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As mentioned earlier, the range of an axis depends on multiple factors like dataSeries attached to it, range of the dataPoints of a given dataSeries, etc. Based on the JSFiddle shared by you the minimum y value in the first series is 0.04, in such cases dataPoints goes out of viewport making it difficult to visualize because of which the auto-calculated range has a negative minimum. This feature is by design.
However, you can customize the range of axisY by setting values of minimum and maximum properties. Please take a look at the respective documentation pages for more information and live example.