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Sunday, 27 July 2014

Response to the claim 1/3 of Native American DNA came from the Middle East - now that would be a Great Surprise

During the last couple of years I have been asked several times to respond to claims by Mormons that recent human genomics research offers support for the belief that Native Americans have Jewish ancestors. The paper causing the excitement was published in the Jan 2013 issue of Natureone of the most prestigious scientific journals. The article in question was written by Raghavan et al. and entitled “Upper Palaeolithic Siberian Genome Reveals Dual Ancestry of Native Americans.”  The paper would have gone unnoticed by Mormons had a National Geographic journalist not sensationalised it with the following hyperbole.

"Great Surprise"—Native Americans Have West Eurasian Origins.

Oldest human genome reveals less of an East Asian ancestry than thought.
Nearly one-third of Native American genes come from west Eurasian people linked to the
 Middle East and Europe, rather than entirely from East Asians as previously thought, according to a newly sequenced genome.

Not surprisingly some Mormons reading these headlines have seized upon this research as conclusive proof that Native Americans have Middle Eastern, and thus potentially Jewish, DNA (1, 2, 3, 4). Even President Newsroom cited Raghavan's research in the Church's official "Book of Mormon and DNA Studies" essay, claiming it challenges previous conclusions and proves the picture isn't clear. But the conclusions being challenged have nothing to do with recent Hebrew migrations. The Raghaven study is focussed on a 25,000-year-old paleolithic DNA sample which tells us something about major human migration events that took place over 20,000 years ago. There is nothing in the Raghavan research that supports the Book of Mormon or challenges the mainstream scientific views about the colonization of the New World. Native Americans are still all descended from ancient Asian ancestors.

The Context of the Research 

Raghavan's research adds another detail to a broad scientific understanding of the timing and route our ancestors took as they colonised the globe. The common ancestors of all humans lived in sub-Saharan Africa. They began migrating "out of Africa" about 80,000 years ago and by about 50,000 years ago had colonized Western Asia, India and Southeast Asia and Australia (Fig.1). Eastern Asia was colonised by people derived from this southern migration event. By about 40,000 years ago people arrived in Europe and Central Asia via a northern route, finally reaching the Americas between 15 and 25,000 years ago.

Fig.1.   Major routes and timing of human colonisation of the world 
(Wellcome Trust,

Scientists have found no evidence that we all descend from a single man and women (Adam and Eve) who lived on the earth about 6,000 years ago. This is simply not what happened. The volumes of evidence in support of the mainstream scientific views are vast and span numerous disciplines. It is the truth and Mormons should face it. When the individual Raghavan's team studied was alive, humans had not even reached the Americas so it is difficult to comprehend how it tells us anything about mythical Jewish migrations in the last few thousand years. 

Fig. 2.  The extent of human colonization of the world 25,000 years ago 
and the location of Raghavan's Siberian sample.

The 2014 Raghavan Study 

Raghavan's team isolated DNA from the bones of a 24,000-year-old individual and sequenced its entire genome. They then examined 156,000 DNA markers (SNPs) to reveal how closely related this individual is to hundreds of other people from contemporary populations (Fig. 3). The more DNA markers two individuals share the more closely related they are. 

Fig. 3.  Heat map of relatedness between the Siberian (MA-1) and individuals from numerous 
geographical locations around the world. The graded heat key on the left indicates the 
degree of relatedness with red indicating high relationship and black low relationship. 
(See Raghavan et al. 2014)

The major finding of the study is that the Siberian individual (MA-1) is not closely related to other Central and Eastern Asians (dark blue dots) and much more closely related to Native Americans (red dots). In addition, this Siberian appears to be related to people now living in Europe and Western Asia (yellow, light blue-green dots). This suggests that this Siberian individual's ancestors had migrated from Western Eurasia into Siberia, but when they arrived they did not mix very much with Asian populations living further east. Consequently, when some of this Siberian's descendants migrated on to the Americas, they didn't carry many DNA markers found in East Asian populations.

Another way of illustrating the results of the study is shown in Fig. 4 below. All Eurasians and Native Americans descend from people who lived in West Asia (near modern day Afghanistan and Pakistan) about 50,000 years ago (see also Fig. 1.). These people carried with them large numbers of DNA markers that can be defined as West Asian. When the ancestors of the Siberians and Europeans/Middle Easterners migrated away from each other, both groups carried the same set of West Asian (blue) DNA markers with them. This is why the Siberian individual carried DNA markers also found in Europeans and Middle Easterners. They shared common ancestors about 15,000 years earlier (50,000 years ago).   

However, once they became separated from each other, each group began to accumulate DNA markers that were unique to each group. This is indicated by the green (Eur/ME) and purple (Siberian) shading on the tree (Fig. 4). Once the Siberian groups encountered East Asians some of their DNA lineages (red) also entered Siberian populations, and some of these DNA markers found their way to the Americas.

Fig. 4.  Origin of DNA markers in Native Americans and some Eurasian populations 
and the approximate timing of their occurrence 


Virtually all Eurasian and New World populations descend from populations that migrated out of Africa and colonised West Asia about 50,000 years ago. Eastern Asia is likely to have been first colonised by populations that split away from a southern migration through India that ended in Australia. The Raghavan study tells us that Siberians are mostly derived from people who migrated into Central Asia via a northern route that resulted in little admixture with Eastern Asian populations. The research paper is focussed on very ancient migrations and tells us nothing about the likelihood or occurrence of recent Jewish migrations to the pre-Columbian New World.

Saturday, 31 May 2014

Keith Crandall's Claims

In 2013 the Foundation for Apologetic Information and Research (FAIR) published a video entitled DNA and the Book of Mormon Explained. The DVD is aimed at defending the flagging Mesoamerican Limited Geography Theory and contains amazing claims by a number of LDS scientists and apologists. The boldest claims in the video are those of Keith Crandall, who joined BYU in 1996 and was baptised in 2004. Crandall was Chair of the BYU Department of Integrative Biology from 2006 until 2012 when he resigned to take up a position at George Washington University in Washington D.C.   

Three times in the video Keith Crandall claims Middle Eastern DNA has been found in the Maya.

