The Book of Mormon and the Origin of Native Americans from a Maternally Inherited DNA Standpoint

The Book of Mormon and the Origin of Native Americans from a Maternally Inherited DNA Standpoint

Ugo A. Perego


Where did Native Americans come from? When did they arrive
in the Western Hemisphere? Which route(s) did they follow? How many
colonization events were there? These and other fascinating questions have been
at the center of debates among scholars from different disciplines since the
rediscovery of the New World by Europeans more than five hundred years ago.
Archaeologists, linguists, anthropologists, and geneticists are still
investigating the processes that took place through the millennia that led to
the peopling of America’s double continent. The considerable number of
scholarly papers that have been published on DNA and Amerindians is a
demonstration that “despite the 80-year history of genetic studies in the
Americas, the real work is now [only] beginning to fully elucidate the genetic
history of [the] two continents.”1

At first, Europeans believed that
the New World inhabitants were somewhat connected with the biblical account of
the lost ten tribes (2 Kings 17:6), leading them to look for cultural and
linguistic similarities between contemporary Jews and Native Americans.2 The evidence amassed to this point indicates that although sporadic
pre-Columbian contacts with the Old World cannot be completely ruled out,3 the majority of Native Americans share a genetic affinity with Asian

The notion that some or all
American Indians are of Hebrew descent is still popular among Latter-day
Saints. The Book of Mormon tells of three relatively small parties (the
Jaredites, Lehites, and Mulekites) that left their native homeland in the Old
World at different times and through divine guidance traveled to a new promised
land, presumably on the American continent. The Book of Mormon contains only
marginal information about the demographic dynamics and the geography of the
land occupied by the people it describes. Instead, the volume claims to be
primarily an abridgment of thousands of years of mostly spiritual and religious
history and not a full account of the people. For example, the text does not
give direct information about whether other populations were already
established in the land at the time of the migrants’ arrival. This lack of
information leaves many open questions that have profound implications for the
genetic characteristics that we would expect to find in present-day Native
American populations. The extent to which these Old World groups expanded and
colonized their new habitat, the level of admixture they may have experienced
with local indigenous populations (if any were present), and the locations of
their settlements would all influence the genetic landscape we would observe in
Native Americans today. Furthermore, it is implausible that ancient record
keepers would have had a comprehensive knowledge of all the goings-on of the
entire vast landmass of the Americas, considering that from northern Canada to
Patagonia is about 8,700 miles, a greater distance than that from Portugal to
Japan! Despite these many complex factors, since the publication of the Book of
Mormon in 1830, Mormons and non-Mormons alike have resorted to speculation in
an attempt to fill in the historical and geographical details that are either
completely missing or only briefly alluded to in the Book of Mormon text.5

Even in light of statements by
individual Latter-day Saint church leaders and scholars on this topic through
the years, the church advocates no official position on the subjects of Book of
Mormon geography and the origins of Amerindian populations.6 Together with
all other members, LDS Church leaders are entitled to their own opinions and
reasoning on this subject, as demonstrated by “pre-DNA” comments such
as that of President Anthony W. Ivins, a member of the First Presidency, at the
April 1929 General Conference: The Book of Mormon “does not tell us that
there was no one here before” the Book of Mormon peoples. “It does
not tell us that people did not come after.”7 Others have
expressed similar opinions more recently.8

Over the past decade, critics of
the Book of Mormon have promoted the idea that since the majority of Amerindian
DNA lineages are closely related to Asian populations, and since no perfect
genetic affinity to the Middle East has been found, it must be concluded that
the Book of Mormon account is fictional. This argument is sometimes bolstered
in part by a common sentiment among Latter-day Saints generally that all Native
Americans are descendants of the Old World migrants described in the Book of Mormon
text, particularly Lehi’s colony. To contend with these arguments, some Mormons
dismiss DNA studies as being unreliable for reconstructing history, while
others are quick to embrace any news of possible Middle Eastern DNA in the
Americas as conclusive proof that the migrations to America described in the
Book of Mormon are real.

In this article, I will provide
an updated review on the properties of mitochondrial DNA (mtDNA) and explain
how these pertain to the study of ancient population expansions, specifically
focusing on the origin of Native Americans. This topic is especially relevant
to the current debate on the applicability of DNA evidence to the question of
Book of Mormon historicity, as such evidence is based mostly on mtDNA data
published during the past two decades. The major arguments in this debate have
been presented at length in previous publications9 and will not
be restated herein. The most pertinent supporting material that follows will
provide a foundation to the reader regarding the basics of mtDNA heredity, a
review and update on the most recent mtDNA data available pertaining to the
origins of Native American populations, and a summary of how this information
relates to the larger DNA and Book of Mormon discussion. It is important for
readers to understand that while mtDNA and other genetic motifs are useful in
elucidating some historical questions,10 it may not
be possible to achieve a full resolution of questions arising between secular
and religious history.

Mitochondrial DNA

The hereditary features of mtDNA
provide unique information that geneticists use to study the ancient history of
humanity. Such studies are based on the foundational principles of population
genetics. It is essential to have a working knowledge of these principles when
evaluating genetic studies relating to the Book of Mormon, because those who
argue against its authenticity overlook some of these concepts.

MtDNA is found in mitochondria, which
are the organelles within each cell responsible for life-sustaining processes
such as cell energy metabolism, cell division, and programmed cell death
(apoptosis). Each cell may contain thousands of mitochondria, and each
mitochondrion may contain hundreds of mtDNA genomes. A significant hereditary
feature of mtDNA is that it is maternally inherited, a fact that affects the
extent of historical information one can learn from its analysis.

The mtDNA molecule comprises only
16,569 bases and is therefore very small when compared to the nuclear genome
(i.e., the 3.2 billion bases of genetic material that make up the twenty-three
pairs of chromosomes found in the cell’s nucleus). The first complete mtDNA
genome was sequenced in 1981 at Cambridge University and is called the Anderson
or Cambridge Reference Sequence (CRS).11 In 1999
Andrews and colleagues resequenced the original Cambridge mtDNA, which is now
referred to as rCRS.12 This sequence became the industry standard used to compare complete or partial
mtDNA data produced to date. Instead of reporting long lists of genetic bases
for each mtDNA sample, a typical report includes only differences (i.e.,
mutations) from the rCRS. This set of mutations is called a haplotype, the mtDNA genetic profile descended from the maternal
lineage of an individual. As a general rule, mutational events occur randomly,
and their accumulation over time has resulted in the differentiation of the
many mtDNA lineages observed in today’s world populations. Analysis of these
lineages can therefore be structured hierarchically in a treelike format called
a phylogeny (fig. 1). A phylogeny attempts to
model the true hereditary history of mtDNA across populations.

Similar to the Y chromosome
(Ycs), mtDNA does not recombine with the DNA from the other molecules. That is,
mtDNA is inherited as a fully intact DNA segment between generations, with
variations from mother to child arising rarely due to random mutations. While
the Ycs is inherited along the paternal line, as noted before, mtDNA follows an
inheritance pattern found on the opposite side of the family tree, along the
unbroken maternal line (fig. 2). A mother’s mtDNA is passed to all of her
children, but only the daughters will pass their mtDNA to the next generation.
Although there has been one documented instance of male-inherited mtDNA in
humans, this is considered an exceptionally rare (almost unique) exception,
mainly associated with a pathological status.13

The mtDNA
genome has two parts: the control region,14 which
includes three segments called HVS1, HVS2, and HVS3,15 and the
coding region (where all the mtDNA’s genes that produce proteins essential to
life are found). Genetic data from an individual’s mtDNA is obtained by the
following methods, with each successive approach yielding more information:

1. Inspection of restriction fragment length polymorphisms (RFLPs) using
enzymes that break the DNA into smaller fragments at specific short (usually
four to six base pair) sequences. Depending on the presence or lack of
mutations, the fragment will or will not be broken and the resulting fragment
length indicates the presence or lack of the mutation.

2. Assaying single nucleotide polymorphisms (SNPs), where the type of base
at a specific location is identified for comparison with the reference

3. Sequencing of part or all the control region (up to approximately 1,000

4. Sequencing of the
complete mtDNA genome (all the 16,569 bases—the highest level of mtDNA
molecular resolution attainable).

