Sympathetic nerve system acts on your entire body, increasing metabolic rate to compensate for increased demand. Respiration rate, therefore, increases in order to provide more oxygen to the alveoli in your lungs, which is transferred via red blood cells to the muscles doing the work of jogging. When you stop and cool down, your parasympathetic nerve system kicks in, and returns your body slowly to it's natural state, or homeostasis. Respiration rate is among the first systems returned to normal by the parasympathetic nerve system after a jog.
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