LDS Church Part Two: Interpreting the DNA Data and the Book of Mormon
Part Two: Interpreting the DNA Data and the Book of Mormon
By John A. Tvedtnes
Comment on Article
Part 1 of 3 - Unwarranted Assumptions
During the past few years, a number of anti-Mormon writers and groups have been pushing the idea that DNA Studies of Native Americans prove that the Book of Mormon is false. They claim that these studies prove that all Native Americans have Asian ancestry. When Latter-day Saint scholars have shown that this does not contradict the Book of Mormon, the critics have sought to discount scholarly research that suggests that the peoples mentioned in the Book of Mormon were not alone in the New World and that events depicted in that volume took place in Mesoamerica. In doing this, they have relied on popular opinions about these people and events rather than on the text itself. [ii]
While generally not questioning the results of the DNA studies, I find serious problems in the interpretation placed on these results by critics of the Book of Mormon. For example, the original studies do not claim that the results exclude the possibility that Lehi (or even other groups) migrated to the Americas; the critics added that claim. Indeed, one non-Latter-day Saint scientist, looking at the DNA studies, has concluded that there is, indeed evidence for migration to the New World by various groups, including people from the ancient Near East. We shall return to this later.
A Priori Assumption
All DNA studies begin with the a priori assumption that the New World was populated from Asia via a land bridge called Beringia, thought to have connected Siberia with Alaska during the last ice age. The idea originated in 1589 with José de Acosta, a Jesuit missionary from Spain.
Today, the Bering Strait separates the Asian and North American continents by a mere 53 miles. The water depth in this region is 98 to 164 feet, and there are numerous islands in the strait. During the time of the last ice age, so much of the sea water was frozen into glaciers that the sea level in this area dropped by about 300 feet, leaving a narrow land passage where water exists today.
This has led anthropologists to postulate man's arrival in the New World 13-14,000 years ago, when there was an ice-free corridor in the midst of the glacial masses leading from Beringia to the United States. This idea has archaeological support from Paleoindian sites. More recent DNA studies push the arrival of humans in the Americas back to at least 30,000 years B.P., leading to deep divisions in the ranks of archaeologists.
Prior to the development of DNA research, anthropologists relied on phenotypical studies, noting facial similarities between Asiatics and Native Americans and the fact that newborns in both Asia and the Americas are born with a dark blue spot in the lower back, adjacent to the buttocks. For skeletal materials, the shape and measurements of skulls and teeth were used to determine genetic relationships. The frequency of the various blood types was also considered to be a marker of an Asian origin for Native Americans, despite the fact that all blood types are found on each of the world's continents. [iii]
DNA and Ancestry
It was a monk named Gregor Mendel (1823-1884) who first noted the principles underlying biological inheritance. Unrecognized in his own day, his groundbreaking discoveries led to the science of genetics. The discovery of chromosomes and the genes of which they are comprised narrowed the processes of procreation and regeneration down considerably. The presence of deoxyribonucleic acid, commonly called DNA, found in the nucleus of all cells, was believed to lie behind these processes and was the stuff of which genes are made. In the fall of 1951, James Watson and Francis Crick began unraveling the structure of DNA and eleven years later, in company with Maurice Wilkins, who had performed the initial X-ray crystallography studies of DNA, they received the Nobel Prize for Medicine.
Strands of nuclear DNA (nDNA) are long polymers built of millions of nucleotides that are linked together by what are termed bases, to form a double helix. Nuclear DNA controls heredity on the molecular level, storing the necessary information in a sequence of bases along the polynucleotide chain. These bases or nucleotide sequences are built of four organic substances, adenine (A), cytosine (C), guanine (G), and thymine (T), linked by phosphate and sugar molecules. The sequence of these bases is the underlying chemical mechanism that contains all of the information necessary for a fertilized egg to produce a biological form, including human beings. In that respect, it can be likened to a computer code. [iv]
In a process known as replication, the two halves of the nDNA helix separate and each reproduces its counterpart. This is possible because thymine always pairs with adenine and guanine always pairs with cytosine. On a larger level, the chromosomes (which can be seen via an optical microscope) double, then separate with two halves of the cell, in a process known as mitosis. When the missing bases are recreated, it leads to the production of two separate cells, each of which has the same genetic material as its twin. Thus, as some body cells die, they are replaced by others that result from mitosis. [v]
A similar process occurs in the production of gametes or reproductive cells (ova and spermatozoa) in the testes and ovaries. This process, known as meiosis, involves the division of cells as in mitosis, plus an additional division in which the chromosomes are not replicated. Consequently, each gamete has only one set of chromosomes rather than pairs of chromosomes. Because of this, each parent passes to his/her offspring only 50% of his/her nuclear DNA inherited from his/her parents. Which DNA is passed to one's offspring depends largely on how it was divided up during the production of gametes. With 23 chromosomes in each gamete, each one comprising a large number of genes, the number of variations among male or female gametes is rather high. Crossover or exchange of genetic material between paired chromosomes during meiosis increases the variety of DNA that can be passed on. This makes it possible for each child to have a different genetic makeup from that of his/her siblings while sharing much of the inherited genetic material. [vi]
Over time, minute changes or mutations occur in the nucleotide chains, often by substitution of one base for another. [vii] This results in inherited genetic material from a common ancestor having a different chemical composition in individuals descended from that ancestor. Thus, corresponding loci (called alleles) on the nucleotide chain can differ between individuals even when the alleles in question came from the same source. This is called polymorphism, which in effect denotes a variety of alleles descended from a common source.
