DNA sequences on the Y chromosome undergo mutation over time and vary among individual males. Like Y-linked traits, these variants—called genetic markers—are passed from father to son and can be used to study male ancestry. Although the markers themselves do not code for any physical traits, they can be detected with molecular methods. Much of the Y chromosome is nonfunctional; so mutations readily accumulate. Many of these mutations are unique; they arise only once and are passed down through the generations without recombination. Individual males possessing the same set of mutations are therefore related, and the distribution of these genetic markers on Y chromosomes provides clues about genetic relationships of present-day people.

Y-linked markers have been used to study the offspring of Thomas Jefferson, principal author of the Declaration of Independence and third president of the United States. In 1802, Jefferson was accused by a political enemy of fathering a child by his slave Sally Hemings, but the evidence was circumstantial. Hemings, who worked in the Jefferson household and accompanied Jefferson on a trip to Paris, had five children. Jefferson was suspected of fathering the first child, Tom, but rumors about the paternity of the other children circulated as well. Heming’s last child, Eston, bore a striking resemblance to Jefferson, and her fourth child, Madison, testified late in life that Jefferson was the father of all Hemings’s children. Ancestors of Hemings’s children maintained that they were descendants of the Jefferson line, but some Jefferson descendants refused to recognize their claim.

To resolve this long-standing controversy, geneticists examined markers from the Y chromosomes of male-line descendants of Hemings’s first son (Thomas Woodson), her last son (Eston Hemings), and a paternal uncle of Thomas Jefferson with whom Jefferson had Y chromosomes in common. (Descendants of Jefferson’s uncle were used because Jefferson himself had no verified male descendants.) Geneticists determined that Jefferson possessed a rare and distinctive set of genetic markers on his Y chromosome. The same markers were also found on the Y chromosomes of the male-line descendants of Eston Hemings. The probability of such a match arising by chance is less than 1%. (The markers were not found on the Y chromosomes of the descendants of Thomas Woodson.) Together with the circumstantial historical evidence, the matching markers strongly suggest that Jefferson fathered Eston Hemings but not Thomas Woodson.