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II. The Mystery of an Illegitimate Son of the Third President of the United States
1. Who was Thomas Jefferson's illegitimate son?
Thomas Jefferson (1743-1826) was one of the leaders in the American War of Independence. He helped drafted the Declaration of Independence. He served as the first U.S. Secretary of State, the second Vice President and the third President. Together with Washington, Lincoln and Roosevelt, he is considered one of the four greatest presidents in American history. Despite all his world renown accomplishments, he was a controversial person. For over one hundred years, rumors about his love affair with his black slave and having illegitimate children generated a great deal of heated debates and controversy. At last, this mystery in American history was resolved by Y chromosome DNA decoding.
Jefferson's wife, Martha, was a beautiful white woman. Unfortunately, after Martha Jefferson gave birth to their youngest daughter, Molly, she died in 1782. At her deathbed, she begged her husband never get married again. With tears in his eyes, the 39 year old Jefferson agreed. Jefferson kept this promise and never had another wedding in his life. Five years after the death of his wife, Jefferson was appointed as the U.S. ambassador to France. The 19 year old Sally (1773-1835), Martha's half sister, went with him to Paris to take care of him. Sally's grandmother was a black slave who gave birth to Sally's mother with her white master. According to the prevailing law, Sally's mother was still a black slave. Sally's mother and Jefferson's father-in-law or his wife Martha's father was Sally's parents. Even though Sally, a beautiful girl with only had one quarter Negro blood, however, in accordance with the prevailing law, she was still a slave depraved of any freedom. Therefore, she did not have the title as his wife even though she lived with Jefferson for 30 years.
Sally gave birth to four children. In view of her position as a humble slave, people did pay much attention to her children. Her eldest son, Woodson Was born in 1790 and the youngest son Eston In 1808. Eston had one eighth Negro blood in him but he looked very much like Jefferson. Moreover, he had political talent which eventually landed him in political circle in Wisconsin.
However, now President Jefferson never admitted to having these children with Sally to protect his own political reputation. For a period of time, this matter often became a political bargaining chip and later became an inheritance lawsuit. For the last hundred years, this matter has been an unraveled mystery.
In 1997, there was a turning point in this historical mystery. Dr. Eugene A. Foster, a famous professor of pathology proposed the a plan to search with the Y chromosome in order to unravel the mystery surround the blood linkage in Jefferson's children. At that time, the confirmation of father-son relationship with Y chromosome testing was already well established. Moreover, the mitochondrial Eve hypothesis was established as well. It so happened that in this same year the Y chromosome Adam hypothesis was first proposed. Theoretically and technologically, the time was ripe for Professor Foster's plan to be actualized.
2. The Y chromosome analysis finally unraveled the mystery surrounding Jefferson's illegitimate children.
The simplest way to solve the mystery surrounding Jefferson's illegitimate children is to compare the Y chromosome from the remains of Jefferson and the self proclaimed descendants of his. However, it is almost an impossible task to reopen the coffin and do autopsy on the past president. The only feasible way was to use what the Y chromosome theory proposed, namely to use DNA from modern humans to search for the ancestors of president Jefferson. This method requires the comparison of the Y chromosome from Jefferson's descendants with those of the descendants from the illegitimate children. If results found to be similar, then, the possibility exists that they were Jefferson's descendants. If dissimilar, then the "suspected descendants" were not Jefferson's descendants.
It is unfortunate, Jefferson's only son died at age 9. Therefore, there are no descendants. Fortunately, President Thomas Jefferson had an uncle named Field. He had many descendants. After much effort, Professor Foster finally contacted the fifth generation of Jefferson¡¯s uncle and collected their blood samples. At the same time, Professor Foster successfully collected blood samples from the descendants of slave Sally's eldest son Woodson And youngest son Eston. Together with collective effort from several molecular biologists, the confirmation was eventually a success.
In the November 1998 issue of Nature, the DNA analysis was published (Reference 3 ). A summary of this report with explanation is shown in the Figure below. From this Figure, one can see that on the 11 STR loci, Eston's descendants STR and the STR from five Jefferson's descendants were similar. With question, Eston had inherited the Y chromosome from Jefferson's family. However, a contrary conclusion was reached with Sally's eldest son, Woodson.
 Figure 3-4 DNA confirmation of father-son relationship of Jefferson and Eston
In 2001, the independent committee commissioned by the Thomas Jefferson Heritage Society issued a 565-page report saying that Eston may be the son of Thomas Jefferson's brother Randolph Jefferson. The DNA evidence is simply too cruel. It is no way to deny that Eston was part of the Jefferson's family. This independent committee was too clever for they knew that the Y chromosome must be the same between these two brothers. There is no way to prove or disprove the "brother's son" claim. Obviously, this also points out the limitation of tracing ones genealogy with the Y chromosome.
We will not further dig into the aforementioned controversy as to who is right and who is wrong. In fact, there are several follow-up studies on the Y chromosome of the Jefferson family ( Reference 4 ).
The Cold Spring Harbor Laboratory in New York and another international organization whose laboratory had produced over eight Nobel Prize winners are the most authoritative organizations in tracing the patrilineal and matrilineal genealogy of the various people groups in our world . Its branch "Genome Research" revises the "Y-Chromosome Phylogenetic Tree" of the entire world's population based the test results of Y chromosome analyses collected world wide (Reference 5). The Y chromosome of Thomas Jefferson's family eventually belongs to the K2 haplogroup (see Figure 4-7). Yet, everyone of us must belong to a specific haplogroup. We can say that everyone of us is a leaf on this Phylogenetic tree.
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