28 seconds 
“The most recent DNA evidence that I’ve seen, in terms of peopling of the Americas, shows this Middle Eastern haplotype at greatest frequencies in the Mayan people; so if that’s your perception of where Lehi and company set up shop then the DNA evidence would be consistent with that.”

25 minutes 07 seconds  
"…the fact is, based on this paper by Noah Rosenberg from the University of Michigan that there are in fact Middle Eastern haplotypes in where we as Latter-day Saints would expect them to be; in the Mayan population, as opposed to across all North and South America.  

37 minutes 37 seconds 
"…there is an interesting bit of data that probably only an LDS scientist would pick up…[chuckle]…which shows for the Mayan people and maybe one or two other cultures close geographically to the Yucatan area…there’s actually a nice infusion of Middle Eastern…what they call Middle Eastern genotypes in those populations." 

Crandall also tells viewers the DNA studies are very difficult to understand, and because the critics are not population geneticists like himself, they couldn’t understand the research.

3 minutes 25 seconds 
“The real issue is that these guys don’t actually look at the population genetic literature, they don’t understand the population genetic literature because they’re not population geneticists…so they couldn’t interpret these kinds of data. It's a very tricky kind of literature and a tricky kind of data to wrap your brain around. But it’s pretty patently obvious when you look at their data in this one figure in particular.  If that's what you’re looking for it's there.” 

The truth is these studies are now routine and they are done in hundreds of plant and animal populations. I have been actively engaged in forest tree population genomics research for well over a decade and have published research in the field. I am very familiar with the population genomics research that Keith Crandall cites because we did identical types of analyses in trees. 

A tricky kind of data

When asked for references to his claims Crandall directs people to two published papers, Li et al. 2008 and Rosenberg et al. 2005). In contrast to earlier studies on mitochondrial DNA, this research was focussed on nuclear DNA variation. In the paper by Li et al. (2008) they studied the nuclear DNA of 938 unrelated individuals from 51 global populations at 650,000 common single-nucleotide polymorphisms (SNPs). SNPs are points in the genome where single base differences occur in the human population.

   A SNP is a single-letter change in DNA
  Image courtesy of Lauren Solomon, the Broad Institute

SNPs are part of the natural genetic variation found within all human populations. In Li's research they  showed that global populations can be clearly distinguished on the basis of the hundreds of thousands of SNPs they carry. This is illustrated in the figure below

In the above diagram the information from 650,000 SNPs is condensed into a single thin vertical line for each individual. This line has coloured segments whose length corresponds to the proportion of their DNA derived from particular global regions. Individuals are then grouped with other individuals who share similar DNA. 

If you focus on the data for the Mayan population, which is expanded in the figure below, you will notice that their ancestry also includes DNA likely to have originated in East Asia (orange) and Europe (green). This is the DNA Crandall interprets as "Middle Eastern genotypes". However, this claim is incorrect, and none of the authors of the papers Crandall cites conclude, as he suggested, that Middle Eastern DNA was found in the Maya.

If we look at more Native American populations we see exactly the same sort of thing. European and African admixture is found in many Native American populations (Figure 3). 

The most likely origin for the European DNA in the Maya is post-Columbus admixture. After Columbus, large numbers of Europeans and Africans migrated to the Americas and many of these early colonists intermarried with indigenous Native Americans. Scientists try to avoid including individuals with this mixed ancestry, but it is especially hard to do this in populations that mixed very early with European and African colonizers. 

Post-Columbus admixture confirmed

Admixture in the Maya has since been examined in much more detail in a paper by Hellenthal et al. 2014. Hellenthal tracked the geographical origin of post-Columbian DNA admixture in the Maya to Europe and Africa (see figure below). None of the admixture came from Middle Eastern populations which were included in his study. What is especially telling is the DNA data Hellenthal used was obtained from the same individuals used in the Li et al. (2008) research. This report confirms that Crandall's "Middle Eastern genotypes" are in fact European and African admixture. See my Mesoamerican DNA post for more details on the Hellenthal study.

Figure 4. Geographical origins of Maya DNA. The orange circles represent post-Columbus admixture (European and African) that entered Mayan populations about 350 years ago. The blue circles represent much older ancestral links to other Native American, East and Central Asian populations. The area of each circle reflects the proportion of the donor population's contribution to the DNA of the Maya. Source: Chromosome Painting Collective / February 18, 2014

It appears that in his eagerness to please his FAIR colleagues Keith Crandall saw things in the research that are simply not there. The truth is that scientific research has consistently failed to uncover reliable evidence for the presence of any ancient Hebrews, or their genes, in pre-Columbian Mesoamerica or throughout the New World.

Wednesday, 9 April 2014

My unanswered letter to President Henry B. Eyring in November 1998

10 Stavewood Court
Samford Qld 4520

30th November 1998

Dear Elder Eyring,

I have been a member of the Church for almost thirty years and until recently I served as a Bishop. I am also a molecular biologist currently working at the University of Queensland. I asked to be released soon after I stumbled across some scientific research that greatly concerned me. I did not feel I should be Bishop while I harboured doubts.

The research is in the field of human population genetics. Numerous research groups from around the world are studying the mitochondrial (mt) DNA of humans to determine the relatedness of different populations. An area of particular interest to many scientists is the origin of the American Indians. Several thousand American Indians have been tested from almost 100 populations throughout North, Central and South America and about 99.5% of the individuals tested have mtDNA that is most closely related to the mtDNA of some populations in Eastern Asia. The remaining 0.5% have mtDNA that is either African or European, and is likely to have been introduced after the arrival of Columbus since the frequency of these mtDNA types in populations with virtually no western contact is essentially nil. Lehi and his family would certainly have had mtDNA most closely related to other European populations.

When I first spoke with my Stake Presidency they questioned the validity of the research and asked me to contact Elder Hafen in the Australia/Pacific Area Presidency. He put me in touch with Dr Scott Woodward, Professor of Microbiology at Brigham Young University. I have corresponded with Scott on a number of occasions over the last few months and I have tried to arrange through him an opportunity to talk with you about this issue.

