The Book of Mormon, one of the four books of scripture of The Church of Jesus Christ of Latter-day Saints (see Standard Works), is an account of three groups of people. Two of these groups originated from Israel. There is generally no support amongst mainstream historians and archaeologists for the historicity of the Book of Mormon.
Since the late 1990s and the pioneering work of Luigi Luca Cavalli-Sforza and others, scientists have developed techniques that attempt to use genetic markers to indicate the ethnic background and history of individual people. The data developed by these mainstream scientists tell us that the Native Americans have very distinctive DNA markers, and that some of them are most similar, among old world populations, to the DNA of people anciently associated with the Altay Mountains area of central Asia.
Overview of the genetic challenges to the Book of Mormon story
The genetic challenge
The understanding of Joseph Smith, and, traditionally, of Mormons in general, is that the Book of Mormon indicates that the Lamanites, descended from Lehi, are a "remnant of the House of Israel" and were the "principal ancestors of the American Indians". This traditional understanding was stated in the preface to the Book of Mormon from 1981. A literal reading of that preface suggests that modern-day Native Americans are descended from the party of Israelites that migrated to the New World around 600 BC from the Jerusalem area. If this were the case, the DNA of Native Americans should correlate with Middle Eastern genetic markers, consistent with Hebrew descent. But the DNA of Native Americans indicates a different, Asian, origin. Some claim it is because of this incongruity that the introduction was changed (to try to reconcile Book of Mormon assertions with the lack of expected evidence). In 1929 President Anthony W. Ivins of the LDS church's First Presidency cautioned church members: “We must be careful in the conclusions that we reach. The Book of Mormon teaches the history of three distinct peoples … 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.” 
LDS researchers compare existing genetic evidence with the Book of Mormon story
Mormon researchers such as anthropologist Thomas W. Murphy (who is a member of the Church of Jesus Christ Latter-day Saints, henceforth LDS) and former-LDS and molecular biologist Simon Southerton state that the substantial collection of Native American genetic markers now available are not consistent with any detectable presence of ancestors from the ancient Middle East, and argued that this poses substantial evidence to contradict the account in the Book of Mormon. Both Murphy and Southerton have published their views on this subject (Southerton 2004).
Followup of genetic claims in the media
Southerton's work was later used as a source for an article written by William Lobdell and published in the LA Times on 16 February 2006, which contains the following. “For Mormons, the lack of discernible Hebrew blood in Native Americans is no minor collision between faith and science. It burrows into the historical foundations of the Book of Mormon, a 175-year-old transcription that the church regards as literal and without error.”
Lobdell's article prompted a response from Latter-day Saint supporters, including several articles referenced on the official LDS web site (see external links below).
The origin of groups described in the Book of Mormon
Statements regarding the Hebrew ancestry of Book of Mormon people
An introductory paragraph added to the Book of Mormon in the 1981 revision states in part: "After thousands of years, all were destroyed except the Lamanites, and they are the principal ancestors of the American Indians." (see lds.org) That addition from 1981 was changed in a 2006 edition, that stated only that "the Lamanites...are among the ancestors of the American Indians." This change, church leaders said, was in harmony with the claims of the Book of Mormon itself, and what some Latter-day Saints had long perceived. For example, in 1929 President Anthony W. Ivins of the LDS church's First Presidency cautioned church members: “We must be careful in the conclusions that we reach. The Book of Mormon teaches the history of three distinct peoples … 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.”
The origin of the Jaredites
According to the Book of Mormon, the Jaredites were a group of people that left the Tower of Babel, but does not give any information that would allow conclusions to be drawn about their genetic or genealogical background. Jaredites could be ancestors to some Native Americans if there were some survivors of the concluding war described in the Book of Ether. This theory is advocated by several LDS scholars due to a variety of contextual clues.(Sorenson 1992) This is where some writers believe that the Lamanites get their Asiatic heritage.(Nibley 1988, p. 250) Amateur apologist Jeff Lindsay notes that a migration into the mountains of Asia is possible for portions of the "lost tribes of Israel."
The Middle Eastern Origin of Lehi
The Book of Mormon tells the story of a small group of Israelites, led by a prophet named Lehi, who fled Jerusalem around 600 BCE and traveled to the Americas. Two of Lehi's sons, Laman and Nephi, become the fathers of two separate nations, the Lamanites and the Nephites. The parent DNA of these two nations would likely have come from one of five people: Lehi, his wife Sariah, Ishmael, his wife (unnamed), or Zoram. Little information is given in the Book of Mormon about the genetic background of these people, but it is stated that Lehi is a descendant (possibly, but not necessarily, patrilineal) of Manasseh. It is uncertain whether other people travelled with Lehi's party to the Americas. For the context of the debate regarding genetics and the Book of Mormon, it is usually assumed that Lehi and his party had mostly Middle Eastern genes.
