Lehi’s “Missing” DNA

The subject of DNA and the Book of Mormon is a persistent topic of discussion. For a couple of decades now, scholars have realized that DNA is a powerful tool for unraveling human history, understanding relations of different populations, and tracing ancient migration movements. Nonetheless, even DNA has its limitations on what it can tell us about the past.[1] Can DNA shed any light on the migration of Lehi’s family? The latest paper from Interpreter, written by Ugo Perego, a population geneticist who has worked extensively on the origins of Native Americans, and Jayne Ekins, an international lecturer and published scholar on molecular biology and genetic genealogy (both ancient and modern), provide the latest, most up-to-date discussion of the topic.

Using DNA, scientists have shown that Native Americans are most closely related to East Asians.[2] There does not appear to be any clear relationship between indigenous Americans and peoples from the Middle East. Although this has led some to conclude that this proves that the migration reported in 1 Nephi is merely fiction,[3] such conclusions fail to appreciate the limitations of DNA science.[4]

The Lehites would have met and interacted with indigenous peoples almost immediately.[5] This interaction makes tracing their DNA lineage very complicated. Most DNA studies are dependent on DNA from the mitochondria (mtDNA, passed from mother to offspring) and Y-chromosome (YcDNA, passed on from father to son), because such DNA passes along matrilineal and patrilineal lines without recombining, making it highly stable over several generations. These genetic markers only represent 0.01 percent of a person’s DNA.[6] The rest of the genome (the other 99.9 percent) consists of DNA that recombines every generation, making it difficult to trace its origins. Everyone has about 1,024 ancestors who lived just a few hundred years ago. Go back another couple hundred years and the number of ancestor slots goes up to 1,048,576. Go back a thousand years, and an individual living today has about 10,737,417,000 ancestors from that generation (though there would be overlapping lines). But the genetic markers would only be able to detect two (if you are male, one for females) of these ancestors.[7]

Given the above, it should be no surprise that few of these genetic lineages survive over time. In fact, every 20 generations only 2 out of 18, on average, get passed on.[8] Forensic DNA scientist John M. Bulter notes that a comprehensive study in Iceland reveals, “the majority of the people living today in Iceland had ancestors living only 150 years ago that could not be detected based on the Y-chromosome and mitochondrial DNA tests being performed and yet the genealogical records exist showing that these people lived and were real ancestors.”[9] Butler then drives the point home:

To the point at hand, if many documented ancestors of 150 years ago cannot be linked to their descendants through Y-chromosome and mitochondrial DNA tests from modern Iceland, then it certainly seems possible that the people who are reported in the Book of Mormon to have migrated to the Americas over 2,600 years ago might not have left genetic signatures that are detectable today.[10]
The likelihood of Lehite DNA surviving is particularly disadvantaged by factors known to geneticists as genetic drift, founder effect, genetic bottlenecks, genetic swamp out, and other phenomena, all of which practically guarantee that their genetic markers would be eliminated or undetectable.[11] David A. McClellan, an integrative biologist with specialization in human genetics, explains that these factors constitute violations of the Hardy-Weinberg assumptions, upon which the findings of population genetics rest. Since both the Book of Mormon narrative and the post-Book of Mormon history of the Americas manifest these and other violations, the recovery of Lehite DNA is complicated and unlikely.[12]

Even in the highly improbable event that their genetic markers were to survive, we unfortunately have no sample of DNA from any of the Lehite (or Mulekite) founders, and we lack sufficient information to guess what their mtDNA or YcDNA might have been like.[13] Ugo A. Perego adds that post-Columbian admixture with European lineages also complicates the picture.

