I think I found the one you're looking at. Looks like it had been well smoked, and the location of the dark spot is about in the place where the tenon would end in the bottom of the mortise. That, combined with the oval shaped shank means that the dark spot you are seeing is from the years of tars and oils seeping through the thinnest part of the shank in that spot. I'd be willing to bet money that there's a similar spot on the underside as well.
Nothing to worry about though, just make sure you clean her out well! Looks like a heck of a deal too!