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In the following image, the dotted vertical lines depict the spectrum of a shepard tone that is one semitone lower than that represented by the solid. Again, the upward-pointing arrow indicates the "fundamental."

You will note that unlike spectra of natural sounds (like musical instruments and human voices, etc.), the spectra in Shepard tones involve partials that are both above and below the so-called fundamental.  In this situation, the notion of "fundamental" becomes questionable.  This situation is amplified by the fact that, while with natural sounds each succesive partial (even if it has little energy), constitutes a doubling, in frequency, of the fundamental.  By contrast, each partial within a Shepard tone is exactly an octave above the next lower one.