Plant geneticist Simon Southerton was a Mormon bishop in Brisbane, Australia when he woke up the morning of Aug. 3, 1998 to the shattering conclusion that his knowledge of science made it impossible for him to believe any longer in the Book of Mormon.

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.

1. If the past Mormon prophets did not really have any inspiration informing them of the true origins of the pre-Columbian peoples of the Americas and Polynesian islands, why did they personally pretend to know? Why did Kimball make his remarks about American Indian children of church members turning lighter? Why did BYU sponsor a group called "Lamanite Generation" that included all native Polynesians and American Indians as Lamanites? Why do numerous DandC revelations generally refer to North American Indian populations as Lamanites?
2. If there were pre-Lehite inhabitants of the Americas, who came over before the time of Noah's flood, why weren't these original inhabitants of the Americas wiped out in the great flood?
3. At a minimum, is it not the responsibility of inspired Prophets and Apostles to (i) refrain from teaching false doctrine; and (ii) correct erroneous doctrines that are accepted by most, if not all, of the members of the Church? (Why do apologists always think that their great religious leaders can be so easily excused for failing miserably in these responsibilities? And why do the past Prophets and Apostles have such a miserable track record in this regard?)
4. What does it say about the likelihood of the Book of Mormon's authenticity that DNA evidence supports the Siberian land bridge/east-Asian origin theories that were derided by Mormons for so long, while, at best, providing no support whatsoever for the Book of Mormon stories, if not outright refuting them?
5. If so many Mormons over the past several generations have misunderstood the implications of the Book of Mormon regarding the origins of pre-Columbian Americans and Polynesians, what is it that they have "testimonies" of? Do they really understand anything about the Book of Mormon? "The Church is true. The Prophets are true. The Book of Mormon is true. Just don't ask us to carefully define what our testimonies of these things mean and don't try to hold the Church, the Prophets or the Book of Mormon accountable for any past pronouncements. It may have all been a misunderstanding that has been clarified now by our illustrious apologists."

1. President Hinckley spoke one-to-one with Scott Woodward in 2002 or 2001, at which time President Hinckley instructed Scott Woodward to stop some or all of his DNA research at BYU. Scott Woodward mentioned the content of this meeting with President Hinckley during a faith-inspiring message to members of his Belmont Apartments single student ward, BYU 1st stake, while he was serving as Bishop.
2. At the time of the meeting, Scott Woodward was scientific director of the Molecular Genealogy project at BYU. This project aimed to create a large DNA genealogical database to allow people to trace their ancestral homelands through their DNA.
3. At the time of the meeting, Scott Woodward had carried out DNA tests on over 6,000 Native Americans, mostly from Peru. At least 98% of their mitochondrial DNA lineages were most similar to Asian mitochondrial DNA lineages. The results of this research remain largely unpublished today.
4. Some time after this meeting, the BYU Molecular Genealogy research project was moved off campus to the Sorenson Molecular Genealogy Foundation in Salt Lake City. For a period, Scott Woodward was not affiliated with BYU.

The Book of Mormon: Another Testament of Jesus Christ is exactly what it claims to be - a record of God's dealings with peoples of ancient America and a second witness of the divinity of the Lord Jesus Christ. The strongest witness of the Book of Mormon is to be obtained by living the Christ-centered principles contained in its pages and by praying about its truthfulness.

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. Those interested in a more detailed analysis of those issues are referred to the resources below:

"The authors are correct in saying the historical origins of most Jewish communities are unknown. With no evidence that modern Jewish mtDNA constitutes a valid control of the genetics of ancient Israel, claims of Israelite lineage cannot be either confirmed or denied based on DNA evidence."

"The authors are correct in saying the historical origins of most Jewish communities are unknown."

"With no evidence that modern Jewish mtDNA constitutes a valid control of the genetics of ancient Israel, claims of Israelite lineage cannot be either confirmed or denied based on DNA evidence."

"Geneticists use the Y chromosome and mitochondrial DNA to track the movement of populations because each is passed unchanged from parent to child, escaping the genetic shuffle that occurs on the rest of genome between generations. Since the Y chromosome passes down only from father to son, and mitochondrial DNA is always inherited from the mother alone, the two elements serve to track the genetic history of men and women respectively."

Was Hebrew DNA recently found in American Indian populations in South America? According to Scott R. Woodward, executive director of Sorenson Molecular Genealogy Foundation, a DNA marker, called the "Cohen modal haplotype," sometimes associated with Hebrew people, has been found in Colombia, Brazil and Bolivia.

According to Woodward, the way critics have used DNA studies to attack the Book of Mormon is "clearly wrong." And it would be equally wrong to use similar DNA evidence to try to prove it.

This is because "not all DNA (evidence) is created equal," Woodward said.

