The Book of Mormon has traditionally been presented as a historical account of the first inhabitants of the Americas – “the principle ancestors of the Native Americans”. This interpretation, still dominant among members of the LDS Church, remained in the introduction to the Book of Mormon until recently. It is commonly referred to as the hemispheric geography model because it locates the events and descendants of the Book of Mormon peoples across the entire western hemisphere, including North, Central, and South America.
According to the text, the populations grew rapidly to ‘cover the face of the whole earth, from the sea south to the sea north, from the sea west to the sea east’ (Helaman 3: 8), and the voyaging Israelites arrived in a land ‘kept as yet from the knowledge of other nations’ (2 Nephi 1: 8-9). Joseph Smith himself declared the whereabouts of the Lamanites before commissioning missionaries to preach to them. “And thus you shall take your journey into the regions westward, unto the land of Missouri, unto the borders of the Lamanites” (D&C 54: 8, see also D&C 28:8-9; 30:6; 32: 2).
Joseph Smith routinely used the term ‘Lamanite’ to describe North American indigenous peoples. He said, “The Book of Mormon is a record of the forefathers of our western tribes of Indians; …By it we learn that our western tribes of Indians are descendants from that Joseph who was sold into Egypt, and the land of America is a promised land unto them, and unto it all the tribes of Israel will come, with as many of the Gentiles as shall comply with the requisitions of the new covenant. 
See Archaeology and the Book of Mormon for a review of LDS claims and an exploration of evidence we should expect to find.
THE DNA CHALLENGE
Comprehensive DNA surveys of approaching 20,000 Native Americans and Polynesians have failed to find any plausible scientific evidence of pre-Columbian Hebrew migrations into the New World or Pacific Islands. In fact, scientists find such claims highly implausible. Dr. David Glenn Smith, a molecular anthropologist at U.C. Davis, pointed out that “Genetic research, particularly that using mitochondrial and Y chromosome markers, provide quite emphatic refutation of any such relationship between Jews and Native Americans.” 
In fact, scientists studying Native American populations were not as surprised by the DNA research as Latter-Day Saints might expect. That’s because there are no apparent cultural connection between them and ancient Hebrew peoples. For over a century, the consensus view among archaeologists, geneticists, anthropologists, geologists and biologists is that the Americas were first populated by migrants from the environs of Lake Baikal in southern Siberia who crossed an Ice Age-exposed Beringian land bridge into the New World 14-20,000 years ago.
While evidence against the Book of Mormon and its miraculous origins has been steadily accumulating for more than a century, modern DNA techniques provide new and irrefutable evidence to further bolster decades of anthropology, archaeology and linguistic study. It is difficult for anyone who studies archeology at any level to take seriously the idea that the Book of Mormon has any historical validity.
- Scientific American: Ancient Genome Suggests Native Americans Really Did Descend from the First Americans
- Lamanites No More: DNA and Lost Ties to Father Lehi, Joel Groat
Human DNA Geneology
DNA is a long chain-like molecule comprised of four repeating units called bases, represented by the letter A, C, G and T. Genetic, or hereditary information, is stored in the order of these bases and is passed from generation to generation in all living things. Human genealogy is made possible because DNA accumulates mutations, commonly referred to as ‘markers’, and does so at a relatively stable rate over long periods of time. While rare, these markers allow construction of DNA pedigrees by grouping DNA lineages with common markers in their DNA sequences.
The best scientists in the world have been at work tracing the ways in which ancient humans populated the world from Africa spreading out to Europe, Asia, and then to the Americas. It is most likely that any Middle-Eastern DNA to be found in the New World came from ancestors of the ancient Asian peoples who migrated here through Siberia. To argue that there are populations that are no longer extant in the remaining DNA would be to argue that there are no descendants of those who would have left the DNA. It seems an odd thing for the LDS Church to argue that the DNA proves that there are no remaining descendants of those Lamanites for whom The Book of Mormon is supposedly written.
Mitochondrial DNA Studies
The first human molecular genealogists focused their attention on mitochondrial DNA, a small DNA molecule (about 16,500 bases) with a simple pattern of inheritance. Mitochondrial DNA is passed intact from mothers to their offspring and the DNA it contains can be used to construct maternal ancestries. DNA markers can be used to define specific DNA lineage families (haplogroups), and family trees of related haplogroups have now been constructed for humans. Human mitochondrial lineages can be classified into one of about 25 large haplogroups on the basis of a few dozen markers. Each haplogroupis denoted by a letter of the alphabet.
