Ugo Perego, director of operations at the Sorenson Molecular Genealogy Foundation, told the Deseret Morning News that technological advances in DNA testing during the past couple of years have helped prove with "99.9 percent certainty" that two early Latter-day Saints thought by some to be Smith's children are not his descendants. They are:
• Mosiah Hancock, son of Clarissa Reed Hancock, who was married to Levi Hancock.
• Oliver Buell, son of Prescindia Huntington Buell, who was married to Norman Buell.
Perego said that brings to five the number of people that some believed were Smith descendants whose paternal DNA does not match up with his. To date, at least seven other early Latter-day Saints have been identified in various historical documents or in later writings as potential Smith offspring, he said.
In 2005, Perego said DNA testing also ruled out three other alleged male descendants Moroni Llewellyn Pratt (son of Mary Ann Frost Pratt, married to Parley P. Pratt), Zebulon Jacobs (son of Zina Diantha Huntington Jacobs Smith, married to Henry Bailey Jacobs) and Orrison Smith (son of Fanny Alger).
Some candidates are surrounded by what he called "strong historical evidences like journal entries," while other alleged descendants have little historical basis to be related, other than "speculation based on conclusions that sometimes may have been too rushed," Perego said.
In Hancock's case, "historically, there is nothing about him. In fact, another son of Levi Hancock is more in question, named John Reed Hancock." Mid-20th century historian and author Fawn Brodie, in her book "No Man Knows My History," had "quite a lot about John Reed Hancock," he said.
Brodie also believed Buell was Smith's child, born during the early church's days in Far West, Mo., he said. "She goes quite far to explain why she thought this was the case. The time was perfect because (Prescindia's) husband was gone from the church, and there was a plural marriage that took place while he was gone."
Brodie also offered as evidence a photo of Buell resembling two of Joseph and Emma Smith's sons, writing that his "physiognomy ... seems to weigh the balance overwhelmingly on the side of Joseph's paternity."
Historians say Smith was married to as many as 30 women before he was killed by a mob in June 1844.
Perego also has gathered DNA samples on about 120 descendants of Josephine Rosetta Lyon, daughter of Sylvia Sessions Lyon, who was one of Smith's wives. But Y chromosome evidence, used to determine paternal relationships from father to son, is not present for Lyon because she is female. The effort to determine Lyon's parentage is ongoing, he said.
His most recent findings were presented as a paper at the annual John Whitmer Historical Association conference in Kirtland, Ohio, in late September. The group's officers since have asked Perego to put his presentation into an article format suitable for publication in their next annual journal.
The list of approximately 12 people alleged to have been Smith's children "may grow over time," Perego said, noting historical documents continue to surface. "I'm not saying the list I have is definitive or complete at all. But out of those we have data for, there is no evidence from DNA at this point that Joseph Smith had any children from women other than Emma Smith.
"In the future, if DNA data will be able to be collected and tested, we might know otherwise. But right now, we're able to eliminate five children from that list. There may be some cases we might never be able to test at all."
While Y chromosome DNA is passed from father to son and is most accurate in identifying living people, mitochondrial DNA is passed from mother to daughter and is more often used in paleontology and archaeology, Perego said. As a result, there are distinct limitations on the testing that can be done to date because such testing on a living and cooperative male descendant requires an unbroken male line.
Perego has mapped Smith's DNA by retrieving samples from living descendants of two sons he had with Emma Smith Joseph Smith III and Alexander Hale Smith. "Their Y chromosomes were identical, so we know for 100 percent sure what Joseph Smith's Y chromosome looked like. We can now use that standard to verify any other alleged sons," which he did with those who have been eliminated as possible descendants.
"For 160 years people have been writing in books or speculating that these people could have been Joseph Smith's children. When people write something in a book, many people refer to that almost as a fact. Brodie went on and on about Buell, talking about the timing and the picture everything seems to indicate Buell was Joseph Smith's son. But the DNA says otherwise."
Perego said he was not only able to eliminate Smith as their father, but also was able to confirm that the men who were married to Hancock's and Buell's mothers were actually their biological fathers.
As he finds living descendants of people in question, Perego said he will be happy to continue to test them. "I think this will always be a work in progress. Hopefully, someday we'll be able to test some of the girls as well, when genetic testing is developed to accurately conclude if some of these girls were or were not his descendants."
Plural wife Sylvia Sessions Lyon left a deathbed affidavit for her daughter, Josephine, telling her that her father was Joseph Smith. In terms of circumstantial evidence, "that is probably the strongest case out there, but it involves a daughter. I've collected maybe 120 samples from descendants of Josephine, but as of today, there is not an accurate method" to prove parentage.
Perego's work is an independent project that Sorenson has allowed him to work on, rather than something the foundation does full-time, he said. His motive, he said, is truth, not glory.
"As a scientist, I like to look for truth. If there is a book that says this person was Joseph's son, and I have evidence that's not right, it's important for me to offer an alternative explanation from science that people can refer to. New authors in the future can then take that new genetic evidence into consideration.
"My goal is not at all a crusade to prove or disprove either that Joseph Smith practiced polygamy or that he had children from women other than Emma. I have no agenda to prove or disprove.
"There are legitimate cases of individuals studying family history who have a pedigree chart in front of them that shows" Smith as a third-great-grandfather.
"Because there is some evidence like a book or a rumor in the family, individuals don't know who to put on their pedigree chart. We're talking about real people who want to know who they are descended from.
"Most have told me they don't really care if they come from Joseph Smith or from someone else. They just want to know which one."
For information on DNA testing for family history research, see Sorenson's Web site at www.SMGF.org.
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