During the 1990s, a number of
studies were published presenting mtDNA data obtained from RFLP and control
region sequences (often only HVS1, approximately 300 bases), many of them
highlighting several Native American populations.16 The mtDNA
data produced during that decade allowed scientists to investigate for the
first time the mtDNA variation from diverse populations. From this they
advanced the first theories about the origin of anatomically modern humans and
the processes of expansion that resulted in the colonization of the continental

Starting around the year 2000,
researchers employing new technological advances began to produce complete
genome sequences as the standard for the most rigorous mtDNA population
studies.17 However, the process of generating a full mtDNA sequence is still labor
intensive and relatively expensive. Recently, a study reviewing all the
published mtDNA full sequences reported that only a very small fraction of
these data are of Native American origin, leaving a considerable gap to fill in
the scientific literature.18

The opportunity to acquire
complete mtDNA sequences brought several benefits to the field of population
genetics, including resolution of questionable phylogenies based on control
region data (this region has a higher mutation rate and is therefore affected
by recurring mutations), identification of smaller clades within the large
world mtDNA tree, better understanding of events that characterize the
expansion and migration routes followed by our early ancestors, and an improved
understanding of the expected mutation rate of the mtDNA genome, yielding a
better calibration of the molecular clock—the mathematical underpinnings
of historical date estimations based on genetic data.

It is important to remember that
population geneticists face the continuing challenge of correlating their
findings with those of other disciplines, including linguistics, anthropology,
and archaeology. A multidisciplinary approach allows a consensus to be formed
for date estimates and helps to cross-verify findings among different fields of

MtDNA Haplogroups

differentiation of mtDNA has been generated by the sequential accumulation of
new mutations along radiating maternal lineages. Over the course of time, this
process of molecular divergence has given rise to separate mtDNA lineages that
are now called haplogroups—that is, groups of haplotypes sharing similar
characteristics. Haplogroups are named following a simple but standardized
nomenclature procedure, alternating letters with numbers and starting with a
capital letter (e.g., K1a4, H1a, A2d2, C1b2a) (fig. 1). Coincidentally, the
first time haplogroup names were given was when the sequence variation of
mtDNAs from Native American populations was investigated. Four major mutational
motifs were identified, and they were therefore originally named A, B, C, and

The mtDNA process of molecular
differentiation was relatively rapid and occurred mainly during and after the
recent process of human colonization and diffusion into different regions and
continents. Thus, serendipitously, the different subsets of mtDNA variation
tend to be restricted to different geographic areas and population groups.
Older mtDNA lineages had more time to accumulate a greater number of mutations,
while younger mtDNA lineages accumulated fewer mutations and therefore
underwent less variation. Mainstream population geneticists are in agreement
that, based on the available mtDNA data, the most recent common female
ancestor, from whom all mtDNAs in modern humans derive, lived in Africa about
200,000 years ago and that an initial migration out of Africa took place around
70,000 years ago, represented by an mtDNA lineage known as L3. This lineage
left the Horn of Africa by migrating eastward and following a southern coastal
route along the Indian Ocean; and while moving farther east about 63,000 years
ago, it gave rise to two mtDNA “daughter” branches known as haplogroups
M and N. An offshoot of N shortly after was haplogroup R. Lineages M, N, and R
are the female ancestors of all the known non-African lineages that eventually
colonized the rest of the continents. These lineages are also known as macro-
or superhaplogroups. The Americas were the last of all the continents to be
colonized by Homo sapiens, approximately 10,000–20,000 years
ago (fig. 3).

The Basics of Population Genetics

Using the mtDNA mutations as a
guide, it is possible to trace all modern mtDNA lineages back to a single
African female ancestor. Geneticists have named this ancestor the African “Eve,”
but despite this name, she was not necessarily the only woman on the planet.
The mtDNA lineages corresponding to other women simply disappeared because
their offspring failed to produce additional continuous female lineages (a
phenomenon known in population genetics as genetic drift), because of natural
or manmade calamities that wiped out a significant portion of the population
(an event referred to as a population bottleneck), or because they were
selected against due to the detrimental effect of specific mutations. This
African “Eve” was the only one that was successful in perpetuating
her mtDNA lineage through the generations. Therefore, because of genetic drift,
population bottlenecks, or natural selection, the mtDNA lineages observed in
today’s population do not reflect the full range of mtDNA variation that
occurred throughout human history. A recent example from a study in Iceland
based on genetic and genealogical data clearly demonstrated how the majority of
people living in that country today are just a small representation of people
that lived just three hundred years ago.21 This work is
a powerful illustration and a rare example of a controlled study where
genealogical, historical, and genetic data are available to unequivocally
demonstrate the effect of genetic drift and natural selection in a fairly
isolated population. The effect of these population genetics processes occur
globally (including in organisms other than humans) and are not exclusive to
the Icelandic population. Most relevant to our current discussion, these
principles have also affected populations in the Western Hemisphere. Although
some would like to dismiss the Icelandic model and suggest that it is more an
exception than the rule,22 these population genetics laws cannot be ignored: they are the fundamental
force that shaped the modern genetic landscape worldwide. It is a well-known
fact that mtDNA lineages have disappeared in the past and that they will
continue to disappear in modern times. This process has occurred everywhere in
the world, and the Americas are no exception.23

Native American DNA

With regard to measuring the
genetic variation observed among the indigenous people of the Western
Hemisphere, molecular anthropologist Michael H. Crawford has stated this
problem succinctly and repeatedly in his book The Origins of Native Americans:

The Conquest and its sequelae squeezed the entire Amerindian
population through a genetic bottleneck. The reduction of Amerindian gene pools
from 1/3 to 1/25 of their previous size implies a considerable loss of genetic
variability. . . . It is highly unlikely that survivorship was genetically
random. . . . Thus, the present gene-frequency distributions of Amerindian
populations may be distorted by a combination of effects stemming from genetic
bottlenecks and natural selection. . . . 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.24

Subsequent research has supported
this notion. In an article dealing with ancient DNA from Native American
populations that was published in the American Journal of Physical Anthropology,
the authors made the following statement: “Genetic drift has also been a
significant force [on Native American genetics], and together with a major
population crash after the European contact, has altered haplogroup frequencies
and caused the loss of many haplotypes.”25

These statements from experts in
the field of modern and ancient DNA from Native American populations (experts
not involved with the Book of Mormon and DNA debate) give insight into the
influence of the major population-altering events of the Columbian and
pre-Columbian eras on the genetic variation of modern Native Americans. Their
mtDNAs were not immune to the evolutionary processes of genetic drift and
population bottleneck that have been observed in a similar fashion in other
populations. One cannot overstate the importance of considering both random as
well as environmental factors when studying history using DNA samples from
modern populations, including that of Amerindians. Population genetics
principles guide geneticists who study human history, and genetic drift and
population bottlenecks are among the most basic factors considered in their

Some wonder
if ancient DNA samples might shed additional light on the history of ancient
populations such as the ancestral Native Americans. This approach can be
valuable when the necessary samples are available and the DNA is of good
quality. Note, however, that
several limitations must be carefully considered when studying ancient DNA:

a.   Accessibility to the ancient remains: In many cases Native American and
First Nation groups consider their burial grounds sacred and are quite
resistant to DNA testing being performed on their ancestors’ remains.
(Moreover, they are often resistant to testing being done on themselves.)26

b.   Contamination: Skeletal remains in museums or personal collections may
have been handled improperly over time. Thus any attempt to retrieve endogenous
DNA from them may be compromised by the presence of DNA belonging to those who
have touched the samples since the time of their excavation.

c.   Confidence that the data obtained are genuine: A general practice when
analyzing ancient DNA samples is to compare the data obtained with samples from
the modern population. If identical or similar haplotypes are found in the
modern population, then it is assumed that the data obtained from the ancient
specimen are reliable. However, if no matches are found in the modern
population, it can become difficult to ascertain if the data obtained belong to
a lineage no longer in existence or if the genetic signal comes from contamination
or postmortem damage.

d.   Failed sequencing due to environmental factors: Even in cases when bone
fragments are found and proper excavation techniques are in place, the success
rate of extracting and analyzing ancient DNA is approximately 1 in 3. Extreme
heat, high humidity, gamma rays from the sun, and other factors can accelerate
DNA degradation. During the last decade, thanks to new technological
advancements and a better understanding of how
to work with ancient DNA,27 results have improved and the data are more reliable. However, much of the data
published in the 1990s was susceptible to less rigorous collection and lab
procedures that may have resulted in unreliable DNA data and conclusions.

