Depending on what you think of this line it is a mystery or not. This is actually a mystery caused perhaps by the internet because prior to the advent of the wide spread use of the net I don't believe this was an issue. In any case Anna Wharton fails us with John's line since she does not show it. However, several extensive works the Ellenwood-Wharton Genealogy in particular backed up by Quaker Meeting Minutes prove certainly to my satisfaction that John Wharton married Mary Cutler September 12, 1770 at Bucks, PA Falls MH and that this John Wharton is the same as the son of Joseph and Hannah. There are some who feel that the John Wharton who married Phoebe Bradshaw is the John Wharton of the Philadelphia clan, but from all the research I have been able to conduct I have not been able to find any relationship between that John Wharton with Mary Cutler's John Wharton.
In any case there is extensive research available on this family and rather than repeat it here please go to WHARTON Surname Resource Center for the details.