I see a serious conflict between the research and things contained in the Book of Mormon. The introduction to the Book of Mormon states that the Lamanites are the principal ancestors of the American Indians. It states this because it is very clear from the contents of the Book of Mormon. This is what all my friends in the Church believe because all the prophets have declared it; it is scriptural (D&C and Book of Mormon); and it is clearly stated in other Church books such as Jesus the Christ and A Marvellous Work and a Wonder. Scott is the Church authority on this research and he has told me of his deep concern at the conflict between the church position regarding the Lamanites and the data. I think you should speak to Scott very soon about this research. I admire his strength but I don’t think it is right that he should feel alone on this.

I have also become aware of the position of the intellectuals at BYU regarding the historical setting of The Book of Mormon. Some don’t seem to be concerned if all the Lamanites have died out. Several of the scientists I have spoken to rely heavily on the work of John L. Sorenson to support their belief that when Lehi arrived in America there were millions of people already there. These “other” people were incorporated into the Lamanite and Nephite populations, used to help build their temple and fight their wars. I cannot accept this scholarship as it is very clear to me that the Book of Mormon makes no mention of any group of people that didn’t originate in Israel or thereabouts. I am also certain that many Latter-day Saints will struggle with this concept as I have.

My firm testimony of the reality of my Heavenly Father and His Son Jesus Christ remains. My once firm testimony of the truthfulness of the Book of Mormon is shattered. I am concerned that there are many people who may become very distressed about this as my wife and myself have been. I have wanted to speak to an Apostle about this issue for some time. I am certain it is only a matter of time before the wider Church community finds out about the research via the press and many will want answers. I don’t think the answers from BYU will satisfy many. I think it is crucial for the leaders of the Church to know about the situation, because they are ultimately responsible.

I wish I didn’t have to share these things with you. I would be happy to hear from you about this matter. If I am wrong in any way please correct me.

Kind regards

Simon Southerton

Ph (07) 3289 1814

Thursday, 27 February 2014

DNA vs the Mesoamerican Limited Geography

The 20th century saw an explosion in scientific understanding of the prehistoric colonisation of the Americas. There is now broad scientific agreement Native Americans essentially all descend from Siberian big game hunters who walked to the New World over 15,000 years ago. Coincidentally, as the science blossomed, LDS scholars have steadily shrunk claims about the footprint of Book of Mormon peoples. First they acknowledged the presence of "other" native people in the Americas who probably arrived after the Book of Mormon period. They then conceded native people probably arrived first. Recently, apologists have begun incorporating large numbers of native people into the scriptural history. These dwindling apologetic claims have mostly centred on Mesoamerica, in particular the complex civilisations of the Maya. Their populations were large, they lived at the right time, and most importantly, they were the only New World culture with a system of writing. 

Scientists have failed to uncover genetic links to the Middle East among Native Americans in general and Mesoamericans specificallyThe latest whole genome marker studies have revealed in high resolution the complete absence of Semitic DNA in the Maya. At least 99.99% of the pre-Columbian DNA of the Maya is of Siberian origin. The same technology, now accessible from, allows ordinary Mormons to explore their ethnic origins. Many Native American and Polynesian Mormons will soon be wondering where their Semitic DNA has gone. Its time that these futile, damaging and untrue ethnic claims were laid to rest. The Maya, just like other Native Americans, are unrelated to Semitic peoples and their cultures and major civilisations owe nothing to the Old World. 

The shrinking geography 

The most substantive response to my book Losing a Lost Tribe (2004)and the DNA issue in general, is The Book of Mormon and DNA Research (2008), a collection of essays previously published in The Farms Review and The Journal of Book of Mormon Studies. The editor of the volume is non-scientist Daniel Peterson, a once prominent Mesoamerican apologist who is Professor of Islamic Studies and Arabic at Brigham Young University. Peterson was removed from his position as editor of The FARMS Review within the Maxwell Institute in June 2012 and now runs an independent online apologetic journal known as Interpreter

For years Daniel Peterson has been claiming that my criticism of the Book of Mormon, in light of DNA, has relied on a hemispheric interpretation of the book. That is, that the Book of Mormon people arrived in a vacant land and went on to colonise both hemispheres. If Peterson had taken the trouble to read my book he would have found that I spent far more time addressing the limited geography theories than the hemispheric geography. Like most apologists, Peterson has found it much easier to dismiss me based on things I never wrote.

But there is something that I said back in 2006 that Peterson has latched on to and repeated often, including in his introduction to the DNA research essays. He repeats it to make it look like I have carefully avoided addressing the limited geography theory.
"In a very real sense, this debate is (or should be) over. Just two or three years ago, the Signature Books Web page still featured an admission from Simon Southerton, an Australian plant geneticist and former Latter-day Saint who is now the most vocal critic of the Book of Mormon on DNA grounds, that "In 600 BC there were probably several million American Indians living in the Americas. If a small group of Israelites, say less than thirty, entered such a massive native population, it would be very hard to detect their genes today." This confession effectively concedes a major portion of what several in this volume argue regarding Amerindian DNA and the Book of Mormon." 
– Daniel Peterson, Introduction, The Book of Mormon and DNA Research, 2008

Peterson is particularly selective with his quotations. In order to keep up the pretence that I don't address the limited geography (which I did in 2004 and 2006) he has consistently avoided mentioning what I said in the remainder of the paragraph.

"However, such a scenario does not square with what the Book of Mormon plainly states and with what the prophets have taught for 175 years. The Book of Mormon records that soon after their arrival in the Americas, the descendants of Lehi “multiplied exceedingly and spread upon the face of the land” (Jarom 1:8). By about 46 BC, after which time they had joined with the Mulekites, they had multiplied until they “covered the face of the whole earth, from the sea south to the sea north, from the sea west to the sea east (Hel. 3:8). By the time of the final conflagrations around 400 AD, the Israelite populations numbered in the many hundreds of thousands if not millions. There is not a single mention in the text of groups of people living in ancient America, other than the Jaredites, Lehites and Mulekites. All three population groups had very large populations. It is hardly surprising then that Joseph Smith and all other church leaders have regarded Native Americans to be the descendants of the Lamanites. The God speaking to Joseph Smith in 1830-31 referred to the “borders of the Lamanites” when talking about missionaries being sent to teach Native Americans who had been relocated to Missouri (D&C 28: 9; 54: 8)." (

The comment I made in 2006 was correct at the time, given the extent of the mitochondrial and Y-DNA studies that had been carried out. But the statement I made then is now wrong. Whole genome population studies were not feasible in 2006 but that is not the case today. It is now possible to scan entire genomes for hundreds of thousands of DNA markers and to detect traces of historical mixing between ancient populations with incredible clarity. 