e.   Limited quantity of
data obtained: Because ancient DNA is highly degraded, only small fragments of
genetic material can be sequenced. Most of the ancient DNA data available in
the public literature comes from sequencing short segments of the control
region. To date, only a few complete mtDNA sequences (the full 16,569 bases of
the mtDNA genome) from ancient human remains have been successfully produced
(e.g., five Neanderthals and the Tyrolean Ice Man, Ötzi).28

In summary, even though ancient
DNA data have the potential to be extremely helpful in phylogenetic studies and
in reconstructing past population events, scientists are still limited by the
amount and quality of data they can obtain from ancient remains.

significant finding that elucidates the usefulness of combining ancient and
modern DNA in the study of Native American populations comes from a recent
publication featuring a short control region segment sequenced from a skeleton
found in Alaska that is approximately 10,000 years old.29 Carbon
dating confirmed that the remains were clearly pre-Columbian, but the genetic
profile obtained did not match any of the earlier identified Amerindian mtDNAs
(A2, B2, C1, D1, and X2a). Previously, a number of studies on Native American
populations revealed a small quantity of samples labeled “others”
since they did not belong to any of the known indigenous mtDNA lineages and
were thought to have been contaminated or to be the result of European
admixture. Based on the mtDNA data retrieved from the ancient Alaskan specimen,
some of those previously unclassified samples were reexamined and are confirmed
as belonging to a novel Native American lineage named D4h3.30 Unfortunately, as explained earlier, it is difficult to access and to obtain
data of good quality from ancient DNA. Therefore, for every reclassified mtDNA
lineage, it is probable that many misclassifications remain unknown or
unresolved.  The case of D4h3 is
likely to be a rare event in shedding additional light on the maternal history
of Native American populations.

Another serious limitation is the
possibility of making inappropriate assumptions about which mtDNA
candidate haplogroups to expect from the small groups described in the Book of
Mormon. A survey of modern populations including Middle Easterners and Asians
would reveal a certain number of mtDNA lineages that occur at high frequencies
and are therefore labeled as region-specific for the modern population, but
such a survey would also uncover a number of mtDNA haplogroups that are more
rare. Most likely, these less frequent mtDNA lineages are the result of
relatively recent migratory events, an occurrence very common throughout
history because of international trade routes (such as those that took place
along the Silk Road) or military expansions (e.g., the Assyrian, Babylonian,
Roman, or Mongol empires). These important historical events are responsible
for a partial reshuffling of the DNA compositions of geographic regions
throughout the world, adding to the genetic diversity of affected locations.
Although the majority of lineages in one region could be considered the typical
mtDNA expected to be observed in a specific location in modern populations, the
reality is that potentially any given mtDNA lineage could also be found at low
frequencies in the same geographic area. Any of these low-frequency haplogroups
could be candidates for genetic types that may have been more common during any
previous time period within the last few thousand years.

This issue touches on the people
of the Book of Mormon because we don’t know their mtDNA affiliation. Lehi’s
group could have included typical Middle
Eastern lineages or rare ones, even some with a close Asian affinity.31 To elucidate this point, I use my own Y chromosome (Ycs) haplogroup as an
example. As explained earlier, Ycs is a uniparental marker that, like mtDNA,
can be traced along one specific family tree branch (in this case the direct
paternal line), and for the most part it does not recombine with the other
chromosomes (fig. 2). Ycs haplotypes can also be grouped in a large
phylogenetic tree based on common characteristics that in most cases can be
associated with specific geographic regions. I was born and raised in Italy and
can trace my paternal ancestry back several generations to the mid-seventeenth
century AD. However, my Ycs
belongs to haplogroup C, which has a frequency in southern Europe of less than
1 percent. Haplogroup C is mostly found in east Asia with a branch (C4) found
among the aborigines of Australia. How did haplogroup C become part of my
paternal ancestry? One possibility is that it is a remnant from an ancient
military expansion from the East (e.g., Mongols or Huns) that reached to
northern Italy. With my three sons, we contribute four instances of this
particular Ycs haplotype in the state of Utah, where we currently reside. If
someone took a survey of Italians in Utah with the purpose of reconstructing
the typical Italian genetic composition, they would include the four of us as
part of that count. This would contribute a higher than normal haplogroup C
frequency found among Utah Italians that would in turn provide a different
scenario from the one observed in Italy. What if I was the first and only
Italian that migrated to Utah? What was considered a rare lineage in the source
population (Italy) becomes the totality of the Ycs lineages for the same
population in Utah. By looking at these data, one may reach the incorrect
conclusion that Italians are paternally related to eastern Asian populations.
This is a direct result of another principle of population genetics, the
founder effect.

same founder effect process can be observed with mtDNA lineages that are
traditionally associated withPaleo-Indians who arrived in the Americas most
likely via Beringia between twelve and 20,000 years ago. Haplogroups A2, B2,
C1, and D1 are the most common mtDNAs found in Native Americans (approximately
95 percent of the population), but they do not reflect the current mtDNA
landscape observed in northeast Asia. For one thing, there are no A2, B2, C1,
or D1 lineages in that part of the world (one of few exceptions is subclade
C1a, found only in Asia and not in the Americas).32 These four branches of the mtDNA world tree are exclusively found in the
Americas and have been separated from all other lineages long enough to develop
their own specific mutational motifs. Secondly, a survey of north Asian mtDNA
lineages would reveal a much more diverse distribution and variety of mtDNA
haplogroups—not a 95 percent frequency of Asian lineages belonging to
subbranches of the roots A, B, C, and D. What happened to the other Asian
lineages? Why are they not found in the Americas too? Genetic drift and founder
effect are again the answer. What we observe today in the Western Hemisphere
are the surviving lineages that Paleo-Indians brought with them to the Americas
at the time of the last ice age. The other lineages were simply lost in the

What about Haplogroup X?

Although the majority of mtDNA
lineages surveyed to date among Amerindians
belong to a subclade of one of the four Pan-American haplogroups (A2, B2, C1,
and D1) having Asian affinity, this does not mean that all the pre-Columbian lineages are of Asian origins. One exception is the less
common and geographically limited haplogroup X. The presence of haplogroup X in
the Americas has caused no small perplexity among scientists studying Native
American origins. Research questions include how haplogroup X differs from the
other Pan-American haplogroups with Asian affinity, its origins, where else it
is found in the world, what route it followed to the Americas, and how long ago
it arrived there.

With regard to the Book of Mormon
and DNA debate, haplogroup X has also played an interesting role at both ends
of the spectrum in challenging or defending the historicity of the Book of
Mormon. On one end are those who criticize the Book of Mormon based on the DNA
data. Conversely, there are some within the LDS faith claiming that the
presence of haplogroup X in the Americas supports the truthfulness of the Book
of Mormon. The mutually exclusive reasoning of these two factions can be
summarized as follows:

Against Book of Mormon historicity:
Like other Pan-American clades, haplogroup X is of Asian origin, arriving in
the Americas via Beringia (the landmass that connected northeast Siberia with
modern-day Alaska during the last ice age). This migration took place more than
10,000 years ago, long before Israel ever existed.

In favor of Book of Mormon historicity:
Haplogroup X is of Near Eastern origin, and its presence in the Americas represents
the surviving legacy of Lehi’s party arriving in the Western Hemisphere some
2,600 years ago.

There are probably as many
gradients between these two views as people trying to address this specific
topic. However, these two points summarize most of the issues surrounding
haplogroup X and the proposed association with the historicity of the Book of

Following the discovery of the
first, more common Native American mtDNA
haplogroups in the early 1990s (originally termed A, B, C, and D and later
renamed A2, B2, C1, and D1 to distinguish them from their Asian “cousins”),
a fifth haplogroup was identified in 1996 by Peter Forster and his colleagues
and named haplogroup X (not to be confused with the X chromosome).33 Contrary to nearly all the world haplogroups, it is not geographically confined
but is found at low frequency among several populations: Europeans, Africans,
Asians, Middle Easterners, and Native Americans. A number of studies following
the initial identification of haplogroup X among Amerindians confirmed its
presence in the Western Hemisphere,34 its variance from the X lineages found in Eurasia and Africa, and its
geographic distribution confined to northern North America.35 The Native
American clade of haplogroup X is known as X2a to differentiate it from the
forms of haplogroup X found in northern Africa and Eurasia. The root of this
lineage is characterized by the diagnostic control region transition C16278T,
and the specific X2a subclade also includes mutations at A200G and G16213A.36

As already discussed, the
Pan-American haplogroups A2, B2, C1, and D1are clearly nested within a tree of
east Asian haplogroups, thus suggesting an Asian
origin followed by a Beringian migration and the differentiation of
Paleo-Indian lineages from the ancestral Asian ones. However, the original
differentiation of A, B, C, and D from their ancestral mtDNA lineages occurred
in ancient south Asia during the early expansion of anatomically modern humans
tens of thousands of years ago (south Asia is a geographic region that is not
any closer to Beringia than is the Middle East).
Lineages found today in central and northeast Asia (e.g., A5, B4a, C4, and D4e,
to name a few) are considered “cousins” but are not ancestral to the
American A2, B2, C1, and D1 haplogroups (fig. 1).