Human beings have 23 pairs of chromosomes in the nucleus of each cell, except when it comes to the gametes (ova and sperm), which are cells used for reproduction. The gametes are haploid, containing just one set of 23 chromosomes, while all the other cells in the body are diploid. Each female diploid cell includes a pair of chromosomes designated X, while each male diploid cell has one X chromosome paired with a Y chromosome. [viii]
When the male and female gametes merge during fertilization to produce a zygote, the chromosomes from the father match up with their female counterparts and the process of replication begins and continues, in humans, for about nine months. Consequently, each of us has received half of his/her nuclear genetic material from his/her mother and half from the father. If the sperm that fertilizes the ovum (egg) has an X chromosome, it pairs with an X chromosome from the mother and produces a girl. If the sperm has a Y chromosome, it similarly pairs with the X from the mother and produces a boy. [ix]
Most DNA is found in the chromosomes located in the nucleus of the cell and is hence called nuclear DNA (nDNA). However, small structures outside the nucleus, called mitochondria (singular mitochondrion), also have DNA strands called mitochondrial DNA (mtDNA). Unlike nDNA, mtDNA is not recombinant, meaning that it does not contain the genome code that enables cells to replicate and, in the case of gametes, to merge the maternal and paternal DNA. Rather, its function is to enable the cell to use the energy provided by nutrients coming via the bloodstream. In addition, mtDNA contains only 37 genes, compared with the tens of thousands in nDNA, and the mtDNA genome represents about .0005% of one's entire genome. Because sperm cells generally lose their mitochondria during the fertilization process, the mtDNA in each human being is inherited only from the mother. [x]
Examining the DNA of an individual and comparing it with the DNA of close relatives can establish the origin of specific genetic markers in the parents, grandparents, or other shared ancestors. Because of the complexity of nDNA, its recombination in each generation, and occasional mutations, it is much more difficult to trace one's genealogy over many generations. [xi] While all of one's distant ancestors have the potential of contributing to one's DNA, in practical terms it doesn't work that way. After many generations of recombination in both maternal and paternal ancestors, some of the nDNA simply is not passed on to the next generation. Indeed, in each generation, each parent passes on only 50% of his/her nuclear DNA inherited from his/her parents, because there are a finite number of positions to fill in each succeeding generation. [xii]
The task is greatly simplified when it comes to determining strict male and female ancestral lines. Since the Y chromosome is passed from father to son, it is possible to determine common paternal ancestry (patrilineage) shared by two or more individuals, especially if they are closely related. Most changes to the genetic makeup of the Y chromosome are due to mutations, though there are occasional gene transfers from other chromosomes (usually the X chromosome with which the Y is paired). Each time a man fathers a daughter, his Y chromosome is lost to that line, unless one of her descendants marries a male who picked it up from her brother or another male relative (e.g., an uncle, a cousin, or a grandfather) of the same patrilineage. [xiii]
Similarly, since only daughters pass their mtDNA to their offspring, one can determine common maternal ancestry (matrilineage) as well. [xiv] In both cases, one must take into account that mutations occur in the DNA so that there are minute changes over time. Thus, while the paternal (Y-chromosome) and maternal (mtDNA) markers passed down through the generations will be similar, there will be individual differences caused by mutation and other factors. It is possible for these paternal and maternal markers to be discernible thousands of years later in descendants whose nuclear DNA no longer resembles that of the ancestor. This is because nDNA, like radioactive elements, has a half-life. In each generation, it loses half of its substance during gamete production and that half combines with the nuclear DNA from the other parent to produce offspring. After many generations, the nDNA inherited from a specific ancestor may be so minute in a descendant as to be undetectable or may have disappeared altogether, either through mutation or the recombination process that occurs during fertilization of the ovum.
