Are you going to print a retraction of your Straight Dope article concerning Thomas Jefferson and Sally Hemings [Return of the Straight Dope, pages 219-21]? The column called the evidence that Jefferson had an affair with his slave “dubious.” Is it still the contention of the Straight Dope that Jeffy’s relatives were the ones to blame? Will Cecil hire Johnny Cochran to refute the DNA evidence? –EdGein14, via AOL

Time to bite the bullet. I was doubtful that Jefferson fathered children by his slave Sally Hemings, but the new genetic evidence creates a strong presumption that he did. However, at the risk of sounding like I’m in complete denial, there are parts of this story that still don’t add up.

To review: In 1802 James T. Callender, a disgruntled ex-employee of Jefferson’s, publicly accused the president of a dalliance with Hemings that had apparently produced three children, the oldest of whom, Thomas, was then 12. What made the charge plausible was the strong resemblance between Jefferson and the light-skinned Hemings kids. Sally herself was only one-quarter African, allegedly the child of Jefferson’s father-in-law and a half-white slave. That would make her half-sister to Jefferson’s wife, Martha (who died before the supposed affair began). The real scandal wasn’t so much that Jefferson had impregnated a slave–a common occurrence in those days–but that he’d kept her as his concubine in the midst of his white family.

Privately Jefferson denied all, but he never publicly answered Callender’s widely publicized charges, which have circulated ever since. The story got new life in 1873 when an ex-slave named Madison Hemings claimed to be Sally and Tom’s son. Hemings’s descendants have long believed the president is their ancestor, but white historians ignored or dismissed these claims, a few conjecturing that Hemings’s kids were fathered by Samuel or Peter Carr, the randy sons of Jefferson’s sister–hence the resemblance to Tom.

In recent times the question came up for another look, and it occurred to some that genetic testing might shed some light. The Y (male) chromosome changes very little when transmitted from father to son. So pathologist Eugene Foster and others decided to take the Y-chromosome DNA of male-line descendants of Hemings’s eldest son, Thomas Woodson (so surnamed because of a later owner), and her youngest son, Eston Hemings Jefferson, and compare it with the DNA of male-line descendants of Jefferson’s paternal uncle (TJ had no surviving sons) and of Samuel and Peter Carr’s grandfather. The results:

Thomas Woodson DNA and Eston Hemings Jefferson DNA versus Carr DNA. No match.

Thomas Woodson DNA versus Jefferson DNA. No match.

Eston Hemings Jefferson DNA versus Jefferson DNA. Match. More than that: dead match. It’s all but certain that Jefferson or a close relative fathered Hemings’s youngest son.

True, it might not have been Jefferson. It could have been his brother Randolph, one of Randolph’s five sons, etc. Looking at the bigger picture: it was a plantation, lots of sexual mixing went on–who knows how the bloodlines might have gotten crossed? On the other hand: (1) it’s been documented that Hemings and Jefferson were in the same place eight or nine months prior to each known birth; (2) there’s the DNA evidence; (3) there’s the Woodson oral history; (4) there’s the Madison Hemings account; (5) Jefferson freed all the Hemings children at age 21, something he did for none of his other slaves; and (6) the Carr theory has been largely ruled out. So the simplest explanation is that TJ was the pop.

Still, think where this leaves us. Hemings’s youngest son wasn’t born until 1808. The most obvious interpretation of the DNA results is that Jefferson didn’t father Tom, the kid who inspired the initial rumor, but he did father the kid who was born six years after the scandal broke. Doesn’t this seem odd? Uncertainty about Tom further confuses matters: Callender cited him by name, but Jefferson’s records don’t mention him, and other sources are contradictory. We aren’t sure if Sally even had a son named Tom.

So unanswered questions remain. Yet Cinder Stanton, senior research historian at Monticello, tells me the evidence of Jefferson’s paternity seems “pretty convincing,” and right now I have to agree.

Art accompanying story in printed newspaper (not available in this archive): illustration/Slug Signorino.