Exposure to regular environmental oscillations such as day/night have allowed organisms to evolve biological mechanisms to adaptively anticipate and prepare for rhythmic environmental change. A network of gene-protein interactions between clock genes and their proteins comprise the molecular clock mechanism at the heart of regulating biological rhythms. Though this is an endogenous and self-regulating system, elements of this network can be entrained by exogenous biotic and abiotic factors. This synchronisation process between environmental cycles and endogenous rhythms is facilitated by cues like light and temperature, which influence clock gene expression patterns.Marine bivalves often inhabit intertidal habitats under the influence of numerous oscillating environmental conditions, though little is known about how they regulate their biological timekeeping. In this thesis, we investigate the molecular regulation of biological rhythms in the ecologically and commercially important blue mussel, M. edulis, over different timeframes. For the first time in this species, we isolate and characterise a number of clock genes (Clk, Cry1, ROR/HR3, Per and Rev-erb) and clock-associated genes (ARNT, Timeout-like and aaNAT). Rhythmic clock gene expression is demonstrated in the absence of light cues, indicative of endogenous clock control. Differential expression of Cry1 expression between males and females under the same conditions indicates sex-specific regulation and/or function. In addition, diurnal temperature cycles modulated the otherwise rhythmic expression of Rev-erb to constant levels demonstrating an interaction of temperature with clock function. Instances of seasonal clock mRNA expression differences were found, in addition to a number of other putative seasonal genes, indicating a possible mechanism by which seasonal cues can inform rhythmic biological processes.Understanding the influence of environmental cues on the molecular clock is essential in predicting the outcomes of future environmental change on fundamental rhythmic processes, in particular the impacts of decoupled environmental cues on the already highly dynamic and stressful intertidal zone