For Native American studies, geneticists have concentrated mostly on mitochondrial DNA (mtDNA, inherited from one's mother), though some studies of the Y chromosome (inherited by males from the father) have also been published. While there is some disagreement on the actual numbers, most geneticists believe that mutation in mtDNA occurs at a steady rate, making it possible to determine how long ago a given haplogroup entered the New World. Most mtDNA studies have concentrated on living populations from whose samples ancestral mtDNA has been postulated. Thus, if certain mtDNA markers are found in contemporary Asian and Native American populations, it is assumed that these came from a common female ancestor.
Most tests of mtDNA sequence a small portion (400, 2.4%) of the 16,569 base pairs in the mtDNA molecule, looking for specific "markers" of matrilineal ancestry. Malhi and Eshleman wrote that, "For both mtDNA and Y chromosome, haplogroups are usually defined by a single nucleotide polymorphism (or SNP) which is a single change or mutation in the DNA sequence. For example, all individuals in mtDNA haplogroup A share a mutation at nucleotide position 663 in the mitochondrial genome." [xv] This does not take into account that other ancestral lines may have developed the same mutation over time. If none of the markers are found, the sample is classified as "other" and, in the case of Native American mtDNA, is routinely assumed to derive from post-Conquest Europeans. The history of genetics research has demonstrated that this explanation is not always correct.
Other mtDNA Haplogroups
Clearly, the mtDNA evidence suggests an Asian origin for the four major Native American haplogroups or matrilineages, designated A, B, C, and D (and perhaps X, which will be discussed later). What Book of Mormon critics fail to note is that other, less important haplogroups have also been found in the New World, which means that none of the research actually excludes ancient immigrations from other parts of the world. Some researchers dismiss these other haplogroups as later admixture from Old World immigrants since the time of Columbus, but studies of this matter are insufficient to establish that there were no other migrations in ancient times. A report issued in 2003 declares that "haplogroup frequencies alone cannot distinguish between admixture and common ancestry." [xvi] The authors also note,
However, it is important to remember that mtDNA is but one marker, and one that is solely maternally inherited, and is unlikely to answer all questions regarding the origins of Native Americans ... Like mtDNA, Y-chromosome data have not on their own conclusively answered questions regarding either source populations within Asia or the number of migrations out of Asia into the New World. Clearly, nuclear markers from more populations should be examined to provide additional data relevant to these controversies, even though it is unlikely that additional data will significantly simplify what is a convoluted and complex scenario of migrations and postmigrational evolutionary forces. [xvii]
Continuing, they write that:
In almost all studies of ancient Native American populations [from skeletal remains], individuals have been discovered who do not appear to belong to one of the five founding lineages. In many cases, this is undoubtedly a result of external contamination of samples lacking DNA or in which the DNA is inhibited from amplifying using the polymerase chain reaction. Nonetheless, the possibility remains that additional haplogroups may be discovered by studies of ancient DNA in the Americas. Such a lineage may have either become extinct or be a yet-undiscovered lineage persisting at low levels in modern populations. [xviii]
The authors of the report note that, "Early studies of Na-Dene populations [of North America] suggested that they possessed high frequencies of haplogroup A but lacked haplogroup B and exhibited only low frequencies of haplogroups C and D, whereas Eskimo-Aleut populations appeared to have high frequencies of haplogroups A and D but lacked haplogroups B and C. However, on closer inspection of a large number of samples, Merriwether, Rothhammer, and Ferrell demonstrated that groups traditionally classified as Eskimo and Na-Dene had measurable frequencies of all four haplogroups when larger samples were assayed." [xix] The lesson to be learned from this is that undersampling cannot give us the whole picture.
A 1991 study of the Nuu-Chah-Nulth tribe of the Pacific Northwest revealed some 28 haplotypes, of which 19 clustered in the four maternal DNA haplogroups (A, B, C, and D), while 9 did not. [xx] Because of DNA changes over time due to mutation and other factors, a given haplogroup typically includes various haplotypes or individual lineage markers that descend from a common source. No explanation was given for the other 9 haplotypes.
