The persistence of circadian rhythmicity during long bouts of hibernation in mammals has been a somewhat controversial topic in the literature. While some studies suggest that circadian clock is active during hibernation, other studies dispute this. Apparently, the truth is somewhere in-between - it differs between species:
Not all hibernating animals retain apparent circadian rhythmicity during the hibernation season. Whereas some species, such as bats and golden-mantled ground squirrels, maintain circadian rhythmicity in Tb throughout the hibernation season when held in constant conditions, other species, such as European hamsters, Syrian hamsters, and hedgehogs, lose circadian rhythmicity in Tb.
The outputs of the clock measured in these studies range from body temperature abd brain temperature, to timing of waking, to metabolic and behavioral parameters. But, to my knowledge, nobody has yet looked if the circadian pattern of expression of "core clock gene" persists during hibernation.
Thus, it was really interesting to see a study on the state of hibernation in a completely different kind of organism - a tree. About a year ago, a group from Spain, did exactly what was needed - they measured the levels of expression of circadian clock genes in the chestnut tree.
They measured the expression of clock genes both during naturally occuring winter dormancy and in the laboratory experiments involving chilling of seedlings combining with exposure to different photoperiods. In both cases, the core molecular mechanism of the circadian clock stopped entirely if the temperature and photoperiod both indicated 'winter', and was revived by warming-up the seedlings or the onset of spring.
Circadian clocks exhibit temperature independence, i.e., the period of the rhythm is not affected by temperature, within relatively broad limits. Apparently, the winter temperatures are outside the lower limit in the chestnut tree. Furthermore, it appears that the chestnut actively stops the clock with the onset of winter.
How can we interpret these data?
Overwintering is the stage in which all energetically expensive processes are minimized or shut down. However, workings of the clock itself are not very energetically expensive, so this is an unlikely reason for the elimination of rhythmicity during winter.
Second interpretation would be that, as the tree shuts down all its processes, there is nothing for the clock to regulate any more. There is also no feedback from the rest of metabolism into the clock. Thus, circadian rhythmicity fades as a by-product of overall dormancy of the plant.
Third, the clock itself may be a part of the mechanism that keeps everything else down. In other words, a clock stopped at (for instance - this is a random choice of phase) midnight will keep giving the midnight signal to the rest of the plant for months on end, keeping all the other processes at their normal midnight level (which may be very low). Thus, the clock may be central to the overal mechanism of hibernation in trees - i.e., the autumnal stopping of the clock is an evolved adaptation.