Every so often, DNA tests throw up unexpected surprises - results that don't match the historical or "traditional" reports.
The classic instance of this is the Bourbon Y-DNA findings. Early and possibly-inaccurate tests yielded a perceived haplogroup of G, which pleased those who thought the French royal line descended unbroken from the Merovingians. But tests on two descendants of Louis XIV and one descendant of his brother Philippe showed that the "true" Bourbon haplotype was a particular subset of R-M269. (Note: This does *not* guarantee that this is also the Capet/Valois haplotype, as the first of the Bourbon kings, Henri IV, was only 9th cousin to the last Valois.) The Merovingianists were, of course, disappointed.
Reasons for the discrepancy are not clear, but one strong possibility is a combination of broken chain of possession and "pious fraud". In other words, the materials originally tested weren't what they were purported to be.
Another and more recent headscratcher is Richard III vs. the Somersets. In this case the test materials were thoroughly authenticated - *but* although Richard's Y-DNA haplotype tuned out to be G, the five Somerset descendants, traced back to John of Gaunt and his mistress/wife Katherine Swynford, didn't match him. In fact, one of the five didn't match the other four either! (There had been rumors of hanky-panky on that particular line a couple of generations back...and apparently the rumors were true.)
So the unresolved questions are, who wasn't whose baby daddy, and when, and on which side? (The discontinuity *may* go back to John of Gaunt himself, who was rumored *not* to have been the son of Edward III, and there are a couple of other weak spots in the Beaufort/Somerset line - on the other side, there's a weak spot at Richard's grandfather, Richard of Conisburgh, who may *not* have been the son of Edmund of Langley and therefore not a grandson of Edward III. Sadly, there are no other known male-line Plantagenet descendants to test, so the only possibility of clearing this up is more ancestral Y-DNA (if any can be found that is still "readable").
Oddball results like an E or J (or other rare) haplotype may mean something...or nothing at all. There have been many, many intrusions into Europe from various directions, at least as far back as the Neolithic and probably farther. One very likely source of dispersion of odd haplotypes is the Romans, who drew men for the Legions from all across the Empire, and marched them all around the Empire without regard to their previous habitations. ("The Romans" is the probable explanation for the Lords Darcy E-M35 haplotype, since their roots likely go back to Roman Gaul.)
So it's not necessary to hit the panic button if you get an unexpected Y-DNA (or, less often, mtDNA) result. It may simply mean that some remote ancestor came wandering into the neighborhood and settled down there.
The bottom line, though, is that if you don't want unexpected surprises, *don't* get involved with genealogy and/or genetic testing! :-D
