Two years later he started writing "Losing a Lost Tribe: Native Americans, DNA and the Mormon Church," published by Signature Books and due in stores next month. Along the way, he found a world of scholarship that has led him to conclude The Church of Jesus Christ of Latter-day Saints belief is changing, but not through prophesy and revelation.
Rather, Southerton sees a behind-the-scenes revolution led by a small group of Brigham Young University scholars and their critics who are reinterpreting fundamental teachings of the Book of Mormon in light of DNA research findings. Along the way, he says, these apologist scholars, with the apparent blessing of church leadership, are contradicting church teachings about the origins of American Indians and Polynesians.
"You've got Mormon apologists in their own publications rejecting what prophets have been saying for decades. This becomes very troubling for ordinary members of the church," Southerton said.
And while the work of the BYU apologists - the term means those who speak or write in defense of something - remains confined largely to intellectual circles, some church members who have always understood themselves in light of Mormon teachings about the people known as Lamanites are suffering identity crises.
"It's very difficult. It is almost traumatizing," said Jose Aloayza, a Midvale attorney who likened facing this new reality to staring into a spiritual abyss.
"It's that serious, that real," said Aloayza, a Peruvian native born into the church and still a member. "I'm almost here feeling I need an apology. Our prophets should have known better. That's the feeling I get."
Southerton, now a senior researcher with the Commonwealth Scientific and Industrial Research Organization in Canberra, Australia, has concluded along with many other scientists studying mitochondrial DNA lines that American Indians and Polynesians are of Asian extraction.
The church teaches that Joseph Smith translated this record from gold plates found on a hillside in upstate New York in 1820, when he was 14. The Book of Mormon was first published in 1830.
In Mormon theology, Lamanites are understood as both chosen and cursed: Christ visited them, yet their unrighteousness left them cursed with dark skin. The Book of Mormon says Lamanites will one day be restored to greatness through the fullness of the gospel. (The original 1830 version of the Book of Mormon said they would become "white and delightsome;" in 1981, the passage was changed to "pure and delightsome.") Though not mentioned specifically in the Book of Mormon, Polynesians have been taught they are a branch of the House of Israel descended from Lehi.
Traditionally, Mormons have understood the Book of Mormon to cover all of the Americas in what is known as the hemispheric model. At a Bolivian temple dedication in 2000, church prophet and President Gordon B. Hinckley prayed, "We remember before Thee the sons and daughters of Father Lehi." And in 1982, the church's then-President Spencer Kimball told Samoans, Maori, Tahitians and Hawaiians that the "Lord calls you Lamanites."
Southerton's book details how these teachings have helped LDS efforts to convert new members, especially among Indians in Latin America and Maoris in New Zealand. He also offers primers on Mormon history and American race relations, quick tutorials on DNA research and syntheses of Mormon-related genetic research and DNA scholarship.
But in light of BYU scholars' recent opinion that the Book of Mormon's events could only have occurred in parts of Mexico and Guatemala - that is, Mesoamerica - the final third of the book is dedicated to examining the work of LDS scholars at the Foundation for Ancient Research and Mormon Studies, or FARMS, established 25 years ago and housed at BYU.
FARMS findings on Mesoamerica are based on the Book of Mormon's "internal geography," that is, descriptions of how long it took the ancient peoples to get from one place to another. The apologists now believe the events occurred only hundreds of miles from each other, not thousands - provoking new questions including how the Americas could have been so rapidly populated with people speaking so many languages without the presence of vast numbers of people who never appear in the narrative.
In particular, he's tried to keep up with FARMS qrticles, which he said are "completely at loggerheads with what the church leaders are teaching."
Church spokesman Dale Bills on Thursday said the church teaches only that the events recorded in the Book of Mormon took place somewhere in the Americas. The doctrine of the church is established by scripture and by the senior leadership of the Church, the First Presidency and the Quorum of the Twelve.
"Faithful Latter-day Saint scholars may provide insight, understanding and perspective but they do not speak for the church," he said.
On its Web site, under the "Mistakes in the News" heading, the church declares, "Recent attacks on the veracity of the Book of Mormon based on DNA evidence are ill considered. Nothing in the Book of Mormon precludes migration into the Americas by peoples of Asiatic origin. The scientific issues relating to DNA, however, are numerous and complex."
The site then offers Web links to five articles, four of which were published last year in the Journal of Book of Mormon Studies, a FARMS publication.
Aloayza believes that is tacit approval of what FARMS is saying.
"There is such a huge divide between what the scholarly elite with the LDS church knows and will discuss and what the ordinary member knows," Aloayza said. "The burden of proof is on the people who are advancing the Book of Mormon as the word of God."
BYU political science professor and FARMS director Noel Reynolds said FARMS research and writings are not aimed at proving or disproving the Book of Mormon. "We understand the difficulties of that. We get dragged into these discussions repeatedly because of books like Southerton's or ordinary anti-Mormon questions," he said.
The work of FARMS shouldn't be considered counter to church doctrine because the geography of the Book of Mormon has "never been a matter of official church pronouncement," Reynolds said.
While believing in a hemispheric model might be considered "naive," he said, "it's also fair to say that the majority of LDS over a period of time have accepted a hemispheric view, including church leaders."
Added FARMS founder and BYU law professor John Welch, "We don't speak officially for the church in any way. These are our opinions, and we hope they're helpful."
Southerton, who no longer is a member of the church, said given the state of DNA research and increasing lay awareness of it, church leaders ought just to own up to the problems that continued literal teachings about the Book of Mormon present for American Indians and Polynesians.
"They should come out and say, 'There's no evidence to support your Israelite ancestry,' " Southerton said. "I don't have any problem with anyone believing what's in the Book of Mormon. Just don't make it look like science is backing it all up."