It is the misuse of evidence that gave critics fuel to make their DNA arguments in the first place. According to Woodward, the critics are attacking the straw man that all American Indians are only descendants of the migrations described in the Book of Mormon and from no other source

"Some LDS scholars suggest that haplogroup X2a-found exclusively in northern North America-could be a proof of Lehi's genetic legacy, but at this time there is not enough data to support these conclusions. Reidla and colleagues in 2003 began exploring the origin and distribution of haplogroup X among the world populations and they concluded that "phylogeography of the subclades of haplogroup X suggests that the Near East is the likely geographical source for the spread of subhaplogroup X2." Regarding the presence of a few sequences belonging to haplogroup X found in the Altai population of central Asia, the authors commented that "under the assumption that these sequences are a random sample of the Altaian haplogroup X [they provide a] a time depth of <6700 years, and it would suggest that Altaians have acquired haplogroup X2 only relatively recently." In other words, haplogroup X2 in modern Asian populations is NOT ancestral to haplogroup X2 found in Native Americans. Reidla and colleagues concluded that "the few Altaian and Siberian haplogroup X lineages are not related to the Native American cluster, and they are more likely explained by recent gene flow from Europe or from West Asia."

"Much can still be said about haplogroup X2 in the Americas. In our paper, two sub-branches of the Native American haplogroup X2a have been classified as X2a1 with an estimated age of 9200-9400 years and as X2a2 with an estimated age of 2300-3800 years. A possible third X2a sub-branch (X2a3?) was identified among the indigenous groups of British Columbia in Canada, but there is not sufficient data at this time to confirm this hypothesis. Furthermore, we reported in this paper the discovery of a previously unidentified X2 lineage in an Ojibwa sample - which we named X2g - that has never been previously observed in Native American populations or elsewhere.

"Lastly, a paper published on PLoS One in 2008 (Shlush et al.) provides important clues about the possible origin of haplogroup X: "No population or geographic region has been identified to date, in which haplogroup X and its major subhaplogroups are found at both high frequency and high diversity, which could provide a potential clue as to their geographic origin. Here we suggest that the Druze population of northern Israel may represent just such a population."

"Our paper in Current Biology does not discuss (and does not dismiss) a potential ancient origin for haplogroup X in the ancient Near East, as proposed by Shlush and Reidla (and their co-authors, including important names in population genetics such as Michael Hammer, Doron Behar, Toomas Kivisild, Richard Villems, Antonio Torroni, Alessandro Achilli, etc.), but we emphasize how this haplogroup marked a separate migratory event that characterized the history of Native American populations. Apart from anyone who believes haplogroup X to be the ultimate proof marking the arrival of Lehi's group to the Americas (something that neither Woodward, nor myself advocate), the bottom line is that there is still much to research about the origin and dispersal of this and the other pre-Columbian lineages."

The use of the word "discovering" is interesting in the opening sentence of Southerton's remarks. It appears that Southerton deliberately wants to give the impression to those who are unfamiliar with studies in population genetics that he is the one to first discover a genetic link between Native Americans and Asian populations.

None of these studies on Native Americans, including the current one published in January 2009 in Current Biology were designed to address the Lamanite/Book of Mormon issue. Data for this study were collected and analyzed with the objective of shedding new light about the origins of Paleo-Indians; not to identify additional migratory events in the following millennia and the role they may have played in re-shaping the genetic pool already existing in America's double continent.

Despite Southerton's continued efforts to discredit the professional integrity of institutions and/or individuals affiliated with the LDS faith, the debate about the origin of Native American populations is still wide open as demonstrated by the great amount of scholarship that scientists from different fields are still producing today.

As a scientist and as a member of the LDS faith, I find no difficulties in reconciling my scientific passion about Native American history with my religious beliefs. I am not looking for a personal testimony of the Book of Mormon in the double helix.

Despite a shared consensus RFLP haplotype, substantial genetic differences exist between the American Indian and European haplogroup X mtDNAs.

Recently, the mtDNA studies have shown that both northern and southern Altaians exhibit all four Asian and American Indian-specific haplogroups (A-D) with frequencies of 57.2% (Sukernik et al. 1996) and 46.8% (Derenko et al. 2000a), respectively, exceeding those reported previously for Mongolians, Chinese, and Tibetans. Therefore, they may represent the populations which are most closely related to New World indigenous groups. Since the detection of all four haplogroups (A-D) in an Asian population is thought to be a first criterion in the identification of a possible New World founder, the candidate source population for American Indian mtDNA haplotypes therefore may include the populations originating in the regions to the southwest and southeast of Lake Baikal, including the Altai Mountain region (Derenko et al. 2000b). The presence of X mtDNAs in Altaians is generally consonant with the latter conclusion.

"In their more candid moments, the ex-Mormon critics admit that their criticisms require that the key assumption of 'only Lehi' be made."

"Research indicates that a woman from the North American continent probably arrived in Iceland some time around 1000AD leaving behind genes that are reflected in about 80 Icelanders today."