Based on the molecular clocks currently used by the scientific community, it would be nearly impossible to distinguish a Eurasian lineage that arrived 2,600 years ago from those brought by Europeans after the discovery of America’s double continent, simply because there would not have been enough time for these lineages to differentiate enough to allow discernment of pre-Columbian from post-Columbian admixture.[14]
In this latest paper with Jayne Ekins, Perego explains that this is because, “The mutation rate of mtDNA is roughly 3,000–9,000 years per mutation, depending on the section of mtDNA analyzed and the molecular clock applied.”[15]

Taking a different approach, McClellan argues that these molecular clocks are based on certain assumptions which do not seem to hold for the Lehite colony.

The rate of fixation of new alleles arising from mutation, however, generally increases in founding populations, making it appear as if the lineages to which populations belong diverged more anciently than in fact they did. If this had occurred, … it most definitely would have violated the assumption of a molecular clock, a basic assumption for reconstructing genetic relationships.[16]
This, combined with the violations of the Hardy-Weinberg assumptions, leads McClellan to conclude:

One would expect that if Lehi’s or Mulek’s genetic signature was found, it would be categorized as “unknown” or “other” or “unrelated.” Based on this information, … [McClellen thinks any potentially surviving Lehite/Mulekite DNA will not be] closely related to any extant ethnic group, but appear to be older—perhaps much older—than 2,600 years.[17]
McClellan’s observations are important because just as there is post-Columbian admixture, a recent discovery suggests “a possible ancient connection between Native Americans and Central/West Eurasia [the Middle East], is further complicating the admixture issue.”[18] This DNA is “much older” (24,000 years ago) than Lehi’s, as is the enigmatic X2a mtDNA lineage in some Native Americans, which has its closest affinities in populations in Iran and Egypt.[19] While it is doubtful that this DNA is connected to the colonizers in the Book of Mormon, the implications of this are significant. Whether we assume the molecular clock assumptions are valid (per Perego), or consider them invalid (per McClellan), if any of Lehi’s DNA, or that of other founders, miraculously made it into present populations, it would be obscured by factors which cannot be controlled for.

A few more recent studies have begun to employ autosomal DNA (atDNA, the other 99.9 percent of the genome) to detect very ancient admixtures, such as the evident mixture of anatomically modern humans and Neanderthals, some 30,000 years ago.[20] Some are tempted to argue that since such an ancient admixture was detected, that Lehite DNA should therefore be detectable as well. However, such incredible successes in the advancement of genetics does not eliminate the limitations outlined above, most of which apply to atDNA as well YcDNA and mtDNA.

The Neanderthal study is actually very instructive regarding the limitations of DNA research. The authors explain:

We detect gene flow from Neandertals into modern humans but no reciprocal gene flow from modern humans into Neandertals. Although gene flow between different populations need not be bidirectional, it has been shown that when a colonizing population (such as anatomically modern humans) encounters a resident population (such as Neandertals), even a small number of breeding events along the wave front of expansion into new territory can result in substantial introduction of genes into the colonizing population as introduced alleles can “surf” to high frequency as the population expands. As a consequence, detectable gene flow is predicted to almost always be from the resident population into the colonizing population, even if gene flow also occurred in the other direction.[21]
Notice that gene flow between populations is not necessarily bidirectional, but even when it is, only the flow into the colonizing population by the resident population is expected to be detectable. Lehi and his family were the colonizing population, while the indigenous peoples were the resident population. “We should not be surprised, then,” writes Ryan Parr, a biological anthropologist who has worked with Native American and ancient Egyptian DNA,

when the small founder groups described by the Book of Mormon, after twenty-six hundred years and more, appear genetically like their closest neighbors, the Native Americans, having assimilated with varying frequencies of Native American mtDNA and Y chromosome haplotypes/haplogroups.[22]
The expectation is that overtime, as Lehi’s family and their decedents intermarried with indigenous peoples, the DNA of the original Lehite colonizers would eventually become lost.

