The answer is that the guitar favors the key of E minor. The natural state of E minor is E phrygian. The fret markers on a guitar mark the roots of the seven modes of E phrygian. E F G A B C D. However, this would create some clutter at the half steps. As a general rule you don’t want to lay two fret markers in a row. This is because a fret marker locates three frets;the marked fret, the previous fret, and the next fret. So instead of marking C, we mark C# which locates C, C#, and D. A similar problem occurs at F midway down the guitar neck. In this case the solution is to mark E which locates D# and F and omit a fret marker at F.