Table 1 Definitions

Homeostasis

Homeostasis regulation is the ability to maintain constant levels of some internal molecules while external conditions change continuously, through physiological regulation. In our simulations we require individuals to keep internal concentrations of a resource and energy molecule at a fixed target level, while the concentration of the external resource fluctuates. Although regulatory structure required to maintain homeostasis is free to evolve, it crucially depends on the ability of transcription factors to act as sensors of ligand concentration, allowing the differential regulation of downstream genes.

Phenotypic plasticity

Phenotypic plasticity is the ability of an organism to change its phenotype through regulation. Although typically used to indicate that an organisms can have different morphologies or other external phenotypic traits under varying external conditions, here we mean that an expression pattern of genes can change in a functional way, depending on the external conditions, to allow an individual to retain fitness in different environments.

Evolvability

Different definitions of evolvability have been given in the literature. At a minimum, evolvability is the ability of a genetic system to generate adaptive mutational variation. This ability is influenced by intrinsic properties, such as the mutation rate, the organization of the genotype to phenotype mapping and the different types of mutation that occur. Here we use the term evolvability to indicate the ability to rapidly adapt to environmental change through a small number of mutations. We study whether and how lineages become more evolvable toward recurring shifts in environmental conditions (adapt faster and need less mutations to regain fitness), by evolution of the genotype to phenotype mapping. We refer to this as evolution of evolvability.