DNA sequence evolution has been studied for decades, with relatively clear understanding of its major patterns and mechanisms. By contrast, little is known regarding the general principles of transcriptome evolution, despite the fact that genes function through their RNA or protein products. For example, it is unclear whether gene expression differences between species are primarily adaptive or neutral. Here we propose to generate and analyze both within and between species transcriptome data in order to understand the general principles and potential mechanisms governing transcriptome evolution. A combination of theory development, modeling and computational analysis, and experimentation will be used.