Individuals from related populations generally share common DNA haplogroups. The number of different markers observed between two haplogroups also gives molecular anthropologists an estimate of how long ago these lineages shared a common ancestor. The distribution of haplogroups throughout the world, and the time depths to common ancestral lineages, provides a reliable tool for scientists to track prehistoric paths of human migration across the globe.
Mitochondrial DNA lineages for 15,555 American Indians from over 200 widely dispersed tribes across the New World have been published over the last 30 years. Approximately 99 percent of these lineages fall into one of five haplogroups: A, B, C, D and X (Table 1). The X haplogroup also occurs in Europe, North Africa and the Middle East but the X lineage family is very old (~30,000 years) and Old World and Native American X lineages are distantly related.
Maternal DNA Lineage in the New World† (number of individuals) † This table includes data on 7,317 individuals published by Simon G. Southerton. 
Asian mitochondrial lineages ancestral to Amerindian lineages occur at their highest frequency in Siberian populations that trace their migratory history to the region surrounding Lake Baikal. The most recent estimates of the time when American peoples shared a common ancestor suggest that the initial migration to the Americas occurred 15-20,000 years ago. This timeframe is consistent with archaeological evidence of the earliest appearance of human habitation in the New World.
Whole Genome Studies
Major advances in DNA technology since the turn of the century have allowed molecular anthropologists to access the vast reserves of genealogical information in the entire human genome (3 billion bases). It is now feasible to screen over 500,000 genomic markers, many of which are unique to specific populations. For example, there are 30-50,000 markers found only in Native American populations and a similar number specific to Middle Eastern populations. This is the same technology used by human genealogy companies like Ancestry DNA and Family Tree DNA to tell us where our ancestors came from, and to find murderers whose DNA is known by their genetic links to family members. No serious scientist or even amateur disputes these genetic facts.
Another powerful feature of the whole genome technology is that it can reveal when different populations began mixing with each other anciently. Each chromosome we pass to our children contains fragments from each of our parents’ corresponding chromosome. The generational process of rearranging chromosomal segments, called recombination, reduces the length of intact chromosomal “tracts” derived from a particular parent in each following generation. The reduction in the length of intact chromosomal tracts can be used to estimate when Native Americans first mixed with other global populations. Shorter tract lengths mean the first admixture event took place a long time ago and longer tract lengths indicate recent admixture.
A large whole genome study of Native Americans was published in December 2018.  The authors screened each of 6,589 Latin Americans derived from 5 countries for >500,000 DNA markers. They detected lots of African and Iberian (Portugal and Spain) admixture: Brazil (83%), Chile (46%), Colombia (60%), Mexico (37%) and Peru (30%). Within this admixture they detected small amounts of Middle Eastern ancestry: Brazil (1%), Chile (4%), Colombia (3%), Mexico (3%) and Peru (2%).
To determine when the admixture arrived in the New World, the authors carried out chromosomal tract length analysis. They found that the very small amount of Middle Eastern DNA in these groups had arrived at the same time as DNA from Portugal and Spain; about 10 generations ago. The Middle Eastern DNA is most likely to have been carried by Iberian Conversos. These are Jewish people who “converted” to Christianity in Spain and Portugal in the 14th and 15th century to avoid persecution or execution. This large Latin American study is effectively a high-resolution genomic investigation of the 1% of non-Asian DNA detected in Native Americans. As with all other genomic studies, it failed to detect any pre-Columbian Middle Eastern (or Hebrew) DNA in Native Americans.
To further illustrate how DNA studies are proving the precise ancestors of other groups of people, let us turn to two specific case studies.
Study 1 – The Lemba
The Lemba are a group of 80,000 South Africans who claim Jewish heritage, practice many Jewish rituals, and claimed to be descended from a small group of Middle Eastern men (perhaps as small as seven) who migrated to South East Africa 2,500 years ago and intermarried with the local women. Modern science backs their claim.
