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A British Heart Foundation team found exercise in mice triggers molecular changes in the part of the heart that generates its natural beating rhythm.
This may explain why elite athletes have low resting heart rates and a higher risk heart rhythm disturbances, they told Nature Communications.
However, the benefits of exercising still outweigh any risks, experts say.
Endurance athletes are generally very fit.
Yet, paradoxically, they are more likely to have heart rhythm disturbances, known as arrhythmias, especially as they get older - although the risk is still small.
Experts have suspected that this is because long-term training for extreme endurance events such as marathons and triathlons slows the heartbeat down.
While normal adults have resting heart rates between 60-100 beats per minute, hearts of endurance athletes can beat only 30 times per minute or even less at night time when there can be long pauses between heart beats.
Cyclists Sir Chris Hoy and Miguel Indurain reportedly had resting heart rates of 30 and 28 beats per minute.
The heart rate is set by the heart's pacemaker, which is controlled by the nervous system.
And so it was assumed that the low heart rate of athletes was a result of the autonomic nervous system going into overdrive.
But Prof Mark Boyett and colleagues, from the University of Manchester, say their new research suggests this is not the case.
Instead, the heart's in-built pacemaker changes in response to training.
By studying mice, they found that endurance exercise led to a decrease in an important pacemaker protein, known as HCN4, and that this was responsible for the low heart rate.
Prof Boyett said: "This is important because although normally a low resting heart rate of an athlete does not cause problems, elderly athletes with a lifelong training history are more likely to need an artificial electronic pacemaker fitted."
But he added: "Although endurance exercise training can have harmful effects on the heart, it is more than outweighed by the beneficial effects."
Prof Jeremy Pearson, Associate Medical Director at the British Heart Foundation, said: "This study shows the heart's electrical wiring changes in mice that exercise for long periods, and these changes in heart rhythm are sustained afterwards.
"If the findings are reproduced in humans they could have implications for heart health in older athletes. But much more research is needed before we could draw that conclusion."
All the running,endurance freaks I've ever known always look bloody sick,pale,skinny,and joint issues later in life.
Whatever floats your boat I suppose.
They can have it.