As pointed, breaks can occur ANYWHERE: for this reason, Thomas Jefferson could have been the biological father of Thomas Woodson (the eldest child of Sally Hemings) -- despite the fact that the latter's male-line descendants today do not share the Jefferson family's Y-chromosome DNA.
As for royalty: paternity is a legal fiction -- and I wouldn't be in the least surprised if there were breaks here and there in the patrilineal descent from the Capetians of France.
That being said, in this particular English case one should not necessarily implicate a royal queen in adultery simply because of the DNA mismatch -- since one is talking here of over 500 years of history.
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The Beaufort line is in my view a tricky one to compare to. They are the result of children born outside of a marriage to a woman who did not have a particularly high status. For her it would have been beneficial to have any children born to her after the death of her first husband to be attributed to a Royal prince. However unlike most royal wives she was not as strictly guarded and or protected from other men.
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The break in the male-line DNA could have happened anywhere. Unfortunately the Y chromosome can only be traced through the Beaufort line who are male line descendants of John Of Gaunt, Duke of Lancaster (4th son of Edward III). There are no other living male-line descendants of the Plantagenets. The mismatch between the Beaufort DNA and Richard's can only really be resolved by comparing it to the DNA of a Plantagenet king if the present monarch would grant his permission. Personally I've always favoured extracting DNA from the remains of King John who is buried in Worcester Cathedral. John is as close to the founder of the Plantagenet line as you can get being the son of Henry II. Whoever's DNA matches his is a true Plantagenet descendant of the male line.
Apparently there were widespread rumours at the time that Isabella, Duchess of York, wife of the founder of the Yorkist branch (Edmund of Langley, 5th son of Edward III) had other male lovers one of whom may have been the true progenitor of Richard III's line and therefore the originator of the break but that's just a rumour of course.
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The identity of the king whose body was found in a parking lot has been confirmed with near absolute certainty to have been Richard III -- thanks to mitrochondrial DNA: evidently there are living matrilineal descendants of his sister, Anne of York.
But the testing on the Y chromosome revealed another story: can anybody provide the exact genealogical link through which this was tested? The patrilineal descendant of the Plantagenets who was provden not to be related to the king, thereby revealing a break?
https://le.ac.uk/richard-iii/identification/genetics/dna-results
The YDNA of the Duke of Beaufort did not match that of Richard III.
When the non-paternity-event took place is impossible to say from that, other lines would need testing to find out.
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