Nephites and Lamanites in the Book of Mormon
According to the Book of Mormon, the terms "Nephites" and "Lamanites" actually lose their original significance pursuant to the visitation of Jesus Christ to the American continent after His resurrection; His coming ushers in a period of peace in which the two conflicting nations merge into one, in which "There were no robbers, nor murderers, neither were there Lamanites, nor any manner of -ites; but they were in one, the children of Christ, and heirs to the kingdom of God." (Southerton 2004, p. 156).). But later on in the narrative, as members of the unified nation fall away from the faith, the term "Lamanite" comes to signify wickedness (rather than blood heritage), whereas "Nephite" comes to signify a follower of Christ, both terms alluding to the previous nations' predominant moral tendencies. Eventually, however, even the righteous "Nephites" grow proud and fall into wickedness comparable to that of those termed Lamanites, though they retain the now rather hypocritical distinction "Nephites." The Nephites do battle with the Lamanites perpetually, until finally around 400 AD the Nephites are said to have been annihilated by the Lamanites in epic battle involving about two hundred thousands Nephities (and possibly larger amount of Lamanites) near hill Cumorah. The nation of the Lamanites is understood to have continued on beyond the close of the Book of Mormon. The Book of Mormon states, in an introductory paragraph added in 1981, that Lamanites are "the principal ancestors of the American Indians" (
Response to the genetic challenge from Book of Mormon defenders
Book of Mormon population models
Defenders of the Church of Jesus Christ of Latter-day Saints have made arguments in return, generally centered on the idea that the Book of Mormon peoples from the Middle East formed only a small contribution to the population of the Americas, so that their genetic heritage may have been diluted beyond what can now be detected. The Limited Geography Model of the Book of Mormon (accepted by most LDS scholars) supports this position. This geographical and population model was formally published in the official church magazine, The Ensign, in a two-part series published in September and October 1984.
The Book of Mormon describes a major group of Hebrew-descended peoples, the Nephites, being entirely wiped out during the fourth century AD, which could have decreased the amount of Middle Eastern DNA substantially. Critics of this model point out that the large remaining group, the Lamanites, are also said to be at least partly of Hebrew origin, and that they are "the principal ancestors of the American Indians." However, LDS supporters point out that "principal" does not necessarily mean "majority" but simply "first or highest in rank, importance, value, etc.; chief; foremost".
Critics of the "limited geography" model say that the Book of Mormon does not make clear reference to any other people groups that may have existed in the Americas that would account for the dilution of the Middle Eastern genetic markers in the New World. Therefore, it is argued, a "traditional reading" of the Book of Mormon suggests that "most, if not all," the ancestry of the pre-Columbian inhabitants of the Americas came from this Hebrew migration in ancient times (Southerton 2004, p. 156).
The Book of Mormon makes reference to groups from "other countries" that could be brought to the New World. In 2 Nephi, Lehi states "the Lord hath covenanted this land unto me, and to my children forever, and also all those who should be led out of other countries by the hand of the Lord" (2 Nephi 1:5). Mormons have taught since the time of Joseph Smith that this is in reference to the European colonizers of the Americas. It is subsequently stated that allowing too many other people in the land would cause them to "overrun the land, that there would be no place for an inheritance" (2 Nephi 1:8). Later, however, "other nations" would have power to "cause them (the Lamanite remnants) to be scattered and smitten" (2 Nephi 1:11). Lehi said further that the remnants would not "utterly be destroyed" (2 Nephi 3:9).
According to the LGT proponents, the most direct evidence of prior inhabitants was when Lehi's party found domesticated animals when they arrived in the Americas (1 Nephi 18:25). This was part of the story line, however, and does not support the Limited Geography Theory, since the Book of Ether explains these animals were brought from the middle east by the Jaredites.
LDS advocates of the mound builder setting for the Book of Mormon, maintain that native peoples of Central and South America are predominantly of Asiatic origin. Mormon tradition, and not LDS scripture, has over generalized the use of the term “Lamanite” in identifying these peoples. Mound builder setting advocates cite recent DNA studies which indicate that certain native peoples of the eastern United States and the Great Lakes region (the same peoples designated in LDS scripture as “Lamanites”) carry a genetic marker (the haplogroup X marker) which correlates anciently with various peoples of Europe and the Mediterranean.