Mayan Samples
The authors of a 2001 study of skeletal remains from precolumbian Maya burials recovered from the Late Classsic/Postclassic site of Xcaret in the Mexican province of Quintana Roo noted that "Many analyses of mtDNA haplotypes in New World contemporary and ancient populations have shown the presence of a small number of individuals possessing none of the markers defining the four founding lineages." [xxi]
In 1998, 102 DNA samples were taken from skeletal remains at the Norris Farms Oneota prehistoric (700 years old) cemetery, with successful extraction of mtDNA from 50 of them. All four of the American haplogroups were found, along with one individual with a haplogroup not previously attested in contemporary Native Americans and designated as N. The researchers wrote, "This new mtDNA lineage might be present in contemporary Amerindian populations but not yet sampled, or it might belong to a lineage that is no longer present in contemporary populations. Alternatively, this new mtDNA lineage might actually be one of the four lineages, but a mutation or reversion has occurred at the relevant diagnostic marker, thereby obscuring the affiliation of this mtDNA type. Another possibility is that this sample was contaminated by modern DNA of non-Amerindian origin." [xxii] In 1998, the researchers summarized a study of mtDNA from skeletal remains of 108 individuals from the same site, of which 6 fell outside the four Asian haplogroups and were lumped together as "other." They noted that "data indicate that the lineages from haplogroups A, B, C, and D are the most common among Native Americans but they were not the only lineages brought into the New World from Asia. The mtDNA evidence . . . suggests a single 'wave' of people with considerable mtDNA diversity." [xxiii]
The variety of findings from mtDNA research was summed up in a 1998 article, [xxiv] in which the authors wrote that
Some of the hypotheses based on the interpretation of mitochondrial haplotypes are conflicting. Mitochondrial analysis has been invoked to support a multiwave-founder colonization of America, whereas, on the other hand, mtDNA markers have also been interpreted as supporting a monophyletic colonization from Asia. Archaeological studies seem to indicate an antiquity in the range of 11,000-33,000 years before the present (YBP) for the first settlements in Beringia and the New World, whereas different laboratories working with mitochondrial polymorphisms have proposed times in the range of 14,000-55,000 YBP for this event. Founder maternal Amerindian lineages initially had been estimated as being four. Now it is assumed that there are > 10-13 such lineages, although there is no agreement on the molecular typification of some of these founder haplogroups. [xxv]
The disagreement over the migration of the four major mtDNA lineages (whether one or more migrations) is further complicated by the fact that geneticists are not in agreement concerning the other mtDNA haplotypes found in Native American samples. Torroni and colleagues believe that only one haplotype from each of the four founding lineages arrived in the New World via migration and that all the additional variation arose in the New World, with other types being attributed to later Caucasian admixture. On the other hand, Merriwether and Ferrell believe that "multiple variants of each lineage entered the New World, and that additional unrelated lineages also entered." They illustrate this by two additional lineages they call X6 and X7, found throughout the New World, Siberia, and Asia, providing "strong evidence that at least nine different founding lineage haplotypes entered the New World," and that "these distributions among Native Americans best fit a single wave of migration into the New World." [xxvi]
Most researchers have tended to dismiss the minor haplogroups detected among Native Americans as admixture following the arrival of Europeans in the New World or to ignore them completely. From the data collected thus far, the critics find it easy to ignore the possibility that Book of Mormon peoples imported any of these haplogroups. When Latter-day Saints point out the inconsistencies, they respond that only the major haplogroups count, since all Native Americans are supposedly descended from Lehi. This information comes not from the text of the Book of Mormon, but from the interpretation some have erroneously placed on the text. [xxvii]
When geneticists examine Native American DNA, they use procedures to screen for each of the four (now five) "Native American" haplogroups. If, after screening a sample without a successful identification, the sample is labeled "other." Ultimately, some of these "others" are found to be related to samples tested from other settlements or archaeological sites, and can then be classified as a new haplogroup. This is what happened with haplogroup X.
