Most organisms that live on or near the surface of the Earth or its oceans have evolved a circadian clock - a daily timer of all biochemical, physiological and behavioral functions.
Daily cycle of light and darkness in the environment is a selective factor - having an internal clock is an adaptation that allows organisms to predict and prepare for instead of passively react to cyclical changes in the environment. The regularity of the light-dark cycle is usually a good predictor for other (perhaps not as precise) cycles of temperature, availability of food, or activity of predators.
It gets trickier for organisms that live in places where the light-dark cycle may be missing for big chunks of the year (the polar regions), or where light-dark cycle is not a good predictor of other relevant events in the environment (e.g,. cannot predict rain in very arid regions), or where light cannot penetrate at all (deep ocean, caves, underground burrows). In such organisms the clock may get uncoupled from some of its functions, e.g., it may still time biochemical but not behavioral events. Or the clock may be temporarily or permanently turned off.
Even animals that constantly live in caves still tend to have functioning circadian clocks even if they are not used by these animals to drive rhythms in behavior. In animals that regularly travel into and out of the caves, like bats, the clock is robust.
A number of organisms have been studied in which the clock may temporarily be turned off. In the chestnut tree , circadian clock stops in winter. In reindeer in the high Northern latitudes, behavioral rhythms (and underlying clock) work only during the short springs and autumns, not during the long polar winters and summers. In social insects, castes that spend their time inside the hive and need to work around the clock also do not have a functioning circadian clock.
The organisms that live in extreme environments tend to be difficult to study. It may be a harsh environment for the human researchers to spend long periods of time in. The organisms may not be easy to bring into the lab to study under controlled conditions. Most of such organisms are far from being standard "laboratory models" which means that little is known about their genetics, biochemistry, physiology and behavior.
Thus, one is limited in choices as to which rhythms to study and what conclusions one can take from such studies. A limited number of overt rhythms can be easily monitored in a standardized manner even in the laboratory. A record of overall physical activity and movement is usually made. Additional measured rhythms may be daily fluctuations in hormones, e.g., melatonin. And tissue samples may be taken over a 24-hour period for analysis of patterns of expression of core clock genes.
This approach may miss stuff. For example, even if there is no cycling of clock genes or overt behavioral rhythms, this does not mean that the clock may not be working anyway - cytoplasmatic cellular clocks, or ensembles of neural cells producing weak rhythms, or hormonal feedback loops between endocrine glands could still be producing daily cycles in some aspects of metabolism not identified by the researchers. The adaptive function of the clock is so strong, if nothing else for coordinating internal events, that is is difficult to persuasively and definitively demonstrate that absolutely nothing in the body cycles around a 24-hours cycle.
An important function of the clock is also in measuring changes in daylength - days get longer in spring and shorter during fall. Even environments that have no daily cycles for a while, or no utility in using light-dark cycles, may have strong seasonality, and seasons are another important aspect of the environment related to time. Most organisms use their circadian clocks to measure the changes in daylength through a mechanism called photoperiodism. So even organisms that have no use for daily clocks, may still retain them for their higher-level function of fine-tuning the annual calendar of events.
Domestication also has an effect on circadian clock as one can argue that the lab and the farm are "extreme environments" in some sense. It is well known that many domesticated strains of laboratory mice, rats and nematodes have lost seasonality. Most of our domesticated animals have vastly prolonged breeding seasons - sometimes spanning the entire year, or adding a Fall season to the existing Spring one - compared to their wild relatives. Domestication may be a strong selective force for abandoning seasonality, which reduces the need for a functional circadian clock as well, especially if human care - feeding, defense, etc. - replace the need for the organism to fend for itself in sync with the cycles of nature.
Now a new player is entering this line of research - barley (Hordeum vulgare). Last week, Faure et al, published an open access paper in PNAS showing that strains of barley from Northern Europe have mutations in one of their photoperiodic genes - EARLY MATURITY8 (EAM8) - and that this gene greatly reduces the amplitude of expression of the core circadian clock genes.
As a result, northern varieties of barley can start flowering early and fast in the season, completely ignoring daylength, just following the normal developmental program. At the same time the disrupted clock allows for much longer daily activity of photosynthesis during long summer days, as it does not shut it down before darkness arrives in the evening.
One can imagine how such mutants were prized in the earlier history of the domestication. As humans moved more and more north, only the barley that could be harvested early and produced large yields was valuable. Late harvest may have been too late: humans may have already moved on, driven by hunger, and left the field to be harvested by birds. Or the harvest, being so small and late, would have been used only for consumption (winter is coming - time to brew some beer!) and not for seed for the next year.
Plant circadian clocks are very complex at the molecular level, involving several different feedback loops in expression, some operating in the morning, others in the evening, etc. Importantly, some of the genes involved in photoperiodism and flowering are intricately connected to the clock and may be a part of some of the clock feedback loops. Most of the past research focused on the way clock genes regulate flowering genes. This is an unusual paper in that it discovers the opposite direction - how a gene involved in flowering feeds back on the clock genes and regulates the way the clock works.
What is exciting about this work is that barley is not a difficult organism to do research on. One does not need heroic efforts or expensive Arctic or speleological gear to study it - it is a domesticated plant, easily grown in fields, glasshouses and labs. Furthermore, much of its biology is already well known, including the similarity between its genes and those of Arabidopsis thaliana, the standard model for plant research.
As a number of strains of barley exist, some southern some northern, there is plenty of material to do comparative studies to figure out exactly which genes and processes were involved in the process of domestication - what was selected for as the humans took their crops with them on their northward migrations. This makes barley potentially a useful standard laboratory model for the general studies of evolution under domestication.
Faure, S., Turner, A.S., Gruszka, D., Christodoulou, V., Davis, S.J., von Korff, M. & Laurie, D.A. Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1120496109
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Image: Wikimedia Commons, public domain.