Circadian rhythms are fundamental biological processes that enhance survival and reproductive fitness by coordinating physiology and behavior with predictable environmental cycles. However, in some species, circadian rhythms are weakened, irregular, or even undetectable, likely reflecting evolutionary responses to extreme environments or specialized ecological niches. Nevertheless, the genetic basis of these atypical phenotypes remains incompletely understood. Here, we investigated the molecular evolution of 20 PER2-associated genes across 71 representative mammalian species. We identified four genes under positive selection in mammalian lineages exhibiting atypical circadian phenotypes, three of which (CDK5, CSNK1E, and GSK3B) are involved in the post-translational regulation of PER2 phosphorylation, suggesting that PER2 phosphorylation regulators may contribute to lineage-specific circadian variation. Notably, CSNK1E, a key kinase regulating PER2 phosphorylation, showed signatures of positive selection and accelerated evolution in cetaceans, which exhibit unihemispheric slow-wave sleep (USWS). In vitro assays showed that dolphin CSNK1E increased phosphorylation at the stabilizing FASP site S662 of PER2 and extended the half-life of the PER2 protein, a molecular feature closely linked to circadian oscillator amplitude and sleep regulation. Increased PER2 phosphorylation may contribute to altered sleep and locomotor activity associated with sustained wakefulness during USWS, as supported by our cellular and whole-animal assays. Consistently, zebrafish overexpressing dolphin CSNK1E exhibited elevated locomotor activity and reduced sleep duration. Overall, our findings provide evidence that evolutionary changes in PER2 phosphorylation regulation are associated with atypical circadian phenotypes and offer novel insights into the genetic mechanisms underlying circadian plasticity in mammals.
