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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. González-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. 

Saturday, 1 February 2014

Tentative Faith Meets Uncompromising Facts: A Response to President Newsroom

In response to the apparent lack of Lamanite DNA in Native Americans and Polynesians, in late January 2014 the LDS Church published an essay entitled “Book of Mormon and DNA Studies”. 

The essay raises many difficult questions for Mormons, not the least being the admission by the church there were many Native Americans in the New World thousands of years before the arrival of Book of Mormon people. Some Mormons may wonder how these people avoided the Flood or how they fit with other Biblical events such as the Tower of Babel. Were they even Pre-Adamites? 

In this post I consider the evolution of Mormon beliefs linked to the ancestry of Book of Mormon people; at some of the science driving that evolution, and then respond more specifically to the DNA essay. 

I grew to adulthood listening to the prophet Spencer W. Kimball, God’s mouthpiece on earth, telling us about millions of living Lamanites. He spoke of how in fulfilment of prophecy the Lamanites were blossoming as a rose in the Latter-days. I probably heard these messages more frequently in Australia because of our proximity to our Polynesian neighbours, many of whom had made Australia their home. According to President Kimball there were 60 million Lamanites scattered across the Americas and throughout the Pacific. Their Lamanite ancestry was acknowledged in dozens of temple dedicatory prayers (and still is), thousands of patriarchal blessings and countless seminary, institute and Sunday School classes. Everyone, including the prophet and apostles, and all my church leaders and friends, knew who the Lamanites were and where they lived. 
"I saw a striking contrast in the progress of the Indian people today.... The day of the Lamanites is nigh. For years they have been growing delightsome, and they are now becoming white and delightsome, as they were promised. In this picture of the twenty Lamanite missionaries, fifteen of the twenty were as light as Anglos, five were darker but equally delightsome The children in the home placement program in Utah are often lighter than their brothers and sisters in the hogans on the reservation. At one meeting a father and mother and their sixteen-year-old daughter were present, the little member girl--sixteen--sitting between the dark father and mother, and it was evident she was several shades lighter than her parents--on the same reservation, in the same hogan, subject to the same sun and wind and weather....These young members of the Church are changing to whiteness and to delightsomeness."
-- Spencer W. Kimball, LDS General Conference, 1960 
"Not until the revelations of Joseph Smith, bringing forth the Book of Mormon, did any one know of these migrants. It was not known before, but now the question is fully answered. Now the Lamanites number about sixty million; they are in all of the states of America from Tierra del Fuego all the way up to Point Barrows, and they are in nearly all the islands of the sea from Hawaii south to southern New Zealand. The Church is deeply interested in all Lamanites because of these revelations and because of this great Book of Mormon, their history that was written on plates of gold and deposited in the hill. The translation by the Prophet Joseph Smith revealed a running history for one thousand years-six hundred years before Christ until four hundred after Christ-a history of these great people who occupied this land for that thousand years. Then for the next fourteen hundred years, they lost much of their high culture. The descendants of this mighty people were called Indians by Columbus in 1492 when he found them here." 
-- Spencer W. Kimball, "Of Royal Blood," Ensign, July 1971

What a difference DNA makes. 

We are now informed in an official church essay on the website “nothing is known about the DNA of Book of Mormon peoples.” In the essay it is acknowledged that scientists believe the overwhelming majority of Native American DNA is derived from Asia but we are told the DNA data is “tentative”. But it is LDS beliefs about Native American ancestry that have proven to be tentative. For almost 180 years LDS leaders have taught that Native Americans and Polynesians are the descendants of Book of Mormon peoples. However, most LDS apologists began shrinking the claims and aligned the Book of Mormon civilizations with the Olmec and Maya in the region of Mesoamerica. Now the Lamanite presence has contracted to the point that it has essentially vanished. 

Mainstream scientific views

Before responding to some of the claims made in the DNA essay I'd like to very briefly review some of the understanding that decades of thorough scientific research has uncovered about the origins of Native Americans. In sharp contrast to changing LDS views about the colonization of the Americas, there has been a century-long scientific consensus about where the ancestors of Native Americans came from and approximately when they arrived in the New World. DNA is not significantly altering the consensus. It is just helping to refine our understanding. 

Virtually all non-Mormon scientists accept that the first Americans entered what is now Alaska about 18,000 years ago, near the peak of the last ice age. At that time sea levels were 130m lower because rainfall at higher latitudes became trapped in glaciers and didn’t return to the sea. Lowered sea levels exposed a wide flat land known as Beringia, where the Bering Strait is now situated. This land was cold tundra but it sustained roaming herds of megafauna. At that time migration south from Alaska into North America was blocked by large ice sheets that covered much of what is now Canada.