For years scientists struggled to
identify a possible Asian source for haplogroup X that could explain its presence
in the Western Hemisphere. Different theories were postulated, including a
possible northern Atlantic migration along the ice cap that connected northern
Europe to northern America during the last ice age. This unpopular
theory—referred to as the Solutrean hypothesis—was supported by
archaeological discoveries revealing the presence of a similar technology in
both continents arising at about the same time period.37

Early studies were limited to the
sequence of a few hundred bases from the control region and therefore were not
able to provide the level of resolution necessary to assess the phylogenetic
relationship between American and Eurasian X lineages. This is particularly
relevant in light of the fact that because haplogroup
X initially could not be found in Asia, there was even more uncertainty
regarding its origin and migration route to the Western Hemisphere. Did
haplogroup X come from Europe via the glaciated northern Atlantic, or did it
follow the same Beringian route as the other Native American haplogroups? If
the latter was the case, why was it not found in northern Siberia or eastern

began looking for the presence of haplogroup X in other areas of Asia and
eventually were able to find it in a small percentage of the Altai population,
on the northern border of Mongolia. In 2001 Miroslava Derenko and his
colleagues published a paper in which they reported the Altaian haplogroup X haplotypes (control region only) together with Eurasian and
American X lineages and suggested that their intermediary position could
possibly represent the population source for haplogroup X in northern North
America.38 Its absence in north Siberian populations could be explained by a rapid
expansion or by its disappearance due to genetic drift. However, when the same
data were analyzed at a higher level of resolution—that of complete mtDNA
sequences—and compared to other X haplotypes, it became evident that the
Altaian mtDNA cluster (called X2e) was considerably younger than the Native
American X2a. Therefore, the Asian branch of X was not ancestral to the
Amerindian X2a, but it certainly could be a sister clade derived from a common,
now disappeared Asian ancestor. The authors suggested that the Altaian Xs were the result of a secondary, more recent migratory event, possibly from the Caucasus region,39 leaving the
question about the origin of Native American X2a unanswered. The authors
concluded their research by stating that “phylogeography of the subclades
of haplogroup X suggests that the Near East is the likely geographical source
for the spread of subhaplogroup X2.”40 Interestingly, they identified a sample from Iran that shared a single, fairly
conserved coding region mutation with the Native American X2a cluster: “We
surveyed our Old World haplogroup X mtDNAs for the five diagnostic X2a
mutations [A200G and G16213A in the control region and A8913G, A12397G, and
T14502C in the coding region] and found a match only for the transition at np
12397 [nucleotide position A12397G] in a single X2* sequence from Iran. In a
parsimony tree, this Iranian mtDNA would share a common ancestor with the
Native American clade.”41 However, the authors suggested that this could have been a case of IBS
(identical by state, where shared mutations in different populations arise by
chance in a parallel manner with no common ancestor) rather than IBD (identical
by descent, where shared mutations that exist in different populations
originated from a common ancestor). In other words, since they could not
explain how the Iranian sample could possibly cluster with the Native American
X2a lineages, they deduced that the common mutation was simply due to chance
and not because of a more recent common ancestry. It wasn’t until 2008, with
the publication of two papers on Middle Eastern populations, that more light on the origin of haplogroup X was shed.42 One of them focused on the Druze population of northern Israel.

The Druze are a religious group
originating as an offshoot of Islam and numbering approximately one million
people living principally in Syria, Lebanon, Israel, and Jordan. The authors of
the paper on Druze mtDNAs observed that most of the X lineages found elsewhere
(Africa, Europe, and Asia) were also detected among the Druze, thus suggesting
that they could indeed have been the source population for the spreading of
haplogroup X throughout the world. Although no Native American X2a mtDNAs were
observed among these people, the Altaian X2e was one of the haplotypes that the
researchers identified, thus confirming a more recent migratory event that led
to the presence of X2e in modern-day southern Siberia. Additionally, in 2009 a
paper describing mtDNA lineages from Egyptian nomads revealed a small number of
haplotypes carrying the same diagnostic coding region mutation shared by the
Native American X2a samples and the one from Iran reported in 2003.43 This finding supports the conclusion that such a mutation may indeed be
ancestral to all of these samples, leaving the door open to future studies that
may contribute additional knowledge about a possibly more recent (when compared
to the Pan-American and Asian haplogroups) relationship between Amerindian X2a
and Middle Eastern haplotypes.

This brief summary of studies
focusing on the origin and diffusion of haplogroup X contains some of the
details that have been used in the Book of Mormon debate over the past few
years. Some Latter-day Saint scholars welcomed the association between a small
group of Native American lineages and people of the Middle East as genetic
evidence that indeed there was a group of seafaring Israelites that arrived in
the Americas within the last couple thousand years. On the other hand, critics
of the Book of Mormon dismissed this possibility by first referring to the
presence of haplogroup X among the Altaians (and therefore supporting the
scenario that this lineage followed the same Beringian route to the New World
at the same time as the other Pan-American mtDNAs).44 As already
discussed, this first hypothesis is now challenged by data from complete mtDNA
sequences that exclude the Asian X lineage from being the potential ancestor to
the American one. A second criticism with regard to a possible association
between Book of Mormon people and the X2a lineage is based on the current
coalescent age of haplogroup X2a, as well as findings based on ancient DNA
studies supporting a longer presence of this lineage in the
Americas—close in time to the origin of other Native American
haplogroups—and therefore predating the events recorded in the Book of

The first issue deals with the
age estimate based on modern DNA. There are currently five molecular clocks
that have been proposed to calculate the age of mtDNA lineages using data from
coding regions or complete sequences.45 Only one of
these mutation rates is based on the complete mtDNA genome (both control and
coding regions), providing an age estimate for
X2a (12,800 ± 6,600 years ago), which is similar to the four Pan-American
haplogroups.46 The ages obtained using the other molecular clocks are fairly comparable. The
X2a distribution limited to northern North America strongly suggests a separate
migratory event from Beringia through the ice-free corridor that was open
between the Cordilleran and Laurentide glaciers at the end of the last ice age.47 In order for X2a to fit within Book of Mormon chronology, the currently
accepted molecular clocks would need considerable recalibration,48 or other samples from the Old World carrying additional mutations shared with
the Native American X2a would be needed. Neither of these two scenarios is
currently likely, and neither may ever become a
means for conclusively demonstrating a link between X2a and Lehi’s party.

The discussion of the X haplotype
illustrates the challenges encountered when attempting to reconstruct
genetic scenarios from modern populations compatible with the Book of Mormon
time line and expected source population. 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. The only truly testable hypothesis that
unequivocally evaluates the historicity of the Book of Mormon from a molecular
perspective would be to know the actual genetic profiles of Lehi’s group,
identify them in the modern Native American populations, and find exact matches
in samples from their Middle Eastern area of origin (assuming that genetic
drift and population bottlenecks had not obliterated the genetic signal over
time). Unfortunately, as already discussed, to attribute a particular genetic
profile to Lehi’s group would be pure speculation, making the testing of this
hypothesis impossible.

Three studies explore the
presence of X2a in ancient times in the Americas.49 As
previously discussed, X2a is defined by five diagnostic mutations (two control
and three coding region transitions). However, researchers of ancient mtDNA
have been limited to a small segment of the control region, and therefore their
classification of mtDNA lineages from ancient samples was based solely on one
basal mutation for the root of haplogroup X (C16278T). This mutation is shared
by all the X lineages worldwide and is also a mutational hotspot—a
nucleotide position that recurrently mutates in the world mtDNA phylogeny.
According to a recent publication surveying 2,000 complete mtDNA sequences,
C16278T was the twelfth most common mutation observed.50 Using this
single site as the diagnostic mutation to place ancient samples into the X
haplogroup already poses a serious limitation to the accuracy of such
inferences. Two of the three papers in question predate the era of gold
standards for ancient DNA studies, which already constitutes a potential
concern in confidently accepting the quality of their results and subsequently
of the conclusion derived from such analyses.