Haplogroup X
A brackish pond (bog) at Windover, adjacent to Titusville, Florida, has preserved the largest North American collection of human skeletal remains and fabric for its time, along with the largest tool collection. Brain tissue was preserved in nearly a hundred of the skeletons and was extracted for DNA analysis. None of the common Native American mtDNA haplogroups (A, B, C, and D) were present, but haplogroup X, known mostly from Europe, was plentiful, suggesting that these ancient remains are of people of European ancestry. [xxviii] Later research concluded that there was a persistence of both nuclear and mitochondrial haplotypes at Windover throughout its entire period of use. "Analysis of the mtDNA sequences suggests that some mitochondrial types are clearly related to extant Amerind types, whereas others, more distantly related, may reflect genetically distinct origins." [xxix]
A study reported in 2000 examined DNA samples drawn from human remains ranging from 300-6,000 years in age, from the Aleut, eastern Utah Fremont, Southwestern Anasazi, Pyramid Lake (Nevada), Stillwater Marsh (Nevada), and Oneota (western Illinois), which were then compared with 41 samples from contemporary North American populations. The report admits that "Haplogroup X is an additional ancestral Amerindian mtDNA lineage and is evident upon screening with additional markers and through sequence analysis. Because most of the samples available for analysis have not been screened for these additional markers, it is not possible to identify haplogroup X in all these data." The researchers also noted that "although haplogroup assignment is straightforward in modern samples, it is not always so easy for ancient samples." [xxx]
A 1999 study examined 70 samples of Native American mtDNA, most of which did not evidence any of the four haplogroups (A-D). Of these, 32 were found to belong to haplogroup X. The researchers concluded that
the wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestral descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups. [xxxi]
The authors also note that, "Haplotypes that are not members of A, B, C, or D and that are characterized by specific mutations have been reported in modern (presumably unmixed) Native Americans and in prehistoric individuals, suggesting that founding haplogroups other than A, B, C, and D were once present in the New World, whether or not they have survived," [xxxii] adding that "it is of interest to determine whether or not additional founding haplogroups were once present, but have since become extinct, in the New World." [xxxiii] They cite a 1996 study by Lorenz and Smith, who worked with mtDNA samples from 829 Native North Americans and classified 50 of them as "other" than the four haplotypes (A-D). Revisiting the data, the new study was able to rescreen mtDNA from 25 of the 50, they found that seven had been mistyped and were reassigned to haplogroups A and C (2 each) and D (3), with some of the others assigned to haplogroup X. [xxxiv]
Initial mtDNA studies suggested that there were four haplogroups (A-D) found among Native Americans that are also attested mostly in Asia, though they are not the dominant haplogroups in Asia. Indeed, the earliest studies did not detect haplogroup B in Siberia. [xxxv] The discovery of a fifth haplogroup, X, led to suggestions that it may be due to a migration from Europe, since X had not yet been attested in Asia but was found in DNA samples from Finland, Italy, and Israel, with possible connections to samples from Spain, Bulgaria, and Turkey. [xxxvi] As it turns out, haplogroup X was later identified at a low frequency (3.5%) among the Altaians of Siberia. [xxxvii] While the critics believe that this seals the fate of the Book of Mormon, it really demonstrates that all of the evidence is not yet in and that new discoveries are the norm. If, following further research, a haplogroup not attested in Asia was found in some Asian populations, could not the same thing happen in the New World as the DNA sampling increases the size of the database?
Critics have suggested that even though mtDNA haplogroup X is represented in the Near East, the time-depth for its arrival in the New World is too great to be attributable to Lehi's group. But the existence of this haplogroup in the New World at the time of Lehi's arrival does not a priori mean that it did not exist among the Lehites. If Sariah and her daughters or the wife of Ishmael and her daughters carried haplogroup X into the New World, it would be different from the X haplogroup found among Native Americans because it would have a different mutational history. But since the same haplogroup is different in various Native Americans because of genetic drift following their separation from other New World inhabitants, none of them are precisely like those of such other inhabitants, nor are they identical to the haplogroup X found in Siberia.
The debate about the origin of haplogroup X continues to this day. Because it is attested in higher percentages among Europeans sampled than Asians and because the Native American X shares affinities with the European X not found in the Asian, [xxxviii] some researchers have suggested that it was brought to the New World from Europe across the north Atlantic by people hunting seals. Archaeologists have demonstrated that the earliest spear points found in the Americas are identical in design and method of production to the Solutrean points found in western Europe (notably France and Spain) for the same time period, and that these points are ancestral to the Clovis points previously thought to be the earliest use of flaked stone tools in the New World.
Dennis Stanford of the Smithsonian Institution, an archaeologist who drew attention to the Solutrean connection, said, "The way the tools are made, the whole tool kit, bone artifacts and some artistic expressions are similar, and burial practices are similar." [xxxix] Stanford noted that "There are so many matching steps in how they made their tools: bifacial flaking, heat treatment, similar ceremonial items, the presence of red ochre. There must be fifty or sixty points of comparison. It can't be chance." [xl] Among the more important New World prehistoric sites with suspected ties to the Solutrean culture of Europe are Meadowcroft Rock Shelter, near Pittsburgh, Pennsylvania, and Cactus Hill, Virginia. [xli]
Significantly, both the Solutrean points and mtDNA haplogroup X are attested in a geographical region most likely to have been affected by a migration from Europe. Haplogroup X is found principally among the Algonquian-speaking peoples of the Great Lakes region, including the Ojibwa, but has also been found among the Nuu-Chah-Nulth and Yakima tribes of the northwest. It is known in about a fourth of Ojibwa natives tested and in lesser amounts among members of the Sioux and Navajo. [xlii] It has also been found in skeletal remains of two individuals found in a fourteenth-century burial in Illinois, demonstrating that it was in North America prior to the time of Columbus.
