  The genotype-phenotype map is an essential object in our understanding of
organismal complexity and adaptive properties, determining at once genomic
plasticity and those constraints that may limit the ability of genomes to
attain evolutionary innovations. An exhaustive experimental characterization of
the relationship between genotypes and phenotypes is at present out of reach.
Therefore, several models mimicking that map have been proposed and
investigated, leading to the identification of a number of general features:
genotypes differ in their robustness to mutations, phenotypes are represented
by a broadly varying number of genotypes, and simple point mutations seem to
suffice to navigate the space of genotypes while maintaining a phenotype.
However, most current models address only one level of the map (sequences and
folded structures in RNA or proteins; networks of genes and their dynamical
attractors; sets of chemical reactions and their ability to undergo molecular
catalysis), such that many relevant questions cannot be addressed. Here we
introduce toyLIFE, a multi-level model for the genotype-phenotype map based on
simple genomes and interaction rules from which a complex behavior at upper
levels emerges, remarkably plastic gene regulatory networks and metabolism.
toyLIFE is a tool that permits the investigation of how different levels are
coupled, in particular how and where do mutations affect phenotype or how the
presence of certain metabolites determines the dynamics of toyLIFE gene
regulatory networks. The possibilities of this model are not exhausted by the
results presented in this contribution. It can be easily generalized to
incorporate evolution through mutations that change genome length or through
recombination, to consider gene duplication or deletion, and therefore to
explore further properties of extended genotype-phenotype maps.