The first paper dealt with a
burial site in Windover, Florida, where 176 individuals were identified and
recovered. The site was carbon-dated at approximately 7,000–8,000 years
ago, and a short section of the mtDNA control region (166 bases from position
16151 to position 16317) was sequenced for fourteen individuals. Two of the
specimens analyzed yielded the recurrent
mutation C16278T, which is also diagnostic for the whole X haplogroup. However,
neither of them reported the common G16213A transition, which would have been
found within the range that was sequenced. Additionally, the mutations of these
two haplotypes are not sufficient to allow an unambiguous assignment to either
haplogroup X2a or any of the other Pan-American haplogroups. The authors
admitted that “given the limited number of Windover samples currently
analyzed and the restricted length of mtDNA sequences analyzed . . . any
inference regarding Windover structure or its relationship to contemporary
Amerind groups is necessarily tentative.”51

The second paper dealing with
haplogroup X2a from ancient DNA was based on specimens retrieved from a Native
American cemetery at the Norris Farm site in Illinois. Archaeologists
classified the site as being part of the Oneota culture and dated it at about
1,000 years ago, a time frame that would somewhat fit  with Book of Mormon chronology.
DNA was extracted successfully from 108 individuals, but only 52 of them were
sequenced for a segment of the mtDNA control region (353 bases, from position 16056 to position 16409). Nearly all
haplotypes were assigned to one of the four major Pan-American haplogroups, with
the exception of two that bore the X-specific C16278T transition and none of
the A2, B2, C1, and D1 diagnostic mutations. However, as with the previous
paper, both samples are missing mutation G16213A, which is found in nearly all
modern-day X2a samples.

Contamination, postmortem damage,
parallel or back mutations, and misclassification due to the limited data
available might explain the presence of C16278T and the absence of G16213A,
which precluded a confident determination of haplogroup X in the ancient burial
sites described in these first two papers.52 Currently,
the first convincing evidence of haplogroup X in pre-Columbian America comes
from a 2002 study reporting ancient DNA data from an approximately
1,340-year-old burial site on the Columbia River
near Vantage, Washington.53 It is not excluded that future studies—including a more detailed and
controlled analysis of the samples from the 8,000-year-old Windover burial
site—may eventually confirm the presence of haplogroup X in
pre–Book of Mormon America. It is also possible that the specimens
analyzed could belong to a rarer or extinct X subclade, distantly related to
the more common X2a found in the modern native population of northern North
America, as demonstrated by the recently discovered X2g lineage found in an
Ojibwa sample.54

What about Other mtDNA Lineages Found in the Americas?

Molecular anthropologist Ted
Schurr addressed the issue of Amerindian lineages not belonging to the
classical Pan-American haplogroups by stating that

various studies have also revealed a high frequency of “private
haplotypes” in individual populations or groups of related Amerindian
tribes. These patterns reflect the role that genetic drift and founder effects
have played in the stochastic extinction and fixation of mtDNA haplotypes in
Native American populations.

A number of haplotypes not clearly belonging to these five
maternal lineages have been also detected in different Native American groups.
These “other” mtDNAs have often been considered additional founding
haplotypes or haplogroups in New World populations. However, most have since
been shown to be derivatives of haplogroups A–D that have lost diagnostic
mutations. The remainder appears to have been contributed to indigenous groups
through nonnative admixture. In addition, the “other” mtDNAs detected
in archeological samples may have resulted from contamination with modern mtDNAs,
or were insufficiently analyzed to make a determination of their haplogroup

The process of discovering
additional pre-Columbian lineages in the Americas is somewhat limited by the
preconceived notion that if a lineage does not fit with the classical Native
American haplotypes, it is most likely the result of a recent migratory event
from the Old World. For example, a 1999 study on the Cayapa tribe of Ecuador
revealed a number of lineages that did not fit with the five known Native
American haplogroups.56 Although the authors believed it could have been a newly identified
pre-Columbian lineage and called it the “Cayapa haplotype,” others
dismissed it as a possible case of European mtDNA introgression.57 However,
it was only when mtDNA data became available from the approximately
10,000-year-old Alaskan skeleton described earlier that the Cayapa haplotype
was confirmed as a genuine pre-Colombian novel lineage.58 From the
initial four Amerindian mtDNA haplogroups discovered in the early 1990s, at
least fifteen Native American founding lineages are currently catalogued, and
it is very likely that more will be identified in future studies.59 Additionally, detailed studies based on complete mtDNA sequences of haplotypes
belonging to peculiar branches of the four Pan-American haplogroups may reveal
interesting distribution patterns reflecting novel migratory events that could
not be detected based on control region data only.

What about Other Genetic Markers?

The purpose of this essay is to
provide an updated review of mtDNA research on Native American populations in
light of the Book of Mormon debate. In the interest of space, it is not
feasible to discuss in detail data from additional genetic systems, but a brief
review of findings will be highlighted.

Ycs data produced to date are still fairly scarce and have produced discrepant
results, suggesting that considerable work to fully investigate the history of
paternal lineages in the Americas is still badly needed. Future studies will
need to test many more samples at a higher level of resolution in order to
achieve a greater dissection and understanding of Amerindian Ycs haplogroups,
including a better calibration of the Ycs molecular clock. Additionally, while
autochthonous mtDNA lineages are still found abundantly among both indigenous
and mixed American populations,60 the European male contribution to the Native American gene pool was devastating
in terms of preserving the Native American genetic signal.
The genetic bottleneck experienced in Ycs lineages was tenfold more
severe than its female counterpart, thus making studies based on this
uniparental paternal marker far less informative in elucidating Native American
genetic history.

With regard to autosomal DNA, the
genetic reshuffling that occurs in each generation creates serious limitations
in the ability to trace specific ancestral lineages unequivocally. When
compared to Ycs and mtDNA markers, the study of
autosomal DNA is far more complex and is less forthcoming in straightforward
interpretation. Recent technological advances now allow for the testing of up
to one million polymorphic autosomal sites for an individual, providing an
unprecedented level of resolution in characterizing an individual’s genetic
profile. From such an abundance of data, statistical analysis can give the
estimated percentage of an ancestral population’s contribution to an individual’s
genetic makeup. This can provide a picture of possible genetic influences from
other populations that may not be reflected in the strictly maternal or
paternal ancestral lineage. However, with regard to the Book of Mormon
discussion, autosomal DNA inheritance is subject to the same population forces
as other genetic systems (genetic drift, genetic bottleneck, and founder
effect), and considering the likely demographic scenario of the Book of Mormon
(i.e., a small group of Old World migrants mixing with a large population of
ancient Asian origins), the probable findings of autosomal studies are unlikely
to contradict results already achieved with mtDNA and Ycs data. Native American
Ycs, mtDNA, or autosomal DNA data analyzed will likely continue to produce a
predominantly Asian signal.

A recent study based on a small
section of DNA found on chromosome 9 had the objective of determining the
origin and number of Paleo-Indian migrations. Based on their analysis, the
authors concluded that “all modern Native Americans . . . trace a large
portion of their ancestry to a single founding population that may have been
isolated from other Asian populations prior to expanding into the Americas.”61 This study was recently mentioned as further demonstration that conclusions by
critics of the Book of Mormon in the past are indeed correct, based on the fact
that the study purportedly reported that all Native American populations
and all individuals analyzed carried the same
autosomal polymorphic mutation also found in Asian populations.62 Book of Mormon opponents, however, disregard several key points in their
arguments. First, as already discussed, the
presence of indigenous populations of Asian origins prior to the arrival of
Book of Mormon people does not affect the historicity of the book itself. These
autosomal findings are in line with what is already known about Native American
populations and do not change arguments already
presented that propose that Book of Mormon
events are compatible with the Asian-dominated genetic landscape found in
Native Americans today. Population bottleneck, founder effect, genetic drift,
and other population-altering forces affect all genetic systems, including
autosomal DNA. It would not be unusual to expect that the small autosomal
contribution of Lehi and his followers could be lost over time when mixing with
an already established population of Asian origin. Additionally, the authors
concluded that “a large portion” and not all the Native American
ancestry can be traced to a single population with Asian affinity. A further
important point comes from the idea of hypothesis construction. This research
was not designed to identify a possible presence of Western
Eurasian–specific markers in the Amerindian populations, and thus it is
not surprising that none were found.