About 14,000 years ago an ice-free corridor opened up allowing migration into North America. The most compelling evidence for this migration is the discovery of thousands of fluted spear points manufactured by Native Americans belonging to the Clovis culture. Clovis points have been found in over 1,500 sites across most of the United States. Organic remains at many of the Clovis sites have been carbon-dated to about 13,500 years before present.  

Locations where 13,500-year-old Clovis points have been found in the United States and Canada. Source: The Paleoindian Database of the Americas.

There is also growing evidence that Native Americans migrated south via the Pacific coast. This colonization is thought to have occurred about 15,000 years ago. Finally, there has been fairly continuous migration back and forth across the Bering Strait by Eskimo groups during the last 7,000 years. No scientist outside of Mormon culture believes that Middle Eastern populations migrated to the Americas prior to Columbus.

The two major routes of migration into the Americas. Note: Eskimos have migrated all over sub-Arctic regions over the last 7-8000 years. These migrations are rarely mentioned in the broader debate but they are relevant.

Some responses to President Newsroom
The conclusions of genetics, like those of any science, are tentative, and much work remains to be done to fully understand the origins of the native populations of the Americas.


The DNA science is neither tentative or inconclusive. It is consistent with scientific conclusions about Native American origins from numerous other scientific disciplines. While nothing is known about the DNA of Book of Mormon peoples, a lot is known about the DNA of Native Americans.
Scientists theorize that in an era predating Book of Mormon accounts, a relatively small group of people migrated from northeast Asia to the Americas by way of a land bridge that connected Siberia to Alaska. These people, scientists say, spread rapidly to fill North and South America and were likely the primary ancestors of modern American Indians.


Native Americans have occupied the New World for at least ten thousand years before the Book of Mormon period. For over a century mainstream archaeologists, geneticists and anthropologists studying Native Americans have believed their ancestors migrated from Asia across dry land (Beringia) exposed during the last ice age. The DNA evidence suggests a slightly earlier date of arrival in North America about 16,000 years ago.
The Book of Mormon itself, however, does not claim that the peoples it describes were either the predominant or the exclusive inhabitants of the lands they occupied. In fact, cultural and demographic clues in its text hint at the presence of other groups.


The claim in the first sentence is contradicted by the book itself.
2 Nephi 1:8-9 "And behold, it is wisdom that this land should be kept as yet from the knowledge of other nations; for behold, many nations would overrun the land, that there would be no place for an inheritance. Wherefore, I, Lehi, have obtained a promise, that inasmuch as those whom the Lord God shall bring out of the land of Jerusalem shall keep his commandments, they shall prosper upon the face of this land; and they shall be kept from all other nations, that they may possess this land unto themselves. And if it so be that they shall keep his commandments they shall be blessed upon the face of this land, and there shall be none to molest them, nor to take away the land of their inheritance; and they shall dwell safely forever."

The essay claims there are cultural and demographic "clues" in the text that support the existence of other people. Scriptures like those above, and many others in the Book of Mormon and D&C, need to be overlooked in favour of clues. There are also numerous statements by prophets and apostles which depict the New World as an empty land prior to the arrival of the Jaredites and Lehites. These are the words of 
Jeffrey R. Holland, a current apostle. 

“Holy scripture records that “after the waters had receded from off the face of this land it became a choice land above all other lands, a chosen land of the Lord; wherefore the Lord would have that all men should serve him who dwell upon the face thereof.” (Ether 13:2.) 
Such a special place needed now to be kept apart from other regions, free from the indiscriminate traveler as well as the soldier of fortune. To guarantee such sanctity the very surface of the earth was rent. In response to God’s decree, the great continents separated and the ocean rushed in to surround them. The promised place was set apart. Without habitation it waited for the fulfilment of God’s special purposes. 
With care and selectivity, the Lord began almost at once to repeople the promised land. The Jaredites came first, with stories of the great flood fresh in their memories and the Lord’s solemn declaration ringing in their ears: “Whoso should possess this land of promise, from that time henceforth and forever, should serve him, the true and only God, or they should be swept off when the fullness of his wrath should come upon them.” (Ether 2:8.) 
A Promised Land - Jeffrey R. Holland, The Ensign, June 1976
At the April 1929 general conference, President Anthony W. Ivins of the First Presidency cautioned: “We must be careful in the conclusions that we reach. The Book of Mormon … does not tell us that there was no one here before them [the peoples it describes]. It does not tell us that people did not come after.”

It is hard to take seriously the words of a member of the First Presidency from 85 years ago while the words of many, more recent, prophets are ringing in our ears. If current church leaders believe the words of President Ivins then they need to be repeated in an equally public forum today.

