We are broadly interested in the evolution of transcriptional regulation, using a combination of experimental and computational approaches. Our research spans scales from single nucleotides to entire genomes. At the finer end of this spectrum, we focus on the functional consequences and fitness components of specific genetic variants within regulatory sequences of several genes associated with traits of interest. At the other end of the spectrum, we develop computational and statistical methods to detect natural selection on regulatory elements and empirical approaches to identify functional variation in transcriptional regulation throughout the genome. At intermediate scales, we investigate natural functional variation within gene networks, including heritability, correlations across the network, natural selection, and associations with organismal traits. We address these questions in sea urchins, primates, and butterflies.