Of greater relevance to the
debate about possible subsequent migrations to the Western Hemisphere, besides
those that occurred after the last ice age, is a recent study published in the
prestigious journal Nature. The authors reported autosomal DNA data that
were successfully sequenced from hair belonging to a well-preserved
4,000-year-old Saqqaq individual discovered in Greenland.63 This
research has contributed greatly to the current understanding of events that
led to the peopling of the Americas. The authors concluded that the genetic
makeup of the ancient Saqqaq individual was very different from that of Inuit
or other Native American populations. Instead, he was closely related to Old
World Arctic populations of the Siberian Far East, being separated from them by
approximately two hundred generations (roughly 5,500 years). These data suggest
a distinctive and more recent migration across Beringia by a group of people
that were not related to the ancestors of modern-day Native Americans, who
arrived on the American continent nearly 10,000 years earlier. As the senior
author emphasized, the lack of genetic continuity between the ancient Saqqaq
individual and the modern population of the New World Arctic stands as a
witness that other migrations could have taken place that left no contemporary
descendants.64 In commenting about the findings of this project, population geneticist Marcus
Feldman from Stanford University said that “the models that suggest a
single one-time migration are generally regarded as idealized systems, like an
idealized gas in physics. But there may have been small amounts of migrations
going on for millennia.” He went to explain that “just because
researchers put a date on when ancient humans crossed the Bering Bridge, that
doesn’t mean it happened only once and then stopped.”65 Moreover, a
multiple population source/migration model for the peopling of the
Americas—which may have included additional routes besides the Bering
Strait crossing—was recently reproposed through the analysis of human
leukocyte antigen (HLA) genes.66


The Book of Mormon is not a
volume about the history and origins of all American Indians. A careful reading
of the text clearly indicates that the people described in the Book of Mormon
were limited in the recording of their history to events that had religious
relevance and that occurred in relatively close proximity to the keepers of the

The fact that the DNA of Lehi and
his party has not been detected in modern Native American populations does not
demonstrate that this group of people never existed, nor that the Book of
Mormon cannot be historical in nature. The absence of evidence is not evidence
of absence. Further, the very idea of locating the genetic signature of Lehi’s
family in modern populations constitutes a truly untestable hypothesis since it
is not possible to know the nature of their genetic profiles. Without our
knowing the genetic signature to be located, any attempt at researching it will
unavoidably result in further assumptions and untestable hypotheses. What were
the characteristics of Lehi’s DNA and the DNA of those who went along with him?
What haplogroup(s) did they belong to? We will never know. Yet this key point
seems lost on those who insist on using genetic evidence as a means to validate
or reject the Book of Mormon as a historical narrative. Attempting to make such
conclusions is a miscarriage of logic comparable to collecting and analyzing
the DNA of thousands of people living in the area surrounding a hypothetical
crime scene from which no DNA could be retrieved from the individual who
committed the crime, thus creating a
comprehensive database of all these people. Will the database include the DNA
signature of the criminal? If so, how could the perpetrator be identified among
the thousands of others? Similarly, would a database composed of thousands of
Native American DNA samples provide the necessary evidence to validate the
existence of a small group (perhaps as few as two mtDNA haplotypes) that
migrated from the Old World and settled somewhere in the Americas? Conversely,
could haplogroup X be undoubtedly inferred as the ultimate proof of the genetic
legacy this group left, without ever knowing their actual original DNA
signature? Mitochondrial DNA is a powerful tool in reconstructing the history
of our race, as demonstrated by the numerous
publications that have been produced over the past two and a half decades.
However, as has been amply demonstrated, knowing a great deal about the genetic
composition of modern-day Native American populations does not give conclusive
evidence of the validity or the implausibility of the Book of Mormon’s

An additional caveat is the lack
of professional training in population genetics by those promoting a supposed
discrepancy between the genetic evidence and the Book of Mormon account. Some
of them claim that their conclusions are strongly supported by trained experts
who have been consulted for unbiased opinions about this particular matter.67 This should raise some concerns, though, since it is fairly obvious that most
people outside of the circle of Mormonism have very limited knowledge of the
Book of Mormon and its contents. As a further counterpoint to the critics’
arguments, these experts seem to be in agreement that DNA lineages from a small
Old World group migrating to an already heavily populated American continent
would disappear.68 Moreover, it is also noteworthy that what these scientists know about what “Mormons
believe” has been provided mainly as one-sided background information from
the critics themselves. To offer a personal anecdote, my scientist colleagues
have asked me about DNA evidence and the Book of Mormon on several occasions. I
respond with a simple summary in which I explain that the DNA lineages of Lehi’s
colony could have been lost due to genetic drift since
the number of people involved was probably fairly small compared to the size of
the resident Amerindian population. I also explain that it is not possible to
distinguish those lineages from post-Columbian admixture, simply because 2,600
years is not enough time for Book of Mormon mtDNA to differentiate Lehi’s
descendants from their Eurasian counterparts. My colleagues typically reply
that they are not convinced that I have accurately represented what Latter-day
Saints believe—namely, that Lehi’s posterity comprises all Native
Americans. These personal experiences give context for evaluating “genuine
experts’ opinions,” based as they are on what the critics may have shared
as background information regarding the Book of Mormon and Latter-day Saint
beliefs. Ultimately, the critics’ arguments hold up only when they prescribe
what it is that Latter-day Saints believe. Since neither the Book of Mormon nor
church doctrine indicates that all Native Americans descend from the Book of
Mormon people, the critics’ arguments are on a weak footing at the outset.

light of the information provided in this essay, it should be evident that the
work of reconstructing the history of Native American populations using
molecular data is still under way. Some questions can be answered while many
more remain, spurring further research. The genetic evidence of the peopling of
the Americas is not fully understood, and it has evolved substantially over the
past two decades. DNA research, and particularly mtDNA data, has been produced
in great abundance during this time period and has provided an initial glimpse
into the history and prehistory of the indigenous peoples of the Western
Hemisphere. This is truly an exciting time to study the genetic history of
Native Americans, for there is much yet to be understood. For example, how is
the high frequency of haplogroup B in Southeast Asia and western South America
reconciled with its rarity in the native populations of north Siberia and
Alaska? The scarcity of archaeological evidence for human settlements on either
side of the Bering Strait provides a degree of intrigue, considering that mainstream scientists currently accept Beringia as the
likely refugium for Paleo-Indians during the last ice age, leaving open the
possibility for alternative routes into the Americas.69 Mitochondrial DNA is doubtless a powerful tool that can reveal details about
the expansion processes leading to the colonization of the world, including
America’s double continent. However, it is not well suited as the ultimate tool
to assess the historicity of religious documents like the Book of Mormon and
the Bible. If the DNA of Lehi and his family cannot be confidently detected in
the modern Amerindian population, does it mean that they never existed? The
principles underlying this question can be further extrapolated to other
religious scenarios. Can we use DNA to decisively prove that the great biblical
patriarchs—Abraham, Isaac, and Jacob—ever existed? What were their
own and their descendants’ mtDNA haplotypes? What about the other great Old Testament figures, such
as Joseph of Egypt, Moses, and Isaiah? Can we use DNA analysis to prove that
Jesus Christ lived? The New Testament mentions that Jesus had brothers and
sisters (Matthew 13:55–56; Mark 6:3) through whom Mary’s mtDNA could have
been transmitted to future generations (and if not through Mary, perhaps
through some of her female relatives). Where is their DNA in today’s
population? Would it be acceptable to conclude that these are fictional
historical figures and the biblical text a hoax because of the lack of genetic
evidence? As I already commented on another occasion: “I find no
difficulties in reconciling my scientific passion about Native American history
with my religious beliefs. I am not looking for a personal testimony of the
Book of Mormon in the double helix. The scientific method and the test of faith
are two strongly connected dimensions of my existence, working synergistically
in providing greater understanding, knowledge, and from time to time even a
glimpse into God’s eternal mysteries.”70 Anyone using
DNA to ascertain the accuracy of historical events of a religious
nature—which require instead a component of faith—will be sorely
disappointed. DNA studies will continue to assist in reconstructing the history
of Native American and other populations, but it is through faith that we are
asked to search for truth in holy writings (Moroni 10:3–5).71


am grateful to the following individuals for commenting on this manuscript: Dr.
Alessandro Achilli (University of Perugia, Italy), Jayne E. Ekins, Diahan
Southard, and Dr. Scott R. Woodward (Sorenson Molecular Genealogy Foundation,
USA), Professor Antonio Torroni (University of Pavia, Italy), and Dr. Amy
Williams (Harvard Medical School, USA).

