Desynchronizing the sleep­­–wake cycle from circadian timing to assess their separate contributions to physiology and behaviour and to estimate intrinsic circadian period

Circadian clocks drive cyclic variations in many aspects of physiology, but some daily variations are evoked by periodic changes in the environment or sleep–wake state and associated behaviors, such as changes in posture, light levels, fasting or eating, rest or activity and social interactions; thus, it is often important to quantify the relative contributions of these factors. Yet, circadian rhythms and these evoked effects cannot be separated under typical 24-h day conditions, because circadian phase and the length of time awake or asleep co-vary. Nathaniel Kleitman’s forced desynchrony (FD) protocol was designed to assess endogenous circadian rhythmicity and to separate circadian from evoked components of daily rhythms in multiple parameters. Under FD protocol conditions, light intensity is kept low to minimize its impact on the circadian pacemaker, and participants have sleep–wake state and associated behaviors scheduled to an imposed non-24-h cycle. The period of this imposed cycle, Τ , is chosen so that the circadian pacemaker cannot entrain to it and therefore continues to oscillate at its intrinsic period ( τ , ~24.15 h), ensuring circadian components are separated from evoked components of daily rhythms. Here we provide detailed instructions and troubleshooting techniques on how to design, implement and analyze the data from an FD protocol. We provide two procedures: one with general guidance for designing an FD study and another with more precise instructions for replicating one of our previous FD studies. We discuss estimating circadian parameters and quantifying the separate contributions of circadian rhythmicity and the sleep–wake cycle, including statistical analysis procedures and an R package for conducting the non-orthogonal spectral analysis method that enables an accurate estimation of period, amplitude and phase. This protocol describes how to design, implement and analyze the data from a forced desynchrony protocol to assess endogenous circadian rhythmicity and to separate circadian from evoked components of daily rhythms in physiology and behavior.