Factors affecting DNA composition of the New World population
LDS scholars also say that the DNA taken from modern day Israelis has been intermixed with DNA from many other nations, thus they do not contain the same traits that Israelites had when Lehi left Israel (Stubbs 2003). Also, modern Native Americans have intermixed, which has changed their DNA from that of their ancestors' as well. It is also noted by LDS researchers that another factor affecting genetic diversity of New World inhabitants is the fact that 90% of the population died as the result of disease introduced by the Spaniards after their arrival (Coe 2002, p. 231).
Michael F. Whiting, director of Brigham Young University's DNA Sequencing Center and an associate professor in BYU's Department of Integrative Biology, concluded in his article "DNA and the Book of Mormon: A Phylogenetic Perspective" that Book of Mormon critics attempting to use DNA "have not given us anything that would pass the muster of peer review by scientists in this field, because they have ignored the real complexity of the issues involved. Further, they have overlooked the entire concept of hypothesis testing in science and believe that just because they label their results as "based on DNA," they have somehow proved that the results are accurate or that they have designed the experiment correctly. At best, they have demonstrated that the global colonization hypothesis is an oversimplified interpretation of the Book of Mormon. At worst, they have misrepresented themselves and the evidence in the pursuit of other agendas." Additionally, although he admits the usefulness of population genetics and of DNA in inferring historical events, he contests that, "given the complexities of genetic drift, founder effect, and introgression, the observation that Native Americans have a preponderance of Asian genes does not conclusively demonstrate that they are therefore not descendants of the Lamanite lineage, because we do not know what genetic signature that Lamanite lineage possessed at the conclusion of the Book of Mormon record." Lastly, he concludes, "[There is] a strong possibility that there was substantial introgression of genes from other human populations into the genetic heritage of the Nephites and Lamanites, such that a unique genetic marker to identify someone unambiguously as a Lamanite, if it ever existed, was quickly lost." and that, "There are some very good scientific reasons for why the Book of Mormon is neither easily corroborated nor refuted by DNA evidence, and current attempts to do so are based on dubious science" (Whiting 2003, pp. 24-35).
LDS researchers have also focused attention on one genetic haplotype as potentially providing evidence in favor of a link between Hebrew DNA and Native American DNA. The haplotype in question, known as Haplogroup Q or Q-P36, is found in 31% of self-identified Native Americans in the US (Hammer 2005, p. 5). It is also found in 5% of Ashkenazi Jews (Behar 2004, p. 357) and 5% of Iraqi Jews. In addition, a rare branch of Q-P36, called Q-M323, is found in Yemeni Jews (Shen 2004, p. 251).
A study published in 2004 by Stephen L. Zegura states that "The mutational age of Q-P36*, the marker defining the entire Q lineage, is 17,700 ± 4,820 years BP", and that its original source is the region of the Altay Mountains near the borders of Russia, Mongolia, Kazakhstan, and China (Zegura 2004, pp. 164-175). Zegura further notes, "as a caveat", that a population might have moved into the region of the Altay Mountains from an earlier source, "presumably from the southwest", because "all Native Americans can ultimately be traced to a dispersal from Africa", in common with all other human populations according to the scientific consensus. Most genetic studies show strong relations between Native Americans and Siberian peoples.
Other research postulates that Q-P36 first arose somewhere in Central Asia (Wells 2001). Table 3 from Zegura's research is the source from which the 17,700 ± 4,820 years BP dates seems to have been extracted. This date applies to the latest common ancestor of Altaians and Native Americans with Q-P36 lineage. This ancestor may or may not be the original Q-P36.
Generally speaking, mutation rates pertain to STR (short tandem repeat) rather than SNP (single nucleotide polymorphism) mutations. The former occur frequently enough to be useful in paternity testing while the latter can be used to make an educated guess about the lineage of an individual. Average STR mutation rates of 2.8 per 1,000 have been observed in father/son pairs. (Kayser 2000)  The Zegura research cited above, used an 'effective' mutation rate of 0.7 per 1,000. This is done on the premise that various factors can make a lineage look younger than it really is. In point of fact, however, the effective mutation rate used by Zegura is theoretical. Applying the observed mutation rate to Zegura's calculations yields a lower bound of 2725 years BP.
