Martha Jefferson died in 1782, and in 1784 Thomas Jefferson took up residence in Paris as American envoy to France, taking Sally Hemings with him. Sally became lady's maid to Jefferson's two daughters. She returned to Monticello with Jefferson in 1826 and was given her freedom before the sale in 1827 of the rest of Jefferson's slaves.
Rumors that Sally Hemings and Thomas Jefferson were sexually involved circulated well before Jefferson assumed office in 1801, and they were published in 1802. The truth of these rumors has long been debated. Evidence in support of the theory that Jefferson was father of Sally Hemings' children is that (1) Jefferson and Hemings were together at Monticello at the time of the conceptions of her children; (2) Madison Hemings, Sally's son, stated in an 1873 interview that Sally named the President as her children's father; (3) Sally's children were said to resemble Jefferson physically; and (4) Sally's children, unlike Jefferson's other slaves, were allowed to slip away, or were manumitted, before Jefferson's death.
The main argument advanced against the proposition was that of personal incredulity.
Some had argued that the resemblance to Jefferson was because the children had been fathered by one of Jefferson's nephews (Samuel or Peter Carr), sons of Jefferson's sister.
In Nature, 1988, the Y chromosomal haplotypes of several of Sally Heming's descendants (in the male line) were compared with the Y chromosomal haplotype of several of Thomas Jefferson's grandfather's descendants (in the male line). Some of these (descendants of Thomas Woodson) did not match, ruling out a Jefferson as direct male line ancestor, but the descendants of Eston Hemings did match, providing strong supporting evidence of the allegation that Jefferson had begotten at least one of Sally Hemings' children.
The Y chromosomal haplotype of the Carr family was found to be different from the Jefferson haplotype.
The National Genealogical Society Quarterly of September 2001 examined the totality of the available historical, genealogical, and scientific evidence and concluded that four children of Sally Hemings were fathered by Thomas Jefferson.
The controversy was distorted by its politicization in 1998 when, during the campaign to impeach Bill Clinton, the Pulitzer Prize winning historian Joseph Ellis defended Clinton by comparing him to Jefferson, whom he said had "also" been sexually dalliant, claiming that DNA tests "proved" Jefferson fathered a child by Hemings.
However, Stephen Goode wrote in Insight Magazine that:
(In fact, the tests did not say anything about the 'likelihood' of Thomas Jefferson, as opposed to his brother as the source of the Jefferson haplotype, but they did rule out the Carr nephews, so neither Goode nor Ellis seem to have been fully candid. Goode is calling Ellis a liar because they differ in what constitutes 'reasonable doubt', and since they both were making political, not scientific, points they can probably both be ignored.)
Also,
While it is certainly true that the DNA evidence alone does not indicate which particular Jefferson was father of Sally Heming's children, the DNA testing was designed to discriminate between two competing theories, the Jefferson paternity vs the Carr paternity, and strongly supported the former.
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