1. Dennis H. O’Rourke, “Human
Migrations: The Two Roads Taken,” Current Biology 19/5 (2009):
R204, (accessed 2 June 2010).

2. Michael Crawford, The Origins
of Native Americans: Evidence from anthropological genetics
(Cambridge: Cambridge University Press, 1998), 2.

3. Geraldine Barnes, Viking
America: The First Millennium
(Suffolk, England: St. Edmundsbury
Press, 2001). Note that no genetic contribution from Vikings has been detected
to date in the modern Native American population. Either they kept to themselves
and were not welcomed by native groups, or their DNA has not yet been
identified in contemporary Amerindians. John L. Sorenson, “Ancient Voyages
Across the Ocean to America: From ‘Impossible’ to ‘Certain,'” Journal of
Book of Mormon Studies
14/1 (2005): 6, notes that the Viking
presence in North America has been considered to be of no historical importance
and goes on to present “decisive” empirical evidence of transoceanic
distribution of flora and fauna in pre-Columbian times. See also Martin H.
Raish and John L. Sorenson, Pre-Columbian Contacts with the Americas
across the Oceans: An Annotated Bibliography
, 2 vols. (Provo, UT:
Research Press, 1996).

4. Antonio Torroni et al., “Asian
affinities and continental radiation of the four founding Native American mtDNAs,” American
Journal of Human Genetics
53/3 (1993): 563–90; and Alessandro
Achilli et al., “The Phylogeny of the Four Pan-American MtDNA Haplogroups:
Implication for Evolutionary and Disease Studies,” PloS ONE 3/3
(2008): e1764.

5. For a summary of the
principal theories of Book of Mormon New World geography, see
(accessed 2 June 2010).

6. Carrie A. Moore, “Debate
renewed with change in Book of Mormon introduction,” Deseret
Morning News
(accessed 2 June 2010).

7. In Conference Report, April
1929, 15–16.

8. See, for example, 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; John L. Sorenson and Matthew Roper, “Before DNA,” Journal of
Book of Mormon Studies
12 (2003): 6–23; and Blake T. Ostler, “DNA
Strands in the Book of Mormon,” Sunstone, May 2005, 63–71.

9. This issue has been dealt
with competently in Daniel C. Peterson, ed., The Book of Mormon and DNA Research (Provo, UT: Neal A. Maxwell Institute for Religious Scholarship, 2008).
Examples of Book of Mormon criticisms based on alleged DNA evidence are found
in Simon G. Southerton, Losing a Lost Tribe: Native Americans, DNA, and the Mormon Church (Salt Lake City: Signature Books, 2004); Thomas W. Murphy, “Lamanite
Genesis, Genealogy, and Genetics,” in American Apocrypha: Essays on the Book of Mormon,
ed. Dan Vogel and Brent L. Metcalfe (Salt Lake City: Signature Books, 2002),
47–77; and Brent L. Metcalfe, “Reinventing Lamanite Identity,” Sunstone,
March 2004, 20–25. A seriously flawed attempt by a nonspecialist to
adduce DNA evidence in favor of Book of Mormon historicity is Rod L. Meldrum, Rediscovering
the Book of Mormon Remnant through DNA
(Honeoye Falls, NY: Digital
Legend Press, 2009).

10. See, for example, Ugo A.
Perego, Jayne E. Ekins, and Scott R. Woodward, “Mountain Meadows Survivor?
A Mitochondrial DNA Examination,” Journal of Mormon History 32/3
(Fall 2006): 45–53.

11. Stephen Anderson et al., “Sequence
and organization of the human mitochondrial genome,” Nature 290 (1981): 457–65.

12. Richard M. Andrews et al., “Reanalysis
and revision of the Cambridge reference sequence for human mitochondrial DNA,” Nature
23/2 (1999): 147.

13. Marianne Schwartz and John
Vissing, “Paternal Inheritance of Mitochondrial DNA,” New England
Journal of Medicine
347/8 (2002): 576–80.

14. Also called the hypervariable
or D-loop region.

15. Sometimes referred to as
HVR1, HVR2, and HVR3.

16. For example, Antonio Torroni
et al., “Native American Mitochondrial DNA Analysis Indicates That the
Amerind and the Nadene Populations Were Founded by Two Independent Migrations,” Genetics 130 (1992): 153–62; Antonio Torroni et al., “mtDNA and Y-Chromosome
Polymorphisms in Four Native American Populations from Southern Mexico,” American
Journal of Human Genetics
54/2 (1994): 303–18; Antonio Torroni
et al., “Mitochondrial DNA ‘clock’ for the Amerinds and its implications
for timing their entry into North America,” Proceedings of the National
Academy of Sciences
91/3 (1994), 1158–62; and Peter Forster et
al., “Origin and Evolution of Native American mtDNA Variation: A
Reappraisal,” American Journal of Human Genetics 59 (1996):

17. Antonio Torroni et al., “Do
the Four Clades of the mtDNA Haplogroup L2 Evolve at Different Rates?” American
Journal of Human Genetics
69/6 (2001): 1348–56.

18. Luísa Pereira et al., “The
Diversity Present in 5140 Human Mitochondrial Genomes,” American
Journal of Human Genetics
84 (2009): 628–40; and Mannis van
Oven and Manfred Kayser, “Updated Comprehensive Phylogenetic Tree of
Global Human Mitochondrial DNA Variation,” Human Mutation 30/2
(2009): E386–94, (accessed 4 June 2010). As of 10
November 2009, the publicly accessible GenBank database contained 6,747
complete mtDNA sequences, but the number of those belonging to known Native
American haplogroups still suffers from
significant underrepresentation. See (accessed 4
June 2010).

19. Alessandro Achilli and Ugo A.
Perego, “Mitochondrial DNA: A Female Perspective in Recent Human Origin
and Evolution,” in Origins as a Paradigm in the Sciences and in the Humanities, ed. Paola Spinozzi and
Alessandro Zironi (Goettingen: V&R unipress, 2010), 41–58.

20. Torroni, “Asian

21. Agnar Helgason et al., “A
Populationwide Coalescent Analysis of Icelandic Matrilineal and Patrilineal
Genealogies: Evidence for a Faster Evolutionary Rate of mtDNA Lineages than Y
Chromosomes,” American Journal of Human Genetics 72/6 (2003): 1370–88.

22. Simon Southerton, “Answers
to Apologetic Claims about DNA and the Book of Mormon,” (accessed 4 June 2010).

(accessed 4 June 2010).

24. Crawford, Origins of
Native Americans
, 49–51, 239–41, 260–61.

25. Beth A. S. Shook and David G.
Smith, “Using Ancient mtDNA to Reconstruct the Population History of
Northeastern North America,” American Journal of Physical Anthropology 137 (2008): 14.

26. Amy Harmon, “DNA
Gatherers Hit Snag: Tribes Don’t Trust Them,” New York Times, 10
December 2006,­-.html?_r=2&oref=slogin&pagewanted=all
(accessed 4 June 2010).

27. Alan Cooper and Hendrik N.
Poinar, “Ancient DNA: Do It Right, or Not at All,” Science 289/5482 (2000): 1139.

28. Adrian W. Briggs et al., “Targeted
Retrieval and Analysis of Five Neandertal mtDNA Genomes,” Science 325 (2009): 318–21; and Luca Ermini et al., “Complete Mitochondrial
Genome Sequence of the Tyrolean Iceman,” Current Biology 18 (2008): 1687–93.

29. Brian M. Kemp et al., “Genetic
Analysis of Early Holocene Skeletal Remains from Alaska and Its Implications
for the Settlement of the Americas,” American Journal of Physical Anthropology 132
(2007): 605–21.

30. 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. A single
haplotype sharing part of the D4h3 motif was also identified in the province of
Shandong, China, out of more than 10,000 Asian mtDNAs.

31. Although some information is
available about the ancestry of Lehi and Ishmael, we know nothing about the
origins of Sariah and Ishmael’s wife, who were responsible for passing their
mtDNA to future generations.

32. Erika Tamm et al., “Beringian
Standstill and Spread of Native American Founders,” PloS ONE 2/9 (2007): e829.

33. Forster, “Origin and
Evolution of Native American mtDNA Variation.”

34. Michael D. Brown et al., “mtDNA
Haplogroup X: An Ancient Link between Europe/Western Asia and North America?” American
Journal of Human Genetics
63/6 (1998): 1852–61; and David G.
Smith et al., “Distribution of mtDNA Haplogroup X Among Native North
Americans,” American Journal of Physical Anthropology 110/3
(1999): 271–84.