DNA vs the Mesoamerican Limited Geography

Peterson summarises the Limited Geography in his inimitable style in the introduction to the DNA essays (see Fig 1).
"The broad consensus of serious Book of Mormon researchers, however, remains today what it has been for many decades: Book of Mormon events took place chiefly within a relatively small area in Mesoamerica. This consensus, reflected in a large number of scholarly publications, is scarcely to be overturned by the appearance of a handful of self-produced books and videos or an engaging fireside speaker or two."
Figure 1. Adapted from John L. Sorenson
An Ancient American Setting for the Book of Mormon p 37.

For decades "serious" or "careful" or "diligent" Book of Mormon researchers have devoted almost all of their attention on Mesoamerica, the relatively small region encompassing southern Mexico and northern Guatemala and Honduras. Numerous scriptural contortions are required to fit this geography with the narrative of the Book of Mormon, which I review in another post on my blog. However, shrinking the geography to Mesoamerica has done nothing to reduce the gulf between mainstream archaeology and the views of LDS scholars. Non-Mormon scholars have found no material evidence of pre-Columbian contact between Mesoamerica and Old World cultures.  

A limited geography isn't the magic cure-all for the DNA problem as the apologists have loudly proclaimed. By shrinking the geography the apologists also shrink the size of the indigenous population the Lehites/Mulekites allegedly entered. They merely increase the proportion of Semitic DNA one would expect to find in the smaller territory. You can't have it both ways. So it is perfectly reasonable to expect genetic studies in Mesoamerica to reveal some evidence of pre-Columbian migrations from the Middle East...if they occurred. 

In this post I focus on DNA research on Mesoamerican populations. There are two key factors to consider when looking for the presence of Semitic DNA. First, what percentage of Mesamerican DNA is not derived from Asians? This is DNA that arose from "admixture" or by mixing with other non-Asian populations. This is the only putative Semitic DNA. Second, what percentage of that admixed DNA is likely to have originated in the Middle East? 

Admixture in Mesoamerican DNA

Mitochondrial DNA (mtDNA) studies have proven to be particularly useful for revealing where pre-Columbian Native American DNA originated. MtDNA genealogies have been preferred to Y-DNA studies for ancestry studies because they largely avoid the confounding admixture due to the male-dominated early colonial parties. Additionally, the people who donated blood for these studies were interviewed to exclude people who are close relatives and those with non-native ancestors. When I published Losing a Lost Tribe in 2004, mtDNA lineages had been determined for just over 500 Central Americans. Just 4 individuals had a mtDNA lineage that didn't belong to the Asian A, B, C, D and X lineage families. Clearly, essentially all natives in Central American populations are descended from Asian ancestors.

In the years since the publication of Losing a Lost Tribe much more research has been published specifically on Mesoamerican populations, which are a subset of Central American populations. We now know the mtDNA lineages of over 1700 Mesoamericans (see table below). The mtDNA evidence suggests that Native Mesoamericans, like all other Native Americans, are largely descended from Asian ancestors. The very small number of non-Asian lineages that are found are almost certainly the result of post-Columbus admixture as they belong to lineage families that are most common in Europe or Africa. 

Only sixteen out of 1727 Mesoamericans (about 0.9%) possess a mtDNA lineage that didn’t originate in Asia. Of the non-Asian lineages, three have been found to be African L lineages, and two match mtDNA lineages found in Spain and Portugal. The remaining 11 lineages are either insufficiently characterised or most likely European lineages as the lineage family they belong to is found at high frequencies in Western European populations. 

The next question is what proportion of admixed DNA present in Mesoamericans could possibly be derived from Middle Eastern populations. 

Origin of Mayan admixture

If we assume 0.9% admixed DNA in Mesoamericans, is it possible to estimate what percentage of this admixed DNA could come from the Middle East? That question was answered in a paper published in the February issue of Science (Hellenthal et al. 2014), which outlines sophisticated methods for identifying evidence of historical interbreeding between populations. In contrast to mtDNA studies, which trace maternal lineages using a few dozen markers, the Hellenthal study examined over 400,000 DNA markers on 22 pairs of chromosomes. This is almost the entire human genome.

When people from different populations interbreed, their offspring's DNA becomes a mixture of each of the "admixing" groups (see Fig 2). As the admixed DNA is passed down the generations the size of the segments (on the chromosomes) become smaller and smaller due to reshuffling of the DNA in each generation. By studying the size of the segments it is possible to estimate how long ago the admixture event occurred. In addition, each population has a distinctive genetic "palette" of chromosomal segments that is essentially unique. By detecting many of these unique population-specific segments in modern populations it is possible to detect where interbreeding populations came from.

Fig 2. Admixture results in reshuffling of donor 
   DNA and a reduction in the size of segments 
derived from each donor.

Hellenthal et al. (2014) have also developed an interactive global map that details the genetic histories of 95 different global populations and allows us to track admixture events in the last 4,000 years. 

Five Native American populations were included in the study, including the Pima from northern Mexico, the Maya from Mesoamerica, and three South American populations. Its a fortunate coincidence that the Maya were included in the study because for several decades LDS Mesoamerican apologists have directly linked the Maya with the Nephite/Lamanite civilisations. Pictures of Mayan ruins are very familiar to Latter-day Saints and commonly appear in church manuals and artwork. This includes a series of twelve paintings by Arnold Friberg included in numerous editions of the Book of Mormon.   

