The DNA evidence looked at a male line descendant of Sally Hemings’ youngest child. That living person’s DNA was compared to a living male line descendant of Field Jefferson (Jefferson’s uncle.) Jefferson had no legitimate direct male line descendants so there were none to test against. DNA was also taken from a living male line descendant of Thomas Woodson (someone that people had suggested as a possible alternative father of Hemings’ children.)
What came out was that Eston Hemings was definitively not the son of Thomas Woodson, and that his male line descendants shared very rare genetic traits with the male line descendants of Field Jefferson.
That’s the scientific evidence available. I do not know if further testing has been done on male line descendants of the other 5 of Hemings’ children, and the limitation of this testing is obviously there is the possibility that one of Field Jefferson’s offspring fathered Hemings’ children, not Jefferson himself.
However when you combine the scientific evidence with the historical, it really removes virtually all reasonable doubt that Thomas Jefferson was the father of all six children.
First, Jefferson’s comings and goings are well documented. Hemings’ six pregnancies coincide with Jefferson’s visits and stays at Monticello, none of them coincide with the known movements of any other Jefferson. Randolph Jefferson (TJ’s brother) or his sons, or Field Jefferson’s grandsons could potentially have fathered Hemings’ children, but Field Jefferson’s grandsons lived very far away, and there is no historical evidence that links them to Hemings. Randolph Jefferson and his sons lived in closer proximity, but there is no historical record at all showing that Randolph Jefferson’s movements or Randolph Jefferson’s son’s movements coincided with Hemings’ pregnancies.
Further, while these are scientific possibilities, it should be noted that the historical record is totally absent of any allegations that Field Jefferson’s grandsons or Randolph Jefferson and his sons fathered Sally Hemings’ children.
Basically you have to give a nod to the grandsons of Field Jefferson and Randolph Jefferson’s family as possibilities. But look at it this way, there is historical evidence that Jefferson’s movements put him at Monticello at the appropriate time for all of Hemings’ pregnancies. So if it was another male Jefferson, then their movements would have to be such that they too were always at Monticello at exactly the same time as Jefferson and exactly when Hemings’ six children were conceived. It is just highly unlikely.
Further, visitors to Monticello recorded entries in their diaries and in letters talking about Jefferson having fathered children with Hemings. This was not a deep dark secret at the time. It was not widely known, bu visitors and such were not kept in the dark on this matter. John Hartwell Cocke was a frequent visitor to Monticello and he wrote in his diary that Jefferson was a “notorious example” of the prevalence of Virginia of “masters with slave families.” A long time Jefferson slave, Israel Jefferson, also confirmed the paternity of Hemings children.
These are people who spent time with the real Thomas Jefferson in the real world, and these were their direct observations. These are people who in general were favorable to Jefferson, were close with him and friendly with him. It is unlikely they would make these things up. Especially John Cocke, why would he record a lie in his personal diary? That was primarily kept private in his own lifetime? Did he envisage that hundreds of years later some historian would read it and that it would embarrass his friend Thomas Jefferson? That’s just not a realistic scenario.
Finally, Jefferson freed some of his slaves throughout his life based on a variety of factors. Jefferson’s legitimate granddaughter noted that Jefferson had a practice of freeing certain slaves who had skills and a light enough compelxion to “pass” that they would be able to establish themselves as freed people. However, these were rare cases and it is worth noting that in none of these cases did Jefferson free entire nuclear families, nor did he free people under 30 years of age.
Only in the case of Sally Hemings’ family did Jefferson give an entire nuclear slave family their freedom, and for all of them they were given their freedom at a young age (before age 30.) This makes them extremely unique among Jefferson’s slaves at Monticello, and is highly suggestive that these were in fact Jefferson’s children and that is why they were given freedom upon reaching legal adulthood (I believe at age 21.)