Despite these evidences, other researchers have suggested that haplogroup X came from Europe or Central Asia across Beringia to the New World, leaving very little trace in Siberia. Ripan S. Malhi and David Glenn Smith noted that the Altai of Siberia "are the only known modern ethnic group whose membership represents all five Native American haplogroups and, assuming the New World was colonized by a single migration, constitute a possible origin of the founders of Native America." This leads them to reject the hypothesis of a European migration of haplogroup X to the New World and discount the suggestion that there are similarities between Clovis and Solutrean cultural artifacts. Because it is found among ancient samples from the Norris Farms, Windover, and Vantage sites and the Amazon Basin, they consider haplogroup X to be "a founding Native American lineage" and reject the idea that it resulted from Viking or more recent European admixture. They note that three Algonquian-speaking Native Americans "exhibit both the haplogroup X with the transition at np 16,213 and the rare Albumin marker Albumin*Naskapi," both of which are found only among North American natives." [xliii]
The haplogroup X saga clearly indicates that there is no consensus on matters relating to migrations from the Old World to the New. Perhaps related to the haplogroup X question is that of the "Red Paint People" of ca. 4000 B.P., whose cultural remains have been excavated mostly in Labrador and Maine. The name given them by modern archaeologists resulted from the fact that they added brilliant red iron oxide to their graves. It now seems clear that they sailed across the Atlantic, for similar graves are found in France, England, and Denmark. [xliv]
The authors of a 2003 study wrote, "we have completely sequenced a haplogroup X mtDNA from the Ojibwa ... A comparison of this sequence with those haplogroup X mtDNA sequences of European ancestry that were published by Finnilä et al. (2001) and by Herrnstadt et al. (2002) shows that this Native American mtDNA carries all of the mutations that define haplogroup X." [xlv] A 2003 study makes it clear that haplogroup X originated in the Near East and the version found in Asia was recently introduced from Europe and is more distantly related to that found among Native Americans.
A maximum parsimony tree of 21 complete mitochondrial DNA (mtDNA) sequences belonging to haplogroup X and the survey of the haplogroup-associated polymorphisms in 13,589 mtDNAs from Eurasia and Africa revealed that haplogroup X is subdivided into two major branches, here defined as "X1" and "X2." The first is restricted to the populations of North and East Africa and the Near East, whereas X2 encompasses all X mtDNAs from Europe, western and Central Asia, Siberia, and the great majority of the Near East, as well as some North African samples. Subhaplogroup X1 diversity indicates an early coalescence time, whereas X2 has apparently undergone a more recent population expansion in Eurasia, most likely around or after the last glacial maximum. It is notable that X2 includes the two complete Native American X sequences that constitute the distinctive X2a clade, a clade that lacks close relatives in the entire Old World, including Siberia. The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East. [xlvi]
In 2000, geneticist Theodore Schurr noted that "Recent claims ... that European stock may have been present in pre-Columbian America do not deny the overwhelming contribution of Asiatic peoples to the ancestry of modern Amerindians." [xlvii] The same could be said of Book of Mormon peoples, i.e., that most of the mtDNA makeup of Native Americans can be Asian even if some of their ancestors came from the Near East.
[i] I am indebted to Matthew Roper for bringing some of the articles mentioned herein to my attention.
[ii] Some of the articles listed in the appendix deal with these issues.
[iii] For a discussion, see John L. Sorenson, "The Problematic Role of DNA Testing in Unraveling
Human History," Journal of Book of Mormon Studies 9/2 (2000): 66-74.
[iv] For a good explanation of how DNA can be used in population studies, see D. Andrew Merriwether, David M. Reed, and Robert E. Ferrell, "Ancient and Contemporary Mitochondrial DNA Variation in the Maya," in Nancy P. Dutro, ed., Bones of the Maya: Studies of Ancient Skeletons (Washington and London: Smithsonian Institution Press, 1997), 208-17. For general information about how DNA works, see the following web sites:
http://www.accessexcellence.org/RC/AB/BA/dnaintro/index.html
[v] It is actually a little more complicated than that, involving RNA and other processes, but the explanation given here is sufficient to understand what is going on.
[vi] Identical twins are an exception because they develop from the same fertilized egg.
[vii] There are actually four kinds of changes: 1) indels, which are insertions into or deletions of the DNA at particular locations on the chromosome, 2) snips, which are single nucleotide polymorphisms in which a particular nucleotide (A, C, G, or T) is changed into another, 3) microsatellite changes, which are short sequences (10-60) of nucleotides that are repeated a variable number of times in succession along the nucleotide chain, and 4) minisatellite changes, in which the repeated sequences are short (usually up to 3-4 nucleotides).
[viii] While this is essentially the case, there are very rare occasions where a human being has two X chromosome and one Y or even three X.
[ix] During meiosis, only 1% of the Y chromosome recombines with the X chromosome, the rest evidently constituting what one could call "maleness."