It also appears that President Ivin's words have been taken out of context. Bear in mind that Mormons believe that the Garden of Eden was in Missouri and that prior to the global Flood all continents were joined together. It's very likely that the non-Book of Mormon people Ivin's had in mind were people who arrived after the close of the Book of Mormon period. 
Here is the full quote of President Ivin's words.  

"We must be careful in the conclusions that we reach. The Book of Mormon teaches the history of three distinct peoples, or two people and three different colonies of people, who came from the old world to this continent. It does not tell us that there was no one here before them. It does not tell us that people did not come after. And so if discoveries are made which suggest differences in race origins, it can very easily be accounted for, and reasonably, for we do believe that other people came to this continent. A thousand years had elapsed from the time the Book of Mormon closed until the discovery of America, and we know that other people came to America during that period."
At the present time, scientific consensus holds that the vast majority of Native Americans belong to sub-branches of the Y-chromosome haplogroups C and Q and the mitochondrial DNA haplogroups A, B, C, D, and X, all of which are predominantly East Asian. But the picture is not entirely clear. Continuing studies provide new insights, and some challenge previous conclusions. For example, a 2013 study states that as much as one-third of Native American DNA originated anciently in Europe or West Asia and was likely introduced into the gene pool before the earliest migration to the Americas. This study paints a more complex picture than is suggested by the prevailing opinion that all Native American DNA is essentially East Asian.

This is a very confusing paragraph. The authors jump from talking about Native American  mitochondrial and Y-chromosome DNA (~100% Asian origin) to a 2013 study on autosomal DNA of a 24,000-year-old Siberian who shared one-third of his autosomal DNA mutations with European or West Asian populations. Many readers could easily conclude that the earlier mitochondrial and Y-chromosome studies were faulty. Conflating the two types of analysis is confusing.

DNA mutations that can be used to distinguish Native American DNA arose after their ancestors separated from their Asian neighbours about 18,000 years ago. They are new mutations that occurred on the way to, or in the New World. The Siberian study is about mutations that arose before 24,000 years ago. They are earlier mutations that occurred during the 10s of thousands of years that humans spent migrating across Eurasia before reaching Siberia. 

It's a bit like looking at a 1975 Ford and concluding it is a Hyundai because it has 4 wheels. The idea to use four wheels arose early in the evolution of the car and most cars around the world now have 4 wheels. But just because two different cars have four wheels doesn't mean they are built in the same factory or country. Yes, Native American autosomal DNA carries vast numbers of mutations that arose 20,000 to 50,000 years ago, when their ancestors were in Eurasia. These mutations are shared by numerous populations spread over vast areas because humans have migrated over vast areas of the globe. Mutations that arose 5,000 or 15,000 years ago have a more restricted distribution, exclusively in the Americas. But these are the most informative mutations for ancestry studies.

The 2013 study is not relevant to the conclusions derived from mitochondrial or Y-chromosome DNA. Its about an individual who lived 24,000 years ago, long before the first Native America set foot in the Americas. If you are interested in a more detailed discussion of the 2013 study (by Raghavan and others) feel free to visit my blog post "The Great DNA Surprise".

Also, I hate to be picky but Native American DNA is essentially Siberian, not East Asian. East Asia includes the Chinese, Japanese and Koreans who are not direct ancestors of Native Americans.
While Near Eastern DNA markers do exist in the DNA of modern native populations, it is difficult to determine whether they are the result of migrations that predated Columbus, such as those described in the Book of Mormon, or whether they stem from genetic mixing that occurred after the European conquest. This is due in part to the fact that the “molecular clock” used by scientists to date the appearance of genetic markers is not always accurate enough to pinpoint the timing of migrations that occurred as recently as a few hundred or even a few thousand years ago.

In the early years of dating using DNA there was considerable debate about which method was the most accurate. The debate has been resolved for about the last 15 years but LDS apologists, like Rodney Meldrum, insists on referring to papers from 1997, the peak of the debate, and using it as evidence that dating is unreliable.

The “Near Eastern DNA” being referred to here is the Native American mitochondrial X lineage. This lineage is not derived from Israel. LDS scientist Ugo Perego has dated Native American X lineages using robust modern methods, and he concluded it arrived in the New World about 15,000 years ago, essentially the same time as the A, B, C and D lineages arrived. 
The X lineage has recently been found in Kennewick Man, a 9,000-year-old skeleton discovered on the banks of the Columbia River in Washington. For more information see my Kennewick Man blog post).
Scientists do not rule out the possibility of additional, small-scale migrations to the Americas. For example, a 2010 genetic analysis of a well-preserved 4,000-year-old Paleo-Eskimo in Greenland led scientists to hypothesize that a group of people besides those from East Asia had migrated to the Americas.

Commenting on this study, population geneticist Marcus Feldman of Stanford University said: “Models that suggest a single one-time migration are generally regarded as idealized systems. … There may have been small amounts of migrations going on for millennia.”