For the Maya, Hellenthal et al. (2014) observed two "donor populations" that participated in an admixture event that occurred in the Maya between 1642CE and 1726CE (see Fig 3). For convenience they called the recent admixture donor "Spanish-like" and the other "Pima-like" to reflect the largest contributing population. The Spanish-like donors (orange circles) largely comprised Western European and African populations. The Pima-like donors (blue circles) largely comprised closely related Native American populations and more distantly related Eurasian populations. No donor DNA originated in any Middle Eastern populations. 
Fig. 3.  Western European and African sources of admixture identified in the Maya. The area of each circle reflects the proportion of the donor population's contribution to admixture in the Maya. Source: Chromosome Painting Collective / February 18, 2014

Interestingly, small proportions of some East Asian populations (Daur and Yakut from northern China and Siberia) appeared as "Spanish-like" recent donors to the Mayan population. If this genuinely reflects post-Columbus admixture it may be linked to the importation of Asian slaves during the early Spanish colonial period. It is also possible that it came across the Bering Strait in the last 4-7 thousand years with the Eskimos. The Apache and Navajo Indians are closely related to Eskimo populations in Canada and Alaska and are known to have migrated as far south as northern Mexico by about 1400CE. More detailed admixture studies on more Native American populations may shed more light on this.  

If we exclude the putative East Asian admixture, the level of admixture in the Maya is about 16% (see Table). The largest proportion of the admixture (88%) is derived from European and North African populations. The remaining 12% of donor DNA among the Maya is derived from Sub-Saharan African populations. It is probable that most of the Africans were imported as slaves by early Spanish colonists to use as labourers in New World plantations. Most of these African slaves were likely to have been purchased in North Africa by the Spanish from Arab slave traders.   

Has Semitic DNA been overlooked?

One thing that makes the detection of Semitic DNA in the Maya particularly straightforward is the fact that Native American and Semitic populations are very distantly related. In fact they have been completely separated from each other for close to 30,000 years. This means that there are many thousands of DNA markers that can be used to distinguish each group. The same is true for African and European populations. We can estimate the maximal proportion of Semitic admixture that may have escaped detection in the admixed DNA. It is somewhere between zero (what was observed) and 0.6 percent; the lowest amount of donor admixture detected in the Maya (the African San Kohomani). We can estimate this by multiplying the observed level of admixture (0.9%) by the lowest detected proportion within that admixture (0.6%). By my calculations the maximal proportion of Semitic DNA that may be present in the Maya, but escaped detection, is 0.009 x 0.0062 = 0.000056, or 0.0056 percent. 

In the past some LDS scholars have attempted to downplay the contribution the Lehites and Mulekites made to Native American populations. Some have argued the two parties may only have comprised 50 people at most and their DNA would be impossible to detect after being diluted in the large native populations. But even if small Semitic groups arrived 3000 years ago their genes would have spread widely through adjacent populations, and it would be almost impossible for their Semitic DNA markers to disappear.    

The very small percentage of admixture that has been detected in Mesoamericans essentially all stems from the very early Spanish colonial period. Admixed DNA has been shown to have entered Maya pedigrees around 1670CE and Semitic DNA has escaped detection. The DNA studies support the conclusion that greater than 99.994% of the DNA of the Maya is derived from Asian migrations over 15,000 years ago.

Contrast this with what the Book of Mormon says about the Semitic people who arrived in the Americas. Their crops thrived and wildlife (cow, ox, ass, horse, goat, wild goat) were found in abundance (1 Ne. 18:24-25). In 588 BC the Lehite populations were prospering “exceedingly” and “multiplying” in the land (2 Ne. 5:13) and by 399 BC they had “multiplied exceedingly, and spread upon the face of the land” (Jarom 1:8). In about 120 BC the “exceedingly numerous” descendants of Mulek (who had also sailed from Israel) joined the Nephites (Omni 1:17). At this time there were so many people in the Book of Mormon civilisations that they couldn’t number them because they had “multiplied exceedingly and waxed great in the land” (Mosiah 2:2). By 46 BC they had spread until they “covered the face of the whole earth, from the sea south to the sea north, from the sea west to the sea east (Hel. 3:8).

Clearly, if the events described in the Book of Mormon 
took place anywhere, they did not take place in Mesoamerica. 

Let's lose the Limited Geography Model

The apologetic response to this devastating evidence will likely be the same as it always has been. Nit-pick the science, reinterpret scripture and demonise the messenger. We only have to look at Peterson (2008) to see this approach on full display. These are some of the pessimistic views Peterson's colleagues held about the power of DNA studies to trace genealogical ties to Israel:

"... given the present state of science, such an experiment is impossible to design and would not be taken seriously by the scientific community." – Michael F. Whiting

"...although it may be possible to recover the genetic signature of a few migrating families from 2,600 years ago, it is not probable. However, the data suggest that there has been a trickle of gene flow to the Americas from non-Asiatic source populations. Though far from verifying or proving the Book of Mormon, these data do allow for the plausibility of its story line." – David A. McClellan 
"... the insurmountable difficulties in identifying the genetic heritage of the chief ancestors of the Lehite peoples." – John M. Butler

"...the chance of scientifically tracing a person's genetic heritage by DNA alone is highly remote." – D. Jeffrey Meldrum and Trent D. Stephens

"Given...the extremely limited picture that contemporary genetics offers of our distant ancestral tree, it is unreasonable to insist that DNA studies alone can prove or disprove an Israelite connection." – Matthew Roper

To be fair to these apologists, their negative (albeit unjustified) comments, were primarily directed at the mtDNA and Y-chromosome research published before 2008. They would have been largely unaware of the whole genome marker research described above. But they will be sorely disappointed if they think sniping about the limited power of DNA technology will buy them much time. For just $99 (Provo, Utah) will now test your autosomal DNA at 700,000 markers, almost twice the number of markers used in the Hellenthal study. will then compare your DNA to samples from around the world to reveal your genetic background and ethnic history. Using the methods published in the Hellenthal study they could tell you exactly where your ancestors lived during the past 4000 years. The power of DNA to reveal human genealogies will be glaringly obvious to thousands of ordinary Mormons, and many Mormons who believe they are descended from the Lamanites are going to be in for a big surprise.

For $99 will generate an estimate of your 
ethnicity based on 700,000 markers

LDS apologists will have few other options but to assume what should be the prophet's role and reinterpret scripture. And based on past performances we are in for some painful scripture twisting in the coming years. All bets will be off. Most of the apologists have grown to adulthood worshipping at the feet of Hugh Nibley, and as far as Nibley is concerned, the Book of Mormon is begging for some serious reading between the lines. 