More than 50% of Lemba Y-chromosomes have been identified West Asian in origin. The DNA evidence suggests a migration date between 2,670 and 3,200 years ago, not far from their claim of 2,500. A study in 2000 found that a substantial number of Lemba men carry a particular haplotype of the Y-chromosome known as the Cohen modal haplotype (CMH), as well as Y-DNA Haplogroup J found among some Jews, but also in other populations across the Middle East and Arabia. However, the genetic studies have found no Semitic female contribution to the Lemba gene pool. This indicates that Israelite men migrated to Africa in ancient times and took wives from among the local people while settling in new communities, just as their origin story suggests.
If The Book of Mormon were a historical record, one would expect that, like the Lemba, there would be DNA evidence to show that some remaining group of Amerindians could trace their DNA back to Jewish origins. It is nearly impossible to see how the trace of such ancestry could be erased, particularly when compared to such a small group in Africa, where it is so clearly provable. Added to this is the problem of no preservation of Jewish culture, ritual, or language in the Americas, not at all like the Lemba.
Study 2 – New Founders
Like the Lemba, clear evidence has been found for the sharing of ancient genomic DNA between Amazonians and native people from Australia, the Andaman Islands and Papua New Guinea. This discovery sheds new light on earlier observations that many prehistoric South American skulls exhibit Australoid features, precisely because they had a shared group of ancestors whose descendants migrated both to America and to Australia.  Native Americans also share ancestry with Denisovans, an archaic human species that lived in Siberia over 100,000 years ago. Both the Australoid and Denisovan genes are believed to have accompanied the original founders as they entered the New World over 15,000 years ago. 
THE CHURCH’S RESPONSE
As evidence steadily accumulates against the Book of Mormon as a historical record of the Hebrew ancestors of the Amerindians, the LDS Church has been compelled to take steps to address the seriousness of the problem.
One of its first responses, which passed unannounced, was a one-word change to the Introduction to the Book of Mormon in 2006. Once “principal” ancestors, the Lamanites were quietly relegated to being “among” the ancestors of the American Indians.
This change appears particularly problematic, as the Book of Mormon itself clarifies the lands to be uninhabited except for Jaredites, Mulek and the family of Lehi. The land was “…preserved for a righteous people,” explicitly “kept from the knowledge of other nations” (Ether 2:7 / 2 Nephi 1:5-9). The Jaredites went “…into that quarter where there never had man been.” The urgent need to bring Ishmael’s daughters on the voyage further reinforces the understanding that the clan would encounter no others upon reaching the Promised Land.
The subtle shift also contradicts prior instruction from multiple general authorities and prophets, such as when Elder Jeffrey Holland reiterated, “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 fulfillment of God’s special purposes.” 
Unable to locate tangible support for the expansive geography described in Book of Mormon and reiterated by the prophets, Church-sponsored apologists began advancing restricted models of early Israelite settlement in the Americas. The limited geography theory, which posits that Book of Mormon events took place in Mesoamerica, was designed to shield the narrative from scientific criticism. This model limits the events depicted in the Book of Mormon to land immediately adjacent to the Isthmus of Tehuantepec (narrow neck of land) in southern Mexico and argues the Jaredites are the Olmec civilization while the Nephite/Lamanites the Mayan civilization—all with no scientific backing.
Then there are those like Rodney Meldrum, a salesman and Creationist with no scientific training, who back a “Heartland” theory that claims all Book of Mormon events took place in North America. Meldrum has been a particularly vocal critic of the BYU-sponsored Mesoamerican Geography, who eventually returned fire with a scorching dismissal of his ‘pseudoscientific snake oil’.  Ordinary members, hungry for evidence to bolster their faith in the post DNA era, are inevitably drawn to these false and misleading narratives.
In 2014 the Church quietly published Book of Mormon and DNA Studies, an essay which distills an avalanche of Mormon apologetics (published solely in LDS journals), and attempts to address population genetics. While the Church has pinned its hopes on the work of limited geography apologetics, the essay makes no mention of geography at all. The essay demotes Book of Mormon peoples to minor players in the continent’s archaeological history, rendering them non-contributors to the continent’s gene pool.
The most striking feature of the LDS Church’s DNA essay is its admission that “nothing is known about the DNA of Book of Mormon peoples” and the vast majority of Native Americans carry DNA that appears to have come from East Asia. To distract people from this dramatic retreat, considerable effort is devoted to speculating why Lehite DNA has not been found. Numerous ways Lehite DNA could have been missed or gone extinct are discussed at length (bottleneck and founder effect, genetic drift, extinction, dilution, etc.). The Church even posits that perhaps Lehite DNA did not resemble the DNA of people in the Middle East. Given that Lehi was of Jewish ancestry (see Alma 10: 3) and Jews are closely related to neighboring Middle Eastern people, this argument is implausible.