A genetic study in 2006 by Pakendorf et al. used Kayser's mutation rate of 2.8 per 1000 to calculate a date of the Yakut expansion consistent with historical and archeological data. Pakendorf states, "…it has recently been proposed that 'effective' mutation rates (Zhivotovsky et al. 2004), which are not based on pedigree studies but on archaeologically calibrated migrations, may reflect the true historical processes better than pedigree rates. Using the average 'effective' rate of [0.69 per 1000] calculated by Zhivotovsky et al. (2004) results in a much greater age of the Yakut male expansion of approximately 3800 years, ... However, these older dates are inconsistent with linguistic and archaeological evidence: ... the split of Yakut from Common Turkic cannot be earlier than 1,500 years BP."  This suggests that the 'effective' mutation rate of Zhivotovsky and Underhill are not universally valid. This leaves open the possibility that most Native Americans are descended from a single male ancestor who lived in Book of Mormon times.
Comparison with the Lemba
The challenge of determining the genetic background of Book of Mormon population groups has been compared with the Lemba ethnic group in southern Africa. The Lemba, a Black, Bantu-speaking people, practiced a religion very similar to Judaism, and had oral traditions that their ancestors were Jews who sailed to southern Africa from an ancestral land called Sena (Southerton 2004, p. 127). They also had a patrilineal priestly clan called the Buba. After the advent of historical genetics, it was found that the Lemba did indeed have a preponderance of genetic markers on their Y chromosome indicating over 80% of their ancestry was non-Arab Middle Eastern; and even that their priestly Buba clan had a high frequency of a set of genetic markers known as the Cohen modal haplotype, which has been found to strongly correlate with members of the Kohanim, or traditional patrilineal Jewish priestly clan, living in Israel (Southerton 2004, p. 128).
It has been calculated that the Lemba separated from the main body of Jews about three to five thousand years before the present. The main group in the Book of Mormon is said to have left the Middle East about 2,600 years before the present. Therefore, it is argued, if the genetic evidence of Jewish descendancy remained so distinctly preserved in the Lemba during thousands of years of being surrounded by unrelated ethnic groups in southern Africa, there seems no reason why the same could not have been true of an analogous group in the Americas over about the same timeframe. In response to criticism regarding Amerindians' lack of these genetic attributes, LDS scholars have said that there is no indication that descendants of Levi were among Lehi's group, making the existence of these specific haplotypes unreasonable. They also say that it is more difficult to test Native American DNA for Israelite heritage since traditions of Jewish descent do not currently exist. The Lemba, on the other hand have maintained traditions of being descended from Cohen, or Levites, making it easier to test for their genetic inheritance (Roper 2003, p. 145).
In the February 2003 issue of Science in Africa Dr. Himla Soodyal states,"Using mtDNA the Lemba were indistinguishable from other Bantu-speaking groups." MtDNA was the basis of both studies on American Indians. The Lemba look like Bantus and speak a Bantu language. Yet there is no doubt that the Lemba have male Israelite ancestors. The Y-chromosomes tell us this.
Ecclesiastical standing of LDS researchers
Murphy and Southerton were both members of the LDS Church when they began publishing their arguments that the Book of Mormon is not consistent with current genetic evidence. Both men were warned by their local stake presidents and other church leaders that public statements against the Book of Mormon's historicity and authenticity could be grounds for excommunication. Southerton refused to recant his published statements stating that the Book of Mormon was not an ancient document. Murphy's published works do not include such a statement, although he has taken this position in interviews for videos produced by Living Hope Ministries, a Utah-based evangelical Christian group specializing in Mormon outreach, and has said in other interviews that "the book might be fiction, but inspired as well." 
Southerton, who was formerly a bishop of an Australian LDS congregation, was excommunicated from the church in August 2005, though the Australian LDS Church disciplinary council that rendered the excommunication verdict allegedly cited adultery rather than Southerton's self-admitted "apostasy" regarding his position on DNA and the Book of Mormon .
Murphy's situation gained significant media attention in 2002 when local church authorities in Washington state ordered a disciplinary council and stated that he would either have to recant his position on the veracity of the Book of Mormon or be excommunicated from the church. The disciplinary council was postponed on December 7, 2002, less than 24 hours before it was due to be held, and finally indefinitely postponed on February 23, 2003. As of 2007, Murphy remains a member of the LDS Church.
- The Doubleday edition of the Book of Mormon's introduction states that the Lamanites are "among the ancestors of the American Indians". Moore, Carrie A. "Debate renewed with change in Book of Mormon introduction" Deseret News, November 8, 2007
- Anthony W. Ivins, Conference Report, April 1929, p. 15.
