Circadian clocks drive daily patterns of physiology and behavior. In many animals, the clocks driving daily behavioral rhythms are located in pacemaker neurons in the brain. However, it remains poorly understood how molecular clocks drive rhythms in neuronal activity and how neuronal interactions drive complex behavioral output. We used genetic, molecular, and neurophysiological techniques to address these questions. Our data indicate more complex relationships between pacemaker neuronal activity patterns and behavioral output than previously recognized.