The disappearance of DNA lineages is not the same thing as the end of descendants for a particular ancestor. In truth, everyone has ancestors whose DNA eventually failed to get passed on.[23] As Perego has explained,

We are much more than the DNA of our ancestors. Most of their DNA disappeared by chance and yet they still contributed to our very existence. Likewise, Lehi’s family does not need to have DNA surviving to our days to be among the ancestors of all modern Native Americans. Someone can have thousands of descendants, all of which would not carry a single genetic base of that particular ancestor.[24]
In fact, despite the lack of discernible Lehite DNA, odds are that Lehi and his sons are ancestors of all, or nearly all, modern Native Americans. According to Perego and Ekins, “based on a simple mathematical calculation, there are scenarios in which Lehi is potentially the genealogical ancestor of all Amerindians, … yet leaving no genetic trace of their presence in the present day.”[25] Modern population genetics has demonstrated that after going back 2000–3000 years, nearly everyone living then is a common ancestor for nearly everyone living now. This is not provable by DNA, but is supported by the very best statistical models.[26] Thus, members of Lehi’s family, living 2,600 years ago, are more than likely “among the ancestors of [all] American Indians.”[27]  

To conclude, even though DNA studies are beginning to utilize the entire genome, they can never definitively prove that there was no Lehite migration, and numerous factors suggest that evidence for such should not be expected. Michael F. Whiting, director of BYU’s DNA Sequencing Center, put it this way: “It would be the pinnacle of foolishness to base one’s testimony on the results of a DNA analysis.”[28]

