On January 28, 2009 Simon Southerton posted the following comments on the discussion board at exmormon.org about my recent scientific publication on Native American origins. He also took the opportunity to criticize Dr. Scott Woodward, former molecular biologist at Brigham Young University and current director of the Sorenson Molecular Genealogy Foundation (SMGF).

Having great familiarity and being personally involved with the subjects mentioned in Southerton’s remarks, I deemed it necessary to provide an alternative and more accurate version of the facts. This is simply a rebuttal to Southerton’s specific posting and it is not meant to be another treatise on the Book of Mormon vs. DNA issue, since there is already a great abundance of LDS scholarship addressing the topic.

Southerton’s posting, each section of which appears below, was retrieved from exmormon.org. Below is each section of his posting, along with my comments.

When I resigned in 1998 after discovering DNA evidence that American Indians were essentially all descended from Asian ancestors, I was counseled by the Area Presidency to get in touch with Professor Scott Woodward, a “world-renowned DNA expert” at BYU. In a handful of email exchanges that I had with Woodward, in amongst his lengthy molecular apologetics, he admitted that he had found it difficult to talk to other people about the DNA work and that after a few years of struggling he had reconciled most of the issues it raised.

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. Dr. Antonio Torroni and Dr. Theodore Schurr were the first two researchers to make public such discoveries in the early nineties (references available upon request) when population genetic studies based on mitochondrial DNA variation were still in their infancy. When Dr. Woodward began his correspondence with Southerton in 1998, he wrote that he was aware of the papers mentioned and was surprised that Southerton thought it was a new problem. In his book Losing a Lost Tribe (Signature Books, 2004), Southerton provides proper citations to these earlier scientific works, but I noticed that in his informal communications he tends to be a bit vague about who did the actual DNA work on Native American populations.

During the communication exchange between Southerton and Woodward in 1998, Woodward expressed how difficult it was for him to explain DNA related concepts to people (Southerton included) who did not want to understand or put serious effort into understanding the concepts involved. Woodward’s “difficulty” was not in reconciling Book of Mormon issues, but in dealing with people that refused to listen.

Woodward’s emails from 1998 were eventually edited by Southerton and forwarded to LDS Church leaders in Utah, with the objective of hurting Woodward’s teaching position at BYU. This event greatly upset Woodward. When in 2004 Southerton visited Woodward at SMGF, he admitted his earlier intentions and apologized for what he did in 1998. I was present at that meeting.

I met Woodward when I visited the Sorenson Molecular Genealogy Foundation (SMGF) in Salt Lake City a few years ago. At the time he angrily defended the Book of Mormon and hinted that SMGF scientists were finding exciting new evidence that supported the Book of Mormon (must be still finding it).

There were four people present at that more than three hour long meeting in 2004: Woodward, Southerton, Luke Hutchison (currently at MIT completing his doctorate studies), and myself. I did not speak much, but I remember vividly the meeting and listened carefully to the conversation that took place.

During that occasion, Woodward did not “angrily defend” the Book of Mormon, but there was definitely some tension in the room due to what Southerton attempted to do to him in 1998. As I already stated, Southerton admitted to sending communications to LDS leaders in an attempt to purposely hurt Woodward’s academic position at BYU, and said he was sorry for what he did. However, we had a hard time believing that he was sincere in his apologies since his recent book Losing a Lost Tribe contained several innuendos about the nature of Woodward’s work with SMGF, insisting on possible connections with the search for Lamanite DNA evidence.

Woodward and Hutchison explained to Southerton the complexity surrounding the issue of identifying unknown Israelite DNA among modern Native American populations, the limited data available at the time, the limitations in building or interpreting phylogenetic trees, and other basic population genetic principles as they pertain to the arrival of a small family group in an already largely populated continent. It was emphasized over and over that DNA may or may not yield in the future any evidence about a non-Asian contribution to the modern Native American gene-pool, but the bottom line is that any attempt of using genetic data to support or attack the Book of Mormon is highly complicated and fails to put this matter to rest. Eventually Southerton admitted that he did not know much about population genetics (he is a plant geneticist) and that he did not understand phylogenies but, nonetheless, he was still “very proud of his book.” That pretty much ended that long debate…

No one at that meeting (except, apparently, Southerton) recalls any mention of “finding exciting new evidence that supported the Book of Mormon,” particularly with regards to the work done at SMGF, as DNA and family history data collected in the first few years of the project were mainly of Anglo-Saxon extraction. However, references were made about the work of researchers from other universities publishing data that did not fit with the classic “Asian” markers as found among the majority of pre-Columbian groups. In some cases, the hypotheses surrounding their possible presence in the Western Hemisphere are still a matter of dispute (these arguments have already been discussed elsewhere and basically they have been promptly dismissed by those criticizing the historicity of the Book of Mormon).

