Data from: Gene network topology drives the mutational landscape of gene expression

Regulatory mutations, coding sequence variations, and gene deletions and
duplications are generally expected to have qualitatively different
effects on fitness during adaptation. We aim to ground this expectation
within a theoretical framework using evolutionary simulations of gene
regulatory networks (GRNs) controlling the expression of fitness-related
genes. We examined the distribution of fitness effects as a function of
the type of mutation and the topology of the gene network. Contrary to our
expectation, the GRN topology had more influence on the effect of
mutations than the type of mutation itself. In particular, the topology
conditioned (i) the speed of adaptation, (ii) the distribution of fitness
effects, and (iii) the degree of pleiotropy which acts as explanatory
factor for all mutation types. All mutations had the potential to
participate in adaptation, although their propensity to generate
beneficial variants differed according to the network topology. In
scale-free networks, arguably the most common topology for biological
networks, coding mutations were more pleiotropic and overrepresented in
both beneficial and deleterious mutations, while regulatory mutations were
more often neutral. However, this observation was not general, as this
pattern was reversed in the other network topologies. These results
highlight the critical role of gene interactions in defining
mutations' contributions to adaptation.