"The first rule of historical criticism in dealing with the Book of Mormon or any other ancient text is, never oversimplify. For all its simple and straightforward narrative style, this history is packed as few others are with a staggering wealth of detail that completely escapes the casual reader. The whole Book of Mormon is a condensation, and a masterly one; it will take years simply to unravel the thousands of cunning inferences and implications that are wound around its most matter-of-fact statements. Only laziness and vanity lead the student to the early conviction that he has the final answers on what the Book of Mormon contains."
—Hugh Nibley, 1952

Here is a small taste of the "cunning inferences" that Nibley-inspired apologists have already dredged from scripture (see Peterson, 2008).

Everybody is a Lamanite! 
Sorenson and Roper argue that the term Lamanite lost its hereditary connotation and instead refers to a broad societal segment. It could be that the term referred to “all those” who were “led out of other countries by the hand of the Lord” (2 Ne 1:5). They argue that the “expression refers not only to the eventual Gentile (European) settlers of the 16th through 21st century but also to those ancient peoples whom the Lord brought as well.”  Apparently Gentiles who inhabited the Americas before, during, and after the Book of Mormon period are potential Lamanites. So who exactly isn’t a Lamanite?

Lamanites are like leaven
According to Meldrum and Stephens, genetic traces of the House of Israel could be thought of as leaven in bread. Since too much leaven can be tasted in bread and decreases its quality, one should not expect to find genetic markers for the children of Lehi or even for the children of Abraham.

Lamanites are unmentionable
In 1992 Sorenson argued that references to Native Americans are vague because they were outside the focus of the Book of Mormon and because the Nephite record keepers thought them too insignificant to mention. As they were not Lehi’s descendants, they were beneath mention in a book devoted to a favoured branch of the House of Israel. Sorenson speculates that acknowledging them would have been seen by Nephite chroniclers as a waste of space on their precious plates.

Interestingly, Roper (Peterson, 2008) argues the complete opposite of Nibley! He believes that the scriptural evidence for Native American “others” being present when the Lehites arrived, is “abundant,” while evidence against the presence of others is “sparse and unimpressive”. Yet since the book was published virtually all of its readers have missed any reference to these "others". One has to wonder if Roper has even read the Book of Mormon or if he has only searched it for evidence to back up his pre-conceived ideas.

Native Americans didn't have real “nations”
Roper also twists references to an unpopulated New World, “kept from the knowledge of other nations (2 Nephi 1:8–9).
” According to Roper, Indian tribes “did not yet merit the description 'nations.'” Ouch.

Come on guys, enough is enough. Its time to do what is right and let the consequences follow. It is insulting to Native Americans to pretend they were an unmentionable peasant underclass recruited into Lehite societies to build Nephite temples and fight in the Nephite-Lamanite wars. The Maya were already well on the road to developing complex civilisations by 800BCE. Why would they hand over the reigns to a small band of Semites who they vastly outnumbered? Why would they adopt Lehite names, and familial hatreds and carry on a pointless 1000 year-long brotherly feud? Its high time that the honourable and decent thing was done and these futile, damaging and racist arguments were laid to rest. 


Peterson, D (2008) The Book of Mormon and DNA Research: Essays from The FARMS Review and the Journal of Book of Mormon Studies. Neal A. Maxwell Institute for Religious Scholarship.

Sorenson L. John (1992) When Lehi’s Party Arrived in the Land, Did They Find Others There? Journal of Book of Mormon Studies 1:1-34.

References to Mesoamerican mtDNA table
1. Bortolini MC et al. (1998) Diversity in protein, nuclear DNA, and mtDNA in South Amerinds - agreement or discrepancy? Ann. Hum. Gen. 62, 133-145.

2. Gonz├ílez-Oliver A et al. (2001) Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo Am. J Phys. Anthrop 116, 230–235.

3. Kemp, B. M. et al. (2005) An analysis of ancient Aztec mtDNA from Tlatelolco: Pre-Columbian relations and the spread of Uto-Aztecan. Biomolecular Archaeology: Genetic Approaches to the Past, ed Reed DM (Southern Illinois University, Carbondale, IL), pp 22–46.

4. Kemp BM et al.(2010) Evaluating the farming/language dispersal hypothesis with genetic variation exhibited by populations in the Southwest and Mesoamerica. PNAS USA 107, 6759-6764.

5. Lorenz JG & Smith DG (1996). Distribution of four founding MtDNA haplogroups among native North Americans. Am. J Phys. Anthrop. 101, 307-23.

6. Merriwether DA et al. (1994) Genetic variation in the New World – ancient teeth, bone and tissue as sources of DNA. Experientia 50, 592-601.

7. Sandoval K et al. (2009) Linguistic and maternal genetic diversity are not correlated in Native Mexicans. Human Genetics 126, 521–531.

8. Schurr TG et al. (1990) Amerindian mitochondrial DNAs have rare Asian mutations at high frequencies, suggesting they are derived from 4 primary maternal lineages. Am. J Hum. Gen. 46, 613–623.

9. Torroni A et al. (1994a) Mitochondrial DNA and Y chromosome polymorphisms in 4 Native American populations from Southern Mexico. Am. J Hum. Gen. 54, 303-18.

10. Torroni A et al. (1994b). Mitochondrial DNA 'Clock' for the Amerinds and its Implications for Timing Their Entry into North America. PNAS USA 91, 1158-62.

11. Salas A et al. (2009) Mitochondrial echoes of first settlement and genetic continuity in El Salvador. PLoS ONE 4(9): e6882. doi:10.1371/journal.pone.00068

12. Gorostiza et al. (2012) Reconstructing the history of Mesoamerican populations through the study of the mitochondrial DNA control region. PLoS ONE10.1371/journal.pone.0044666

Tuesday, 18 February 2014

DNA Essay Exposes Mormon Doublethink


In late January 2014, the LDS Church responded to challenges to Book of Mormon historicity from DNA science in an essay entitled “Book of Mormon and DNA Studies”. I have previously commented on the scientific content of the DNA essay on my blog, but this essay raises another important issue. In their hour of need church leaders have turned to LDS evolutionary biologists to help defend the historicity of the Book of Mormon. The principal scientist used to defend the Book of Mormon (Ugo Perego), and essentially all of the other LDS scientists who have written DNA apologetics, are committed evolutionary biologists. They accept evolution as a fact. Yet these same evolutionary biologists have been the subject of ridicule by senior church leaders from the pulpit at General Conference. It is also particularly disingenuous to suddenly expect ordinary Mormons to be satisfied with the DNA essay when those very members have been conditioned by their leaders to believe evolution is one of the most evil concepts ever taught. It is not only mixed messages about evolution the essay conveys; the essay reveals that Church leaders have been giving mixed messages about scientific discoveries that challenge other key LDS beliefs.