This month in the scientific journal Current Biology, Woodward co-authors a research paper that clearly demonstrates that the ancestors the American Indians arrived in North America over 15,000 years ago via two routes from Asia (http://www.cell.com/current-biology/abstract/S0960-9822(08)01618-7). The founders brought 5 major maternal DNA lineages with them, named A, B, C, D and X. One group of founders brought the X lineage to the region adjacent to the Great Lakes as they migrated between ice sheets across what is now central Canada. The other group followed the Pacific coast, probably bringing the other four DNA lineages (A, B, C and D).

An international team of 16 scientists worked on this research for the past 18 months. Dr. Achilli and I were the leading authors on this project, which was conducted under the mentorship of the corresponding author, Dr. Antonio Torroni. All the other authors contributed to some degree to the developing of the project, the analysis of the data, and the writing of the manuscript. I find it interesting how Woodward was singled out by Southerton for his contribution to this research paper. (By the way, the link provided in Southerton’s post does not work. A summary is available at this address. For a copy of the full article, please contact me directly at ugo@smgf.org).

Geneticists in the past emphasized a single arrival for the first Paleo-Indians and this was in clear opposition with scientists from other fields (linguists, anthropologists, archaeologists, etc.), as they were convinced that there is enough evidence to support a multi-origin of all the modern Native Americans. Our paper shifts the position of population geneticists to be more in line with researchers from other fields.

There are currently eleven recognized mitochondrial DNA lineages among modern Native American populations: A2, B2, C1b, C1c, C1d, D1, C4c, D2, D3, D4h3, and X2a. Approximately 95% of modern Native American maternal lineages belong to one of the first six in this list. The others are considered rare lineages. The paper discusses two of these less common mtDNA haplogroups (D4h3 and X2a). D4h3 was identified as a new Native American lineage for the first time in 2007, when DNA extracted from the remains of a 10,300 year old skeleton found in Alaska yielded a genetic sequence that did not match any of the known Native American mtDNA haplogroups. A careful survey of DNA databases identified a significant number of previously unclassified DNA sequences in modern Native American populations belonging to this new haplogroup, which was eventually called D4h3. Although D4h3 is also of probable Asian origin, this important discovery underlines the problematic issue with genetic sequences that were initially ignored simply because they did not fit with the classic “Asian” haplogroups. It is possible that in the years to come, additional rare lineages will be identified both in modern and ancient samples.

The migratory routes followed by the ancestors of these two rare lineages were drawn based on the available data, as it was inferred by the distribution of mtDNAs collected and analyzed in the modern population. These conclusions may be adjusted at future times based on new data both from DNA and/or from other fields. In fact, the paper starts with this clear statement: “When and from where did the first Americans arrive, and what migratory routes did they follow? Scientists from several disciplines continue to search for answers to these questions, but, despite new important evidence, the debate concerning the peopling of the Americas is far from resolved.” Southerton, on the other hand, thinks that this matter is clearly already resolved.

In this paper Woodward helps bury a pile of apologetic trash from both the Mesoamerican (church approved) and Heartland (church still watching) Geographists who have variously claimed in the past that the X lineage came from Israel. The X lineage is conclusively shown to have arrived in the New World thousands of years before the Book of Mormon period.

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. Therefore, I don’t see how “Woodward” is helping in burying anything here, particularly with regards to Southerton’s personal interpretation of what is considered “church approved.”

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.

But Woodward is not always so open with his research. Back in 1998 Woodward told me that his group had DNA tested 6500 American Indians from Peru. I could hardly believe it. All other research groups combined at the time had only DNA tested about 2000 American Indians across the entire New World! There can be little doubt that Woodward had been hunting for Lamanite DNA but apologists of course would deny this. Woodward clearly found none because those Peruvian DNA lineages remain unpublished over a decade later.

So, if Woodward participates in a research project using his data, he is criticized for doing so, and if he doesn’t, he is criticized anyway. This seems to be the common theme linking the last two sections presented by Southerton. First he praises Woodward for “burying piles of apologetic trash,” then he criticizes him for hunting Lamanite DNA and not publishing the data he has available! Could there be room for a third explanation? Could it be that Woodward and his colleagues at SMGF are not searching for a genetic fingerprint of Lehi’s descendants in the Americas? Could it be that LDS scholars can actually participate in genuine scientific research without being biased by their personal beliefs? Apparently to some people this last option is mere fantasy!