[x] An exception is noted later in this paper.
[xi] The task is not totally impossible, provided one has access to a supercomputer that can perform billions of calculations per second, and provided one also takes into account any mutations over time.
[xii] I acknowledge that it is more complicated than this, but most readers will not want to know more than the basics.
[xiii] For an informative discussion of Y chromosomes, see Neil Bradman and Mark G. Thomas, "Why Y? The Y Chromosome in the Study of Human Evolution, Migration and Prehistory," Science Spectra 14 (1998): 32-37, posted http://www.ucl.ac.uk/tcga/ScienceSpectra-pages/SciSpect-14-98.html.
[xiv] Barring mutations, all offspring of a woman have identical mtDNA, regardless of how many men may have fathered her children.
[xv] Ripan S. Malhi and Jason A. Eshleman, "The Uses and Limitations of DNA Based Ancestry Tests for Native Americans," 11, Trace Genetics web site, http://www.tracegenetics.com/nativeamericandna.pdf.
[xvi] Jason A. Eshleman, Ripan S. Malhi, and David Glenn Smith, "Mitochondrial DNA Studies of Native Americans: Conceptions and Misconceptions of the Population Prehistory of the Americas," Evolutionary Anthropology 12 (2003), 8.
[xvii] Ibid., 15-16.
[xviii] Ibid., 13; emphasis added.
[xix] Ibid., 8.
[xx] R. H. Ward et al., "Extensive Mitochondrial Diversity Within a Single Amerindian Tribe," Proceedings of the National Academy of Science USA 88 (1991): 8720-24.
[xxi] Angelica Gonzalez-Oliver et al., "Founding Amerindian Mitochondrial DNA Lineages in Ancient Maya from Xcaret, Quintana Roo," American Journal of Physical Anthropology 116 (2001): 230.
[xxii] Anne C. Stone and Mark Stoneking, "Ancient DNA from a Pre-Columbian Amerindian Population," American Journal of Physical Anthropology 92/4 (1993): 466.
[xxiii] 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 (1998): 1153.
[xxiv] I have omitted the parenthetical references from the text cited here so readers will not be distracted from the flow of the paragraph. Some of those references will be cited later.
[xxv] Néstor O. Bianchi et al., "Characterization of Ancestral and Derived Y-Chromosome Haplotypes of New World Native Populations," American Journal of Human Genetics 63 (1998): 1862.
[xxvi] D. Andrew Merriwether and Robert E. Ferrell, "The Four Founding Lineage Hypothesis for the New World: A Critical Reevaluation," Molecular Phylogenetics and Evolution 5 (February 1996): 241.
[xxvii] This has been dealt with elsewhere; see the appendix to this article.
[xxviii] Glenn H. Doran et al., "Anatomical, Cellular and Molecular Analysis of 8,000-year-old Human Brain Tissue from the Windover Archaeological Site," Nature 323 [6091] (1986): 803-6. In 2002, the University of Florida Press published a book edited by Doran, Multidisciplinary Investigations of an Early Archaic Florida Cemetery, which includes the following articles: W. Hauswirth and C. Dickel, "Investigations of DNA Isolated from Windover Brain Tissue: Methods and Implications"; David Glenn Smith et al., "Serum Albumin Phenotypes and a Preliminary Study of the Windover mtDNA Haplogroups and Their Anthropological Significance"; D. C. Hyland and T. R. Anderson, "Biomolecular Analysis of CollagenousTissue."
[xxix] W. W. Hauswirth et al., "Inter- and Intrapopulation Studies of Ancient Humans," Experientia 50/6 (1994): 585.
[xxx] Dennis H. O'Rourke et al., "Spatial and Temporal Stability of mtDNA Haplogroup Frequencies in Native North America," Human Biology 72/1 (February 2000): 17.
[xxxi] David Glenn Smith et al., "Distribution of mtDNA Haplogroup X among Native North Americans," American Journal of Physical Anthropology 110/3 (November 1999): 271.
[xxxii] Ibid., 272. To facilitate reading for the nonspecialist, I have omitted the parenthetical references to other articles, some of which are included in this present survey.
[xxxiii] Ibid., 275.
[xxxiv] Ibid., 276, 278-9. The earlier study to which they refer was Joseph G. Lorenz and David Glenn Smith, "Distribution of Four Founding mtDNA Haplogroups Among Native North Americans," American Journal of Physical Anthropology 101/3 (November 1996): 307-23.
[xxxv] Antonio Torroni et al., "mtDNA Variation of Aboriginal Siberians Reveals Distinct Genetic Affinities with Native Americans," American Journal of Human Genetics 53/3 (September 1993): 591-608.