[1] See John L. Sorenson, “New Light: The Problematic Role of DNA Testing in Unraveling Human History,” Journal of Book of Mormon Studies 9/2 (2000): 66–74; reprinted in The Book of Mormon and DNA Research, ed. Daniel C. Peterson (Provo, Utah: Neal A. Maxwell Institute for Religious Scholarship, 2008), 1–21.
[2] See, for example, Ugo A. Perego et al., “The Initial Peopling of the Americas: A Growing Number of Founding Mitochondrial Genomes from Beringia,” Genome Research 20/9 (2010); Ugo A. Perego et al., “Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups,” Current Biology 19/1 (2009): 1–8.
[3] See Thomas W. Murphy, “Lamanite Genesis, Genealogy, and Genetics,” in American Apocrypha: Essays on the Book of Mormon, ed. Dan Vogel and Brent Lee Metcalf (Salt Lake City, Utah: Signature Books, 2002), 47–77; Simon G. Southerton, Losing a Lost Tribe: Native Americans, DNA, and the Mormon Church (Salt Lake City, Utah: Signature Books, 2004).
[4] The most thorough, reader friendly approach to the DNA issue is D. Jeffrey Meldrum and Trent D. Stephens, Who Are the Children of Lehi? DNA and the Book of Mormon (Salt Lake City, Utah: Greg Kofford Books, 2003). For a short, easy to read, and up-to-date treatment, see “Book of Mormon and DNA Studies,” https://www.lds.org/topics/book-of-mormon-and-dna-studies?lang=eng&query=DNA (accessed August 21, 2014).
[5] See John L. Sorenson, “When Lehi’s Party Arrived in the Land, Did They Find Others There?” Journal of Book of Mormon Studies 1 (1992): 1–34. Also see Matthew Roper, “Nephi’s Neighbors: Book of Mormon Peoples and Pre-Columbian Populations,” FARMS Review 15/2 (2003): 89–128; reprinted in The Book of Mormon and DNA Research, 185–218; John Gee and Matthew Roper, “‘I Did Liken All Scriptures Unto Us’: Early Nephite Understandings of Isaiah and Implications for ‘Others’ in the Land,” in The Fulness of the Gospel: Foundational Teachings from the Book of Mormon, The 32nd Annual Sidney B. Sperry Symposium, ed. Camille Fronk, Brain M. Hauglid, Patty A. Smith, Thomas A. Wayment, (Salt Lake City, Utah: Deseret Book and BYU Religious Studies Center, 2003), 51–65.
[6] See John L. Sorenson, Mormon’s Codex: An Ancient American Book (Salt Lake City, Utah: Deseret Book and the Neal A. Maxwell Institute for Religious Scholarship, 2013), 249.
[7] See D. Jeffrey Meldrum and Trent D. Stephens, “Who Are the Children of Lehi?” Journal of Book of Mormon Studies 12/1 (2003): 38–51; reprinted in The Book of Mormon and DNA Research, 157–183.
[8] See Ryan Parr, “Missing the Boat to Ancient America… Just Plain Missing the Boat,” FARMS Review 17/1 (2005): 87, fig. 3.
[9] John M. Butler, “Addressing Questions Surrounding the Book of Mormon and DNA Research,” FARMS Review 18/1 (2006): 105–106; reprinted in The Book of Mormon and DNA Research, 75.
[10] Butler, “Addressing Questions,” 106.
[11] See Michael F. Whiting, “DNA and the Book of Mormon: A Phylogenetic Perspective,” Journal of Book of Mormon Studies 12/1 (2003): 24–35; reprinted in The Book of Mormon and DNA Research, 79–97.
[12] See David A. McClellan, “Detecting Lehi’s Genetic Signature: Possible, Probable, or Not?” FARMS Review 15/2 (2003): 35–90; reprinted in The Book of Mormon and DNA Research, 99–155.
[13] See John M. Butler, “A Few Thoughts From a Believing DNA Scientist,” Journal of Book of Mormon Studies 12/1 (2003): 36–37; reprinted in The Book of Mormon and DNA Research, 23–24.
[14] Ugo A. Perego, “The Book of Mormon and the Origin of Native Americans from a Maternally Inherited DNA Standpoint,” FARMS Review 22/1 (2010): 216; reprinted in No Weapon Shall Prosper: New Light on Sensitive Issues, ed. Robert L. Millet (Salt Lake City, Utah: Deseret Book and the BYU Religious Studies Center, 2011), 193.
[15] Ugo A. Perego and Jayne E. Ekins, “Is Decrypting the Genetic Legacy of America’s Indigenous Populations Key to the Historicity of the Book of Mormon?” Interpreter: A Journal of Mormon Scripture 12 (2014): 257.
[16] McClellan, “Detecting Lehi’s Genetic Signature,” 88.
[17] McClellan, “Detecting Lehi’s Genetic Signature,” 89, brackets mine.
[18] Perego and Ekins, “Decrypting the Genetic Legacy,” 240, brackets mine.
[19] See Perego and Ekins, “Decrypting the Genetic Legacy,” 253–255.
[20] See Richard E. Green et al., “A Draft Sequence of the Neandertal Genome,” Science 328 (May 2010): 710–721.
[21] Green et al. “A Draft Sequence of the Neandertal Genome,” 721, punctuation altered, emphasis mine.
[22] Parr, “Missing the Boat,” 100–101.
[23] See “How Many Genetic Ancestors Do I Have?” The Co-op Lab: Population and Evolutionary Genetics, UC Davis, http://gcbias.org/2013/11/11/how-does-your-number-of-genetic-ancestors-grow-back-over-time/ (accessed August 21, 2014).
[24] Email from Ugo A. Perego to Neal Rappleye, May 14, 2014.
[25] Perego and Ekins, “Decrypting the Genetic Legacy,” 273.
[26] Matthew Roper, “Swimming in the Gene Pool: Israelite Kinship Relations, Genes, and Genealogy,” FARMS Review 15/2 (2003): 159–163; Brian D. Stubbs, “Elusive Israel and the Numerical Dynamics of Population Mixing,” FARMS Review 15/2 (2003): 165–182; both reprinted in The Book of Mormon and DNA Research, 253–256, 263–281, respectively; Gregory L. Smith, “Often in Error, Seldom in Doubt: Rod Meldrum and Book of Mormon DNA,” FARMS Review 22/1 (2010): 86–88.
[27] Introduction to the current official edition of the Book of Mormon, brackets mine.
[28] Whiting, “DNA and the Book of Mormon,” 35.