A Hidden Book of Mormon Geography  

An anonymous Mormon recently commented on my response to the DNA essay.  Brother Anonymous helps us to see why the church is in such a difficult situation with regards the historicity of the Book of Mormon. 

“You do know that plenty of LDS leaders and members believed the hemisphere was inhabited by a lot of other people when the Lehites arrived before your book, right? The church has not "changed it's tune" as a result of any DNA research. The limited geography model, or something like it, was first proposed back in the 1840s. There have been many, many statements from leaders of the church over the last 100 years that state that there were plenty of other people here when Lehi arrived. These authors include Sjodal, Nibley, Sorenson, Smith, Reynolds, and many others, including members of the First Presidency. It is very irritating to see you so consistently act as if your book shook the church from any consistent belief about the Book of Mormon events. I suggest a look into the history of the limited geography model and the research from other sources.” 
– Anonymous 

I can understand Brother Anonymous’ irritation, but since when have Nibley et al. been installed as church leaders? I have never heard the authors he names speaking or being quoted by church leaders in General Conference. Their work is rarely acknowledged in official church literature and they have never published anything on behalf of the church. More importantly, I have heard numerous conference talks by apostles and other church leaders that clearly support a hemispheric view. Why should I take any notice of unofficial writings of Mormon apologists, especially when they don’t square with what church leaders publicly teach? 

The vast majority of ordinary Mormons believe the Book of Mormon is hemispheric, meaning its people arrived in a vacant Promised Land prepared for them and went on to inhabit most of the two continents. That’s why we have the descendants of Lehi mentioned in many dedicatory prayers of temples in Central and South America and Polynesia, some as recently as last year. And it’s why we have thousands of “Lamanites” receiving patriarchal blessings telling them they are members of Lehi’s tribe, Manasseh. Hemispheric views have been widely taught in seminary and institute classes and promoted in the Ensign and New Era for decades. These views are openly taught in Sunday School, Institute of Religion, and LDS Seminary classes and by proselytising missionaries preaching throughout the world. Church leaders have been reluctant or powerless to curtail these beliefs which are woven into the fabric of the faith. From the security of the pulpit at General Conference church leaders have preferred to teach these very traditional views to the broader membership because they know that's what they want to hear. 

LDS scholars, however, believe in a very different Book of Mormon narrative to ordinary Mormons. They have known for decades the hemispheric model is simply not possible given the abundant evidence about America's true founders from a range of disciplines including archaeology, anthropology, linguistics, geology and genetics. Given their impossible situation they have had little choice but to shrink the geographical claims. This is why the limited geography model appeared several decades ago. When the DNA evidence arrived it placed severe limitations on an already strained model, to the point where a vanished model is now the most harmonious explanation for the evidence.
However, church leaders have rarely given clear public support for anything LDS apologists have said. This, I believe, goes to the heart of the problem with the essay. Out of sight of the general membership, the church has supported a small army of LDS scholars whose job has been to fend off attacks on the church and the authenticity of LDS scripture. Church leaders must have known the difficulties these scholars have been dealing with, yet they have rarely acknowledged them publicly. Yet when a member raises difficult questions with their ecclesiastical leaders, they are now invariably referred to these apologists. Consequently, the public words of the leaders do not align well with less publicised views of LDS scholars. The essay exposes a kind of corporate doublethink that has been going on for decades.

Revolving Views on Evolution

The essay takes ordinary Mormons into the scientific world of human molecular biology and population genetics (often referred to as human population genomics). This is a scientific field that is built on a foundation of evolutionary theory. Without the explanatory power of evolutionary theory a population geneticist just sees mountains of meaningless data. However, the Mormon Church has a long history of double-dealing with members about evolution. The overwhelming majority of public statements about evolution by church leaders are highly critical. As recently as 2012, apostles have publicly ridiculed evolutionary biologists at general conference.
“Yet some people erroneously think that these marvellous physical attributes happened by chance or resulted from a big bang somewhere. Ask yourself, ‘Could an explosion in a printing shop produce a dictionary?’ The likelihood is most remote. But if so, it could never heal its own torn pages or reproduce its own newer editions.”
— Apostle Russell Nelson LDS General Conference April 2012

It is inexcusable for a man in Nelson's position, with his level of medical training, to display such ignorance, particularly when his audience is prone to accept every word he says without question. The tradition of mocking evolution by LDS leaders has had a major impact on what most Mormons believe. The Mormon Church is now arguably one of the most anti-life science institutions in the United States. We can see the impact of the Church's doublethink in levels of public acceptance of evolution in Utah. The state ranks 47 out of 50 in the United States, beaten to the bottom by Tennessee and Arkansas. These are statistics that church leaders should view with shame because they are largely responsible for them. To make matters worse, the United States ranks 33 out of 34 western countries (beaten to the bottom by Turkey). 

