DNA evidence has disconnected one branch of my Stiles ancestry. My 7th-great-grandfather Ephraim Stiles Jr., paternal grandfather of Sarah Stiles, is documented as the son of Ephraim Stiles Sr. (c.1669 – 1750-12-31), son of John Stiles (c.1633 – 1683-12-14), but DNA evidence has shown John could not be the paternal grandfather of Ephraim Jr.
The Y chromosome is passed from father to son, and thus can do long-range comparisons of bearers of a surname.
In the Stiles Surname Project, what they call Cluster L (or Group L) has three test kits (as of 2022-03-30) confirming the STR signature of Ephraim Jr., who belongs to haplogroup R1b-Y76590. It is clearly distinct from what they call Cluster D, which consists of 12 people whose ancestries go through John or through an ancestor of his. This shows Ephraim Jr. is not a male-line descendant of John.
The usual supposition in cases of DNA mismatch is that the father of someone is a different man than that documented, for any number of possible reasons, a so-called non-paternity event (NPE). The evidence here narrows it down to one of two generations.
There is a testee named Hitchcock, kit #360003, who is a near-exact match for the Ephraim Stiles Jr. branch.
There were indeed multiple Hitchcock families in the vicinity of Springfield, Massachusetts at the time. There is poor documentation of how, and if, these families are related. More DNA evidence may help with this, and with more work and information we may be able to make guesses as to which Hitchcock is the father of which Stiles.
It also may be that there is a hint in town records of, for example, an illicit relationship, which would connect to this evidence.