When you exercise for a long time, your muscles start to burn and feel sore, which forces you to slow down. You call this fatigue and tiredness, but a recent study from Japan shows that muscle fatigue is caused by damage to the muscle itself ( Medicine & Science in Sports & Exercise, July 2005). This also explains why exercising long and hard enough to feel the burn for an extended period leaves your muscles sore for one or more days afterwards. Athletes call this Delayed-Onset Muscle Soreness (DOMS) and they learn that they have to have this next-day soreness to improve for competition.
Running is much more fatiguing than cycling. When you run, your heel hits the ground and stops your leg from moving. This sudden stopping with each foot strike stretches your contracting muscles and tears them to cause a lot of muscle damage. It’s called eccentric contractions of muscle and occurs with far less force in cycling. You pedal with a smooth rotary motion and do not stop suddenly. The eccentric contractions during running cause a high degree of muscle injuries, limit how far person can run fast, and require far more rest days or easy days than cyclists use in their training programs.
Since muscle fatigue during endurance competitions is caused by muscle damage, anything that strengthens muscles will improve performance in endurance events. The only way to make a muscle stronger is to damage the muscle with hard exercise, feel sore on the next day, exercise more easily on as many days as it takes for the soreness to go away, and then exercise vigorously again. Athletes in competitive sports must exercise at a reduced intensity on the days that their muscles feel sore. This makes muscles more fibrous and resistant to injury so that muscles can withstand greater forces when athletes exercise on their hard days.