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Identifying ancient DNA related to Book of Mormon people
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Gospel Topics: "Much as critics and defenders of the Book of Mormon would like to use DNA studies to support their views, the evidence is simply inconclusive"
"Book of Mormon and DNA Studies," Gospel Topics on LDS.org:
Much as critics and defenders of the Book of Mormon would like to use DNA studies to support their views, the evidence is simply inconclusive. Nothing is known about the DNA of Book of Mormon peoples. Even if such information were known, processes such as population bottleneck and genetic drift make it unlikely that their DNA could be detected today. 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.”
Question: What is Lehi's ancestry?
Lehi and his family are not Jews: They belong to the tribe of Manasseh
Genetic attacks on the Book of Mormon focus on the fact that Amerindian DNA seems closest to Asian DNA, and not DNA from "the Middle East" or "Jewish" DNA. However, this attack ignores several key points.
Lehi and his family are clearly not Jews. They belong to the tribe of Manasseh (Alma 10:3, 1 Nephi 5:14), and married into Ishmael's family, the tribe of Ephraim.  These tribes were carried away captive by the Assyrians, and did not contribute greatly to the current genetic mix of the Middle East.
Furthermore, the Middle East is located at the crossroads of three continents, and has seen a great deal of immigration, mixing, and intermarriage. To use modern Middle Eastern DNA as the "standard" against which to measure what Manasseh and Ephraim DNA must have been like 2600 years ago is not a scientifically sound approach.
Question: How does one identify "Jewish" or "Middle Eastern" DNA?
Identifying DNA criteria for Manasseh and Ephraim may always be beyond our reach
Identifying DNA criteria for Manasseh and Ephraim may always be beyond our reach. But, even identifying markers for Jews—a group that has remained relatively cohesive and refrained from intermarriage with others more than most groups—is an extraordinarily difficult undertaking.
One author cautioned:
Studies of human genetic diversity have barely begun. Yet the fashion for genetic ancestry testing is booming. . . . Other groups, such as Jews, are now being targeted. This despite the fact that Jewish communities have little in common on their mitochondrial side—the maternal line down which Judaism is traditionally inherited. It's the male side that shows common ancestry between different Jewish communities—so, of course, that's what the geneticists focus on. . . . Geneticists—like preachers and philosophers before them—need to avoid promising more than they can deliver. 
Question: Can the Lemba and Cohen modal haplotype associated with Levite lineage be used to either prove or disprove the Book of Mormon?
The Book of Mormon suggest that there were no Levites among the Lehi party
Thomas Murphy uses the "Lemba" as an example of a group proven to be Jewish via DNA testing. But, this example is misleading. The Lemba were identified as Jewish because of a marker called the "Cohen modal haplotype." This marker is carried by about half of those who claim descent from Aaron, Moses' brother, and only 2-3% of other Jews.
But, the Book of Mormon does not suggest—and in fact seems to exclude—the idea that Levites (the priestly family of Aaron) were among the Lehi party. Without priestly families, one would not expect to find the Cohen modal haplotype! Yet, only 2-3% of modern Jews from non-priestly families (to say nothing of Ephraim and Manasseh—remember, Lehi and company are not "Jews") can be identified by this test.  Are these 97-98% of modern Jews then not Jews because the genetic test is negative for them? Excluding the Nephites on the basis of such a poor test that we would not even expect them to pass (since they do not include Levitical families) shows how far the critics will twist the evidence to find fault.
Question: What methods of DNA tests are available?
A number of excellent articles are available on this topic
DNA issues can be complex for the non-specialist (especially those who were in high school more than twenty years ago, before much of the modern understanding of DNA was available). A number of excellent articles are available on this topic.
For those interested in general introductions to DNA science:
- This article provides a basic overview by an LDS bishop who is also a world expert on the use of genetic testing. It is quite short, simple, and straight-forward: John M. Butler, "Addressing Questions surrounding the Book of Mormon and DNA Research," FARMS Review 18/1 (2006): 101–108. off-site wiki
- This article provides more detail, but is still accessible to the non-specialist: David A. McClellan, "Detecting Lehi's Genetic Signature: Possible, Probable, or Not?," FARMS Review 15/2 (2003): 35–90. off-site
These articles discuss the feasibility of testing various hypotheses using the Book of Mormon and DNA:
- Michael F. Whiting, "DNA and the Book of Mormon: A Phylogenetic Perspective," Journal of Book of Mormon Studies 12/1 (2003): 24–35. off-site wiki (Key source)
Mitochondrial DNA (mtDNA)is passed only from mothers to their children
Mitochondrial DNA is passed only from mothers to their children. It has been used in attacks on the Book of Mormon, and yet even known Jewish populations do not share mtDNA.
- A new study now shows that the women in nine Jewish communities from Georgia . . . to Morocco have vastly different genetic histories from the men. . . . The women's identities, however, are a mystery, because . . . their genetic signatures are not related to one another or to those of present-day Middle Eastern populations. 
So, known Jewish groups cannot be linked at all by mtDNA studies, and yet the critics would have us believe that two of the lost tribes (Ephraim and Manasseh—from whom we have no 'control' or 'reference' samples to compare to) can be ruled out as ancestors of the Amerindians via mtDNA testing?
Y-chromosomes are only spread from father to son
Y-chromosomes are only spread from father to son; the female line does not carry them at all. These markers have also been used by critics to "prove" that the Amerindians cannot be descended from Lehi.
Despite claims that Y-chromosome data do not support Book of Mormon claims, there are some markers which should be considered in another light:
Douglas Forbes points out that Y-chromosome SNP biallelic marker Q-P36 (also known by the mutation marker M-242), postulated by geneticist Doron Behar and colleagues to be a founding lineage among Ashkenazi Jewish populations, is also found in Iranian and Iraqi Jews and is a founding lineage group present in 31 percent of self-identified Native Americans in the U.S. 
- ↑ "Book of Mormon and DNA Studies," Gospel Topics on LDS.org (January 31, 2014)
- ↑ "The Prophet Joseph informed us that the record of Lehi, was contained on the 116 pages that were first translated and subsequently stolen, and of which an abridgement is given us in the first Book of Nephi, which is the record of Nephi individually, he himself being of the lineage of Manasseh; but that Ishmael was of the lineage of Ephraim, and that his sons married into Lehi's family, and Lehi's sons married Ishmael's daughters, thus fulfilling the words of Jacob upon Ephraim and Manasseh in the 48th chapter of Genesis..." - Erastus Snow, "Ephraim And Manassah, etc.," (6 May 1882) Journal of Discourses 23:184.
- ↑ Martin Richards, "Beware the Gene Genies," Guardian (21 February 2003), accessed 7 July 2006. off-site; cited by Stewart, "DNA and the Book of Mormon."
- ↑ See "Cohen Modal Haplotype," in David G. Stewart, Jr., "DNA and the Book of Mormon," FARMS Review 18/1 (2006): 109–138. off-site wiki FairMormon link
- ↑ Nicholas Wade, "In DNA, New Clues to Jewish Roots," New York Times (14 May 2002): F1 (col. 1); cited by Stewart, "DNA and the Book of Mormon."
- ↑ See "Y-Chromosome Data," in David G. Stewart, Jr., "DNA and the Book of Mormon," FARMS Review 18/1 (2006): 109–138. off-site wiki FairMormon link (Citations omitted)