Scientists are well aware that many small-scale migrations have occurred among sub-Arctic populations. The Bering Strait is not a complete barrier to migration by sea kayak and Eskimo/Inuit groups have crossed in both directions over recent millenia. This is what the 2010 Paleo-Eskimo paper was about and that is the context of Marcus Feldman’s comments. He wasn’t talking about Amerindian migrations into North and South America.

Why can't we detect Book of Mormon DNA?
At about this point in the essay the marbles start appearing. Having admitted that there is a scientific consensus that essentially all Native American DNA is derived from Asia, the authors give some technical explanations for why DNA could disappear or be difficult to detect. We are introduced to the well established principle in population genetics of genetic drift which includes founder effect and bottleneck effect. These are used to suggest that it may be too difficult to detect small populations of Book of Mormon people using population genetics because:

1. We don't know what the founding DNA (Lehite, Jaredite) looks like

2. It entered large populations and got diluted away
3. It was unlucky DNA and faired worse in New World pandemics
One reason it is difficult to use DNA evidence to draw definite conclusions about Book of Mormon peoples is that nothing is known about the DNA that Lehi, Sariah, Ishmael, and others brought to the Americas.

The problem is not knowing what Lehite DNA looked like. The problem is
 Native American DNA is over 99.5% Asian and it arrived in the Americas in excess of 15,000 years ago. The only non-Asian DNA (0.5%) is either western European or African and derived from post-Columbus admixture. It is also untrue to say we know nothing about the likely DNA lineages of the Book of Mormon founders. They came from the Middle East and most were genealogically Hebrew. They would have carried Middle Eastern or Hebrew DNA lineages, which are extensively characterised.
In addition to the catastrophic war at the end of the Book of Mormon, the European conquest of the Americas in the 15th and 16th centuries touched off just such a cataclysmic chain of events. As a result of war and the spread of disease, many Native American groups experienced devastating population losses. One molecular anthropologist observed that the conquest “squeezed the entire Amerindian population through a genetic bottleneck.” He concluded, “This population reduction has forever altered the genetics of the surviving groups, thus complicating any attempts at reconstructing the pre-Columbian genetic structure of most New World groups.”

Yes, the genetic landscape has changed but why would the descendants of Middle Eastern Jews die out at a vastly higher rate than Native Americans? Over a thousand maternal DNA lineages have been determined from pre-Columbian ancient remains. They all belong to one of the five major mitochondrial DNA haplogroups (A, B, C, D, and X), all of which are derived from Asia. No Middle Eastern DNA has been found.

It could be argued that the descendants of Book of Mormon people would be expected to carry more resistance to Old World infectious diseases because their ancestors had lived with these diseases for thousands of years. Smallpox, one of the major killers in Post-Columbus pandemics, has been present in the Old World for as long as 10,000 years. Middle Eastern populations would be expected to carry higher proportions of alleles conferring resistance to the disease.
Moreover, the shuffling and recombination of autosomal DNA from generation to generation produces new combinations of markers in which the predominant genetic signal comes from the larger original population. This can make the combinations of markers characteristic of the smaller group so diluted that they cannot be reliably identified.

If Middle Eastern DNA entered Native American populations in the last 3 thousand years there is no reason to believe it would disappear completely. Scientists recently discovered that people in non-African populations have a small percentage (1-4%) of Neanderthal DNA in their genome. Then more recently it was discovered that Melanesians and Australian Aboriginals carry a small proportion of DNA from Denisovans, a related hominid species that lived in Asia. These small proportions of “foreign” DNA entered our lineage 30-40 thousand years ago but that DNA was very easy to detect. A simple DNA test can reveal exactly how much Neanderthal or Denisovan DNA we each carry. A similar test could reveal pre-Columbian Jewish DNA in Native Americans but none has been found.
Genetic profiles may be entirely lost, and combinations that once existed may become so diluted that they are difficult to detect. Thus, portions of a population may in fact be related genealogically to an individual or group but not have DNA that can be identified as belonging to those ancestors. In other words, Native Americans whose ancestors include Book of Mormon peoples may not be able to confirm that relationship using their DNA.

This is confusing. If people are genealogically related they must share genetic material, especially autosomal DNA.
As Elder Dallin H. Oaks of the Quorum of the Twelve Apostles observed, “It is our position that secular evidence can neither prove nor disprove the authenticity of the Book of Mormon.”

Then why the essay?

The Book of Mormon makes scientifically testable claims that have continuously been shown to have no basis in fact. The DNA evidence has exposed the true ancestry of Native Americans with amazing clarity and also, unfortunately for the LDS Church, the dubious provenance of the Book of Mormon.