The failure of the essay to address the fact that the continent was colonized over 15,000 year ago invites confusion. After stating virtually all Native American DNA is derived from East Asia, the Church’s essay implies this fact may change by citing a study that suggests one-third of their DNA may be derived from Europe or West Asia. Yet the study cited was probing the genetic makeup of the original founders who left Siberia over 20,000 years ago (see www.nature.com/articles/nature12736). The DNA analysis was performed on bones from Siberia that were 24,000 years old. By not disclosing the true entry time, LDS readers may assume this European DNA may have entered the Americas with the Jaredites after a purported global flood about 4,500 years ago. The Church appears to resort to subterfuge because even it knows the overwhelming Asian ancestry of Native Americans is an unchangeable fact.
To give its readers the impression scientists believe there were numerous small-scale migrations to the Americas, the Church cites a study of Paleo-Eskimos from Greenland. The Church does not disclose that it is well known among anthropologists that indigenous peoples of the Arctic (Eskimos) have moved freely over thousands of years across northern circumpolar regions from eastern Siberia through Alaska, Canada and into Greenland. It is well known that Polar seas and ice were not a complete barrier to Eskimo migrations. There is no other genetic evidence of small-scale pre-Columbian migration into the Americas within the last three thousand years.
Scientific facts are seldom kind to religion in general, but Mormonism’s relatively modern truth claims appear particularly vulnerable to objective scrutiny. Michael Crawford, Professor of Anthropology, summarizes the view shared by nearly all respected New World anthropologists. “I don’t think there is one iota of evidence that suggests a lost tribe from Israel made it all the way to the New World. It is a great story, slain by ugly fact.”  The Brethren are reluctant to publicly discuss these difficult issues, preferring instead to entrust the problem to various apologists and the public relations arm of the Church.
The LDS Church is appealing to ignorance while attempting to retreat to a position beyond the reach of established science. To dispute the claims of science is not uncommon in the LDS Church. It stubbornly clung to the notion that African people were cursed by a dark skin through ancestry from Cain, though scientists had already proven that all humanity descends through African ancestry. The very concept of “race” is extremely dubious in science today, but ancestry through DNA is clear and is the basis of modern scientific understanding of the human genome, as well as much medical research, which the LDS Church happily relies on.
For several decades LDS apologists have been shrinking the geographical scale of the Book of Mormon narrative in response to antipathetic science. Human population genetics is yielding fresh and incontrovertible evidence that the more diffuse contributions of decades of anthropology, archaeology and linguistic study have been unable to deliver. In response most Church apologists have adopted a Limited Geography situated in Mesoamerica.
Most Mormons, including virtually all of the senior leadership have paid little attention to this apologetic scholarship until the emergence of the population genetics. Now, through subtle word changes and an essay buried on its website, the LDS Church quietly admits that Book of Mormon peoples were minor players in the continent’s archaeological history, and non-contributors to the continent’s gene pool. While the Church has relied heavily on the work of Mesoamerican apologists to address the challenge of the population genetics, it has stopped short of identifying where the Lamanites are.
- LDS Gospel Topics Essay: Book of Mormon and DNA Studies
- Response to LDS DNA Essay, Dr. Simon Southerton
 Smith, History of the Church, 1: 315.
 Cited by Thomas W. Murphy, Sunstone Symposium, 2002.
 Losing a Lost Tribe: Native Americans, DNA and the Mormon Church, Signature Books (2004): 213-222.
 See www.nature.com/articles/s41467-018-07748-z.
 Skogland et al. Nature 525 (2015): 104-108.
 Qin and M. Stoneking. Molecular Biology and Evolution 32 (2015): 2665–2674.
 A Promised Land, Ensign, June 1976.
 Gregory L. Smith, The FARMS Review 22, 2010, p. 17-161.
 Michael Crawford, Professor of Anthropology, University of Kansas, quoted in BYU Gene Data May Shed Light on Origin of Book of Mormon’s Lamanites, Salt Lake Tribune, Dan Egan, 30 November 2000.