At the same time as it publicly lampoons evolution, the church funds entire academic departments at BYU whose research is based on evolutionary theory and it pays the salaries of dozens of evolutionary biologists. Perhaps the apostles should get out of their sheltered Church Office Building and see where church money is being spent. For a start they could visit professors and scientists in the College of Life Sciences at BYU. Here, they would meet many members of the church who fully accept evolution. The vast majority of LDS life scientists accept evolution and many apply its principles and concepts in their research. These are Mormons who know enough about the topic to make an informed decision about its validity. In contrast to General Authorities, the statements made by LDS scientists in support of evolution are expressed timidly. The most widely known contemporary LDS defence of evolution was expressed by Henry Eyring, father of current apostle Henry B. Eyring:

  "God has left messages all over in the physical world that scientists have learned to read. These messages are quite clear, well understood, and accepted in science. That is, the theories that the earth is about four and one-half billion years old and that life evolved over the last billion years or so are as well established scientifically as many theories ever are.
  We should keep in mind that scientists are as diligent and truthful as anyone else. Organic evolution is the honest result of capable people trying to explain the evidence to the best of their ability. From my limited study of the subject I would say that the physical evidence supporting the theory is considerable from a scientific viewpoint. 
  In my opinion it would be a very sad mistake if a parent or teacher were to belittle scientists as being wicked charlatans or else fools having been duped by half-baked ideas that gloss over inconsistencies. That isn’t an accurate assessment of the situation, and our children or students will be able to see that when they begin their scientific studies."– Henry Eyring, Reflections of a Scientist 1998

It is a sad mistake that LDS General Authorities continue to belittle evolution and evolutionary biologists. Michael Whiting, a current BYU professor of evolutionary biology and active Mormon gave an excellent lecture to students at BYU where he explains the reasons why he fully accepts evolution. 

“Scientists embrace evolution because it is the central underlying concept in all of biology, and it provides us with an extensive set of tools to address real-world problems such as devising strategies to rescue threatened species and protecting humans against infectious agents. There are few scientific theories that have so successfully summarized such an abundance of observations with such an economy of descriptive processes. This is why evolutionary theory is unabashedly not just good science but great science.”

Towards the end of the seminar Whiting talks about how ordinary Mormons respond when he tells them he studies insect evolution. “How can you do that at BYU? Isn’t evolution diametrically opposed to the teachings of the church?” These Mormons are surprised because the public statements of church leaders don't match the more "private" actions of the church. 

Shades of Young Earth Creationism

The low levels of acceptance of evolution by members of the church are increasingly accompanied by Young Earth Creationist beliefs that earth and all life on Earth were created by direct acts of God between 5,700 and 10,000 years ago. Many believe additional LDS scripture reaffirms these literalist beliefs in a Garden of Eden and a global Flood about 4,500 years ago. Again, members hold these beliefs because church leaders have reinforced them publicly for many years. One particularly egregious example that I was personally troubled by was an Ensign article from 1998 on the Flood and the Tower of Babel which argued that it was a poor understanding of science that led some Mormons to lose their belief in a global flood. The author, Donald Parry, is a BYU Hebrew scholar with no scientific training beyond high school. Parry was roundly criticised by several BYU colleagues for the ignorance displayed in the article. Since then Duane E. Jeffery, a highly respected BYU professor has written a much more scientifically informed article that can be found on page 27 of the October 2004 issue of Sunstone

It is likely that the church, much as it was with its past racial doctrines, is influenced by the culture in which it finds itself. Young Earth Creationism is largely an American "bizarrity" where it claims almost 50% of the population. That is a staggeringly high proportion of the population who hold on to this delusion. In the UK it is less than 15% and in Australia the figure is less than 10%. Levels of Creationist belief in other Western countries hardly merit a mention. 

Most scientists who accept evolution cannot accept that there was a Garden of Eden 6,000 years ago or a global Noahian Flood about 4,500 years ago. These two events require that the human population went through not one, but two excruciatingly narrow population bottlenecks in the last 6 to 10 thousand years. If these events had happened the signs of this have been scrubbed from the genomes of plants and animals. Analysis of human DNA using the most sophisticated population genomics methods available to us tells us no such bottleneck occurred. There is also abundant evidence from numerous other scientific fields that human beings who look just like us have lived on the earth for hundred of thousands of years. The scientific evidence for a global flood is non-existent. If there was a major extinction in the last 5 to 10 thousand years, then the biological and geological evidence has been removed. Many LDS scientists who have pondered these issues have reached the same conclusion. They believe that Noah was a real man, but the Flood was a major localized event for which there is evidence

In contrast to the LDS Church, many mainstream churches are much more accepting of evolution and the sciences in general. Consider the Catholics. The Catholic Church established a Pontifical Academy of Sciences in 1936. 

Casino Pio IV, the home of the Pontifical Academy of Sciences

The academy’s membership includes eighty eminent scientists—many of whom are Nobel laureates—from diverse disciplines, nationalities and religious beliefs. Every other year the academy meets to discuss and debate important issues such as environmental concerns, the implications of genetics, and the origins of life and the galaxies. Each time they meet, the Pope has the undivided attention of some of the world’s brightest scientific minds. Those who attend are expected to display respect for the work of the church, but speakers choose their own topics and debate issues with complete freedom. The Academy almost certainly influenced the Pope's declaration in 1996 that evolution “is more than just a theory." It's hard to imagine the First Presidency and the apostles establishing anything resembling the Pontifical Academy or seeking the advice of scientists, especially non-Mormon ones.

Corporate Doublethink

For many years the scholarship of LDS apologists has invariably been accompanied by a disclaimer that reads something like this.

The views expressed in this article are the views of the author and do not necessarily represent the position of the Maxwell Institute, Brigham Young University, or The Church of Jesus Christ of Latter-day Saints.

The essays on the website do not carry this disclaimer. While unnamed scholars helped write them, and LDS apologists will debate what is and isn't official doctrine until the Second Coming, they have been approved by the highest leaders of the church. In the eyes of most members they represent the official (current) position of the church. 

While many will find the content of the DNA essay reassuring, there are others who are concerned by the further issues the essay raises. In attempting to rescue the Book of Mormon in the face of DNA evidence, the church now appears to be admitting that Native Americans occupied the New World before Adam and Eve arrived, and they avoided any global flood. If the church is now acknowledging Native Americans have lived in the Americas for thousands of years, what is the church's current position on the global Flood? Why, if the leaders were aware of the limited geography for many years, did they publicly continue to promote hemispheric views? Why, if the church employs large numbers of evolutionary biologists has it persisted in ridiculing the theory of evolution and scientists who accept it? The essay will leave many asking why they were taught one thing and now the church is saying something completely different. 

Similar difficult questions could be asked in response to the other essays. The fundamental problem is that leaders of the church have been giving mixed messages to the members. What the church risks losing most with the essays is the trust of its members. Many will be disturbed by the apparent doublethink at the highest levels of the church and will think twice before accepting what the leaders say in the future.