35. Rosaria Scozzari et al., “mtDNA
and Y Chromosome-Specific Polymorphisms in Modern Ojibwa: Implications about
the Origin of Their Gene Pool,” American Journal of Human Genetics 60/1 (1997): 241–44; and Perego, “Paleo-Indian Migration.”

36. Achilli, “Phylogeny”;
and Perego, “Paleo-Indian Migration.”

37. Dennis Stanford and Bruce
Bradley, “Ocean Trails and Prairie Paths? Thoughts about Clovis Origins,”
in The
First Americans: The Pleistocene Colonization of the New World
, ed.
Nina G. Jablonski (San Francisco: Academy of Science, 2002), 255–71; and
Bruce Bradley and Dennis Stanford, “The North Atlantic ice-edge corridor:
a possible palaeolithic route to the New World,” World
36/4 (2004): 459–78.

38. Miroslava V. Derenko et al., “The
Presence of Mitochondrial Haplogroup X in Altaians from South Siberia,” American
Journal of Human Genetics
69/1 (2001): 237–41.

39. Maere Reidla et al., “Origin
and Diffusion of mtDNA Haplogroup X,” American Journal of Human Genetics 73/5
(2003): 1178–90.

40. Reidla et al., “Origin
and Diffusion,” 1188.

41. Reidla et al., “Origin
and Diffusion,” 1187.

42. Shlush et al., “The
Druze: A Population Genetic Refugium of the Near East,” PloS ONE 3/5
(2008): e2105; and Doron M. Behar et al., “Counting the Founders: The Matrilineal
Genetic Ancestry of the Jewish Diaspora,” PloS ONE 3/4 (2008):

43. Martina Kujanová et al., “Near
Eastern Neolithic Genetic Input in a Small Oasis of the Egyptian Western
Desert,” American Journal of Physical Anthropology 140/2
(2009): 336–46.

44. Perego, “Paleo-Indian

45. For details about the five
age-estimate models based on complete mtDNA sequences, see Dan Mishmar et al., “Natural
selection shaped regional mtDNA variation in humans,” Proceedings
of the National Academy of Sciences
100/1 (2001): 171–76;
Toomas Kivisild et al., “The Role of Selection in the Evolution of Human
Mitochondrial Genomes,” Genetics 172/1 (2006):
373–87; Perego, “Paleo-Indian Migration”; Pedro Soares et al., “Correcting
for Purifying Selection: An Improved Human Mitochondrial Molecular Clock,” American
Journal of Human Genetics
84/6 (2009): 740–59; and Eva-Liis
Loogväli et al., “Explaining the Imperfection of the Molecular Clock of
Hominid Mitochondria,” PloS ONE 4/12 (2009): e8260.

46. Soares et al., “Correcting
for Purifying Selection.”

47. Perego, “Paleo-Indian

48. Supporters of X haplogroup as
evidence for Book of Mormon historicity and its geographic setting in northern
North America rely on the unpopular molecular clock proposed by a forensic team
in 1997. This clock was based on control region data only. See Thomas J.
Parsons et al., “A high observed substitution rate in the human mitochondrial
DNA control region,” Nature Genetics 15 (1997): 363–68.

49. William W. Hauswirth et al., “Inter-
and intrapopulation studies of ancient humans,” Experientia 50/6
(1994): 585–91; Anne C. Stone and Mark Stoneking, “mtDNA Analysis of
a Prehistoric Oneota Population: Implications for the Peopling of the New
World,” American Journal of Human Genetics 62/5 (1998):
1153–70; and Ripan S. Malhi and David G. Smith, “Brief
Communication: Haplogroup X Confirmed in Prehistoric North America,” American
Journal of Physical Anthropology
119 (2002): 84–86.

50. Soares, “Correcting for
Purifying Selection.” A similar outcome was observed when querying the
Sorenson Molecular Genealogy Foundation mtDNA database (, accessed
8 June 2010). Out of more than 76,000 samples, C16278T was observed in 8,501
cases in several haplogroups, including all the Pan-American lineages.

51. Hauswirth et al., “Inter-
and intrapopulation studies of ancient humans,” 589.

52. Malhi and Smith, “Haplogroup
X Confirmed” 85.

53. Malhi and Smith, “Haplogroup
X Confirmed.”

54. Perego, “Paleo-Indian
Migration,” 2.

55. Theodore G. Schurr, “The
Peopling of the New World: Perspectives from Molecular Anthropology,” Annual
Review of Anthropology
33 (2004): 556.

56. Olga Rickards et al., “mtDNA
History of the Cayapa Amerinds of Ecuador: Detection of Additional Founding
Lineages for the Native American Populations,” American Journal of Human
65/2 (1999): 519–30.

57. Schurr, “Peopling of the
New World.”

58. Kemp, “Holocene Skeletal

59. Achilli, “Phylogeny”;
Perego, “Paleo-Indian Migration”; Ugo A. Perego, “The Origin of
Native Americans: A Reconstruction Based on the Analysis of Mitochondrial Genomes”
(PhD diss., Université di Pavia, Italy, 2009); Ripan S. Malhi et al., “Brief
communication: Mitochondrial Haplotype C4c Confirmed as a Founding Genome in
the Americas,” American Journal of Physical Anthropology 141 (2010):
494–97; and Ugo A. Perego et al., “The Initial Peopling of the
Americas: a Growing Number of Founding Mitochondrial Genomes from Beringia,” Genome

60. Alessandro Achilli et al., “The
mitochondrial DNA landscape of modern Mexico,” American Society of Human
Genetics, 58th Annual Meeting, Philadelphia, 11–15 November 2008; and
Alessandro Achilli et al., “Decrypting the mtDNA gene pool of modern
Panamanians,” American Society of Human Genetics, 59th Annual Meeting,
Honolulu, 20–24 October 2009. Approximately 80 percent of the samples
tested for the Mexican (n = approx. 2,000) and the Panamanian (n = approx. 500)
mixed populations belonged to one of the four Pan-American haplogroups.

61. Kari B. Schroeder et al., “Haplotypic
Background of a Private Allele at High Frequency in the Americas,” Molecular
Biology and Evolution
26/5 (2009): 995.

62. “A Quantum Leap in DNA
Studies,” (accessed January 2010). This
article has since been removed from Signature Books’ Web site.

63. Morten Rasmussen et al., “Ancient
human genome sequence of an extinct Palaeo-Eskimo,” Nature 463 (2010): 757–62.

64. Cassandra Brooks, “First
ancient human sequenced,”
(accessed 9 June 2010).

65. Brooks, “First ancient
human sequenced.” The second quotation is Brooks’s paraphrase of Feldman.
See Michael H. Crawford, The Origins of Native Americans, 4. In his lengthy
review of data supporting the Asian origins of the Amerindians, he stated that “this
evidence does not preclude the possibility of some small-scale cultural
contacts between specific Amerindian societies and Asian or Oceanic seafarers.”

66. Antonio Arnaiz-Villena et
al., “The Origin of Amerindians and the Peopling of the Americas According
to HLA Genes: Admixture with Asian and Pacific People,” Current
11/2 (2010): 103–14.

67. See, for example, the
introduction to Southerton’s Losing a Lost Tribe or Living
Hope Ministries’ DNA vs. the Book of Mormon (DVD, 2003).

68. “What Happens
Genetically When a Small Population Is Introduced into a Larger One?” (accessed November 2009). This
article has since been removed from Signature Books’ Web site. The exact
question asked was, “If a group of, say, fifty Phoenicians (men and women)
arrived in the Americas some 2,600 years ago and intermarried with indigenous
people, and assuming their descendants fared as well as the larger population
through the vicissitudes of disease, famine, and war, would you expect to find
genetic evidence of their Phoenician ancestors in the current Native American
population? In addition, would their descendants be presumed to have an equal
or unequal number of Middle Eastern as Native American haplotypes?”

69. Dennis H. O’Rourke and
Jennifer A. Raff, “The Human Genetic History of the Americas: The Final
Frontier,” Current Biology 20/4 (2010): R202–7.

70. Ugo A. Perego, “Current
Biology, SMGF, and Lamanites,” (accessed 9 June

71. Jeffrey R. Holland, “Safety
for the Soul,” Ensign, November 2009, 88–90,,5232,23-1-1117-28,00.html (accessed 9
June 2010).