genes can have uniform or patterned expressions, many of which recapitulate gene patterns seen in flies, including genes which are not explicitly put in our model. Recruitment of new genes can affect the evolvability of networks (in general, their ability to produce the variation to facilitate adaptive evolution). We see A.V. Spirov ( ) Applied Mathematics and Statistics, and Center for Developmental Genetics, State University of New York, CMM Bldg, Rm481, South Loop, SUNY at Stony Brook, Stony Brook, NY 11794-5140, USA e-mail: Alexander.Spirov@sunysb.edu D.M. Holloway Mathematics Department, British Columbia Institute of Technology, Burnaby, B.C., Canada, and with the Biology Department, University of Victoria, B.C., Canada e-mail: David Holloway@bcit.ca S.-I. Ao et al. (eds.), Advances in Computational Algorithms and Data Analysis, 29 Lecture Notes in Electrical Engineering 14, c © Springer Science+Business Media B.V. 2009 30 A.V. Spirov and D.M. Holloway this in particular with a 2-gene subnetwork. To study robustness, we have subjected the networks to experimental levels of variability in maternal regulatory patterns. The majority of networks are not robust to these perturbations. However, a significant subset of the networks do display very high robustness. Within these networks, we find a variety of outcomes, with independent control of different gene expression boundaries. Increase in the number and connectivity of genes (redundancy) does not appear to correlate with robustness. Indeed, removal of recruited genes tends to give a worse fit to data than the original network; new genes are not freely disposable once they acquire functions in the network.