Networks of interacting genes are responsible for generating life's complexity and for mediating how organisms respond to their environment. Thus, a basic understanding of genetic variation in gene networks in natural populations is important for elucidating how changes at the genetic level map to higher levels of biological organization. Here, using the well-characterized phototransduction network in Drosophila, we analyze variation in gene expression within and between two closely related species, Drosophila melanogaster and Drosophila simulans, under different environmental conditions. Gene expression levels in the pathway are largely conserved between these two sibling species. For most genes in the network, differences in level of gene expression between species are correlated with degree of polymorphism within species. However, one gene encoding the light-induced ion channel TRPL (transient receptor potential-like) shows an excess of expression divergence relative to polymorphism, suggesting a possible role for natural selection in shaping this expression difference between species. Finally, this difference in TRPL expression likely has significant functional consequences, because it is known that a high level of rhabdomeral TRPL leads to increased sensitivity to dim background light and an increased response to a wider range of light intensities. These results provide a preliminary quantification of variation and divergence of gene expression between species in a known gene network and provide a foundation for a system-level understanding of functional and evolutionary change.natural selection ͉ gene expression ͉ network G enes act together in networks to generate important organismal phenotypes. Understanding the general properties of gene networks and how they adapt to environmental changes is of fundamental importance to evolutionary biology. Elucidating the structure of gene networks represents a major goal of systems biology and ecological genomics in the postgenomic era. Recent approaches have primarily exploited genomic and computational methods to focus on distantly related organisms (1). However, very little is known about the basic microevolutionary properties of known genetic networks, information that is crucial for understanding network function, regulation, and evolution, because key adaptations first emerge at the population level. For example, very little is known about natural variation within gene expression networks in different populations, different species, and under different environmental conditions. How much expression variation is present in a gene network within a population? Do genes that show low variation within one species also show low variation in closely related species? To attempt to answer these fundamental questions, we analyzed variation in gene expression in the phototransduction network under two different environmental conditions within and between species of Drosophila melanogaster and its sibling species Drosophila simulans, which diverged Ϸ3 Mya (2).The Drosophi...