- Lindsay, Jeff, "Does DNA Evidence Refute the Book of Mormon?", 2006, jefflindsay.com (link cited below)
- Sorenson Sept. 1984;Sorenson Oct. 1984
- According to the Limited Geography Model, the Lamanites would likely have intermarried with other groups (not of Hebrew descent) and that the resultant Lamanites (not entirely Hebrew) are the "principal ancestors of the American Indians." See the Introduction to the Book of Mormon.
- "Principal" on dictionary.com
- Regarding the hemispheric geography model, Southerton states: "Since the traditional geography model most closely aligns...with an uncontrived reading of the Book of Mormon, it is not surprising that it is still the most widely accepted view in the church."
- Doctrine and Covenants 10:48-51; 30:5-6; 32:2; 54:8; 57:4
- Morgan, Pat, “Mitochondrial DNA Studies of North American Indians”, Ancient American, No. 79-80, pg. 31
- Olive, P.C, "A Comprehensive Look at DNA and the Book of Mormon"; see also Coon, Vincent, Choice Above All Other Lands, pg. 212-213
- Referring to the introduction of smallpox, influenza and measles, Coe states that "It is generally agreed among scholars that these produced a holocaust unparalleled in the world's history: within a century, 90 percent of the native population had been killed off, including that of the Maya area."
- See Figure 1.
- See Table 2
- See Figure 1
- Beringian Standstill and Spread of Native American Founders
- "Attacks on the validity of the Book of Mormon using DNA data" ((HTML)). Religious Tolerance.org. http://www.religioustolerance.org/lds_migr1.htm. Retrieved 2007-01-23.
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- Murphy, Thomas W. (March, 2004), "Inventing Galileo", Sunstone: 58–61 .
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- Murphy, Thomas W. (Winter, 2003), "Simply Implausible: DNA and a Mesoamerican Setting for the Book of Mormon", Dialogue: A Journal of Mormon Thought 36 (4): 109–131, http://content.lib.utah.edu/cdm4/document.php?CISOROOT=/dialogue&CISOPTR=28355&REC=20 .
- Murphy, Thomas W. ([February, 2003]), "Genetic Research a 'Galileo Event' for Mormons", Anthropology News 44 (2): 20 .
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- Nibley, Hugh W. (1988), Welch, John W.; Matthews, Darrell L., eds., "Lehi in the Desert, the World of the Jaredites, There Were Jaredites", Collected Works of Hugh Nibley (Provo, Utah: Foundation for Ancient Research and Mormon Studies) 5, ISBN 0875791328 .
- Roper, Matthew (2003), "Swimming in the Gene Pool: Israelite Kinship Relations, Genes, and Genealogy", The FARMS Review 15 (2), http://maxwellinstitute.byu.edu/pdf.php?filename=NDY5OTQ3NjYwLTE1LTIucGRm&type=cmV2aWV3, retrieved 2007-06-05 .
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- Sorenson, John L. (1992), "When Lehi's Party Arrived in the Land, Did They Find Others There?", Journal of Book of Mormon Studies (Provo, Utah: Maxwell Institute) 1 (1), http://maxwellinstitute.byu.edu/display.php?table=jbms&id=3 .
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- Southerton, Simon G (2004), Losing a Lost Tribe: Native Americans, DNA and the Mormon Church, Salt Lake City: Signature Books, ISBN 1-56085-181-3, http://www.signaturebooks.com/excerpts/losing.html .
- Stubbs, Brian D (2003), "Elusive Israel and the Numerical Dynamics of Population Mixing", FARMS Review (Provo, Utah: Maxwell Institute) 15 (2): 165–82, http://maxwellinstitute.byu.edu/display.php?table=review&id=507, retrieved 2007-05-23 .
- DNA vs. The Book of Mormon (video), Living Hope Ministries, 2003, http://www.livinghopeutah.org/dna.htm .
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- LDS Church Response by the LDS Church after Murphy's essay in American Apocrypha: More Essays on the Book of Mormon.
- Native American DNA and its Impact on Mormonism by Simon G. Southerton
- MormonCurtain.com (ex-Mormon-based blog) entries on Simon Southerton, including Southerton's essay on his excommunication
- Does DNA evidence refute the Book of Mormon? by Jeff Lindsay
- 'Y chromosomes traveling south: the cohen modal haplotype and the origins of the Lemba--the "Black Jews of Southern Africa"', M.G. Thomas et al., American Journal of Human Genetics, Feb. 2000;66(2):674-86.