Evolution is a process that largely occurs within populations. Contrary to common belief, the evolution of complex genome architecture is not driven by natural selection alone. In small populations, genetic drift overwhelms weak selective forces, yielding populations that evolve “in principle” neutrally. Non-adaptive stochastic forces such as mutation, recombination, and genetic drift, also influence genetic material composition under neutrality. On the other hand, selection optimizes expression levels by operating on sequence polymorphisms at gene regulatory regions. Slightly deleterious mutations on the regulatory regions of genes, that affect the binding of transcription factors may increase in frequency by chance alone. Other non-adaptive processes such as gene duplications can change the distribution of the links on each node (gene) of the network.Here, I propose to study the evolution of gene regulatory networks in the population level, by means of genetic drift and natural selection. I will focus on the effects of mutation, recombination, genetic drift and various forms of natural selection (e.g. stabilizing and positive selection) on the polymorphism patterns of the promoter regions. The goal is to identify polymorphism patterns that are created exclusively by natural selection and not by non-adaptive processes.