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The genotype-phenotype map is an essential object in our understanding oforganismal complexity and adaptive properties, determining at once genomicplasticity and those constraints that may limit the ability of genomes toattain evolutionary innovations. An exhaustive experimental characterization ofthe relationship between genotypes and phenotypes is at present out of reach.Therefore, several models mimicking that map have been proposed andinvestigated, leading to the identification of a number of general features:genotypes differ in their robustness to mutations, phenotypes are representedby a broadly varying number of genotypes, and simple point mutations seem tosuffice to navigate the space of genotypes while maintaining a phenotype.However, most current models address only one level of the map (sequences andfolded structures in RNA or proteins; networks of genes and their dynamicalattractors; sets of chemical reactions and their ability to undergo molecularcatalysis), such that many relevant questions cannot be addressed. Here weintroduce toyLIFE, a multi-level model for the genotype-phenotype map based onsimple genomes and interaction rules from which a complex behavior at upperlevels emerges, remarkably plastic gene regulatory networks and metabolism.toyLIFE is a tool that permits the investigation of how different levels arecoupled, in particular how and where do mutations affect phenotype or how thepresence of certain metabolites determines the dynamics of toyLIFE generegulatory networks. The possibilities of this model are not exhausted by theresults presented in this contribution. It can be easily generalized toincorporate evolution through mutations that change genome length or throughrecombination, to consider gene duplication or deletion, and therefore toexplore further properties of extended genotype-phenotype maps.

toyLIFE: a computational framework to study the multi-level organization of the genotype-phenotype map