So, what about the samples described by Woodward in 1998 to Southerton? These are 6500 samples from Peru collected by the late Joel Myres over a period of eight years (Joel passed away in 2001). Most of the samples were typed for a small segment of the mtDNA control region in Woodward’s lab at BYU (which was standard procedure given the cost and technology of 1998) and meticulously recorded in several files. These data were partially published in two research papers and in a scientific poster (references available upon request). Joel was working on four additional manuscripts at the time of his premature death. The files and the 6500 biological specimen are currently in my office and have been shown and shared with a number of researchers that have demonstrated interest in them. This was indeed a remarkable collection of Native American data from a very fascinating geographic area, particularly for 1998, and for sure a greater number of interesting population, medical, and anthropological papers would have been published if Joel was still living. Southerton’s obsession with Lamanite DNA, stands in clear opposition with the anthropological passion Joel had for Peru.

Woodward is now leading an organization (SMGF) that has much more DNA data on American Indians than any other group in the world. His group has undoubtedly DNA tested thousands of individuals from Central America including Mesoamerica. Woodward knows that Mayans, Mesoamericans, Central Americans etc don’t have Israelite ancestors. How long he will hold on to this truth is anyone’s guess.

Woodward has been leading the Sorenson Molecular Genealogy Foundation (SMGF) since 2001. That is where Southerton met him in 2004. To date, SMGF has collected DNA samples and genealogical data from approximately 105,000 volunteer participants representing more than 170 countries. These samples have been sequenced and linked to corresponding family history records and regularly uploaded in a public database on the project website at www.smgf.org. Additionally, these data have been used to produce a number of scientific publications with researchers from both the US and internationally (see a partial list online). Our dataset includes thousands of samples from Africa, Europe, Asia and the Americas. Southerton insists that all these data, the years of work, the resources employed, the collaborations with scientists from other institutions and universities, the publications, etc. have as an ultimate purpose the discovery of Israelite DNA in the Americas and we are failing at it. Further, in Southerton’s viewpoint not only are we failing at what he erroneously insists is our goal, but we are suffering the failure without admitting it.

The ‘truth’ that Israelite DNA (whatever that might be) has not been found in Mesoamerica is public knowledge, a concept that finds Woodward and me with peace of mind. But Southerton is obsessed with the hopeless idea that Woodward and others at SMGF are still searching restlessly for this genetic link so that we can finally reconcile our LDS beliefs and be done with our work!

Perhaps the time has come for Southerton to recognize the considerable contribution that Woodward and the SMGF team have brought both to the scientific and the genealogical community, continuing to pursue the initial mission of building a genetic database to be used as a valuable research and humanitarian tool. This database was voted as one of the best genealogical resources available on the internet (for the years 2007 and 2008) out of more than 300,000 genealogical websites by the popular Family Tree Magazine.

Thankfully there is a public effort in progress that will be looking at large numbers of American Indians from all across the Americas. https://genographic.nationalgeographic.com/genographic/lan/en/about.html
We can expect that data to be published in a timely manner over the next couple of years.

Southerton concludes his remarks with a reference to the National Geographic’s Genographic Project that has been also collecting thousands of DNA samples worldwide with the objective of reconstructing the history of mankind as it developed thousands of years ago. The Genographic Project is definitely praiseworthy and Woodward and colleagues have met in the past with some of its key researchers. As with other groups, we have been exploring opportunities to collaborate and share our data to further scientific knowledge in the field of anthropology, genealogy, and history. The Genographic Project, just like SMGF, has already published a number of important scientific papers on different populations. Contrary to SMGF, they have not yet published a single paper on Native American populations, but we are exploring the possibility to share our data with them as they had some difficulties collecting the necessary samples among indigenous groups from the Western Hemisphere (see for example an article published in the New York Times).

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. Rather than pick and choose from the scientific literature what fits best with his personal interpretation of the history of the Western Hemisphere, Southerton should attempt his own population genetic study to test the hypothesis for “Lamanite DNA.” He will soon “discover” the limitations with designing such a research project, the difficulties in obtaining and processing the necessary ancient and modern DNA samples (including those for comparison), find “reconciliation” between his conclusions with those from other disciplines (such as linguistic, archaeology, anthropology, paleontology, etc.), find a suitable journal with a high impact factor that will publish his work, and be ready to reply to criticisms from other scientists, including geneticists. Through this experiment he might finally realize the complexity of such proposition and understand that others are not actively pursuing a similar objective.

The Book of Mormon withstood 180 years of criticism and it should be evident by now that man-made philosophies alone can neither destroy nor support its truthfulness. The book itself provides a pattern to know if it is from God or from man. 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. The scientific method and the test of faith are two strongly connected dimensions of my existence, working synergistically in providing greater understanding, knowledge, and from time to time even a glimpse into God’s eternal mysteries.

I have always been fascinated with ancient civilizations and I look forward to my involvement in future genetic studies that would contribute to a greater understanding of human history, including that of Native American populations.

-Ugo Perego