[xxxvi] Virginia Morell, "Genes May Link Ancient Eurasians, Native Americans," Science 280 (24 April 1998), 520; 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 (December 1998): 1852-61.
Part 1 of 3 - Unwarranted Assumptions
During the past few years, a number of anti-Mormon writers and groups have been pushing the idea that DNA Studies of Native Americans prove that the Book of Mormon is false. They claim that these studies prove that all Native Americans have Asian ancestry. When Latter-day Saint scholars have shown that this does not contradict the Book of Mormon, the critics have sought to discount scholarly research that suggests that the peoples mentioned in the Book of Mormon were not alone in the New World and that events depicted in that volume took place in Mesoamerica. In doing this, they have relied on popular opinions about these people and events rather than on the text itself. [ii]
While generally not questioning the results of the DNA studies, I find serious problems in the interpretation placed on these results by critics of the Book of Mormon. For example, the original studies do not claim that the results exclude the possibility that Lehi (or even other groups) migrated to the Americas; the critics added that claim. Indeed, one non-Latter-day Saint scientist, looking at the DNA studies, has concluded that there is, indeed evidence for migration to the New World by various groups, including people from the ancient Near East. We shall return to this later.
A Priori Assumption
All DNA studies begin with the a priori assumption that the New World was populated from Asia via a land bridge called Beringia, thought to have connected Siberia with Alaska during the last ice age. The idea originated in 1589 with José de Acosta, a Jesuit missionary from Spain.
Today, the Bering Strait separates the Asian and North American continents by a mere 53 miles. The water depth in this region is 98 to 164 feet, and there are numerous islands in the strait. During the time of the last ice age, so much of the sea water was frozen into glaciers that the sea level in this area dropped by about 300 feet, leaving a narrow land passage where water exists today.
This has led anthropologists to postulate man's arrival in the New World 13-14,000 years ago, when there was an ice-free corridor in the midst of the glacial masses leading from Beringia to the United States. This idea has archaeological support from Paleoindian sites. More recent DNA studies push the arrival of humans in the Americas back to at least 30,000 years B.P., leading to deep divisions in the ranks of archaeologists.
Prior to the development of DNA research, anthropologists relied on phenotypical studies, noting facial similarities between Asiatics and Native Americans and the fact that newborns in both Asia and the Americas are born with a dark blue spot in the lower back, adjacent to the buttocks. For skeletal materials, the shape and measurements of skulls and teeth were used to determine genetic relationships. The frequency of the various blood types was also considered to be a marker of an Asian origin for Native Americans, despite the fact that all blood types are found on each of the world's continents. [iii]
DNA and Ancestry
It was a monk named Gregor Mendel (1823-1884) who first noted the principles underlying biological inheritance. Unrecognized in his own day, his groundbreaking discoveries led to the science of genetics. The discovery of chromosomes and the genes of which they are comprised narrowed the processes of procreation and regeneration down considerably. The presence of deoxyribonucleic acid, commonly called DNA, found in the nucleus of all cells, was believed to lie behind these processes and was the stuff of which genes are made. In the fall of 1951, James Watson and Francis Crick began unraveling the structure of DNA and eleven years later, in company with Maurice Wilkins, who had performed the initial X-ray crystallography studies of DNA, they received the Nobel Prize for Medicine.
Strands of nuclear DNA (nDNA) are long polymers built of millions of nucleotides that are linked together by what are termed bases, to form a double helix. Nuclear DNA controls heredity on the molecular level, storing the necessary information in a sequence of bases along the polynucleotide chain. These bases or nucleotide sequences are built of four organic substances, adenine (A), cytosine (C), guanine (G), and thymine (T), linked by phosphate and sugar molecules. The sequence of these bases is the underlying chemical mechanism that contains all of the information necessary for a fertilized egg to produce a biological form, including human beings. In that respect, it can be likened to a computer code. [iv]
In a process known as replication, the two halves of the nDNA helix separate and each reproduces its counterpart. This is possible because thymine always pairs with adenine and guanine always pairs with cytosine. On a larger level, the chromosomes (which can be seen via an optical microscope) double, then separate with two halves of the cell, in a process known as mitosis. When the missing bases are recreated, it leads to the production of two separate cells, each of which has the same genetic material as its twin. Thus, as some body cells die, they are replaced by others that result from mitosis. [v]
A similar process occurs in the production of gametes or reproductive cells (ova and spermatozoa) in the testes and ovaries. This process, known as meiosis, involves the division of cells as in mitosis, plus an additional division in which the chromosomes are not replicated. Consequently, each gamete has only one set of chromosomes rather than pairs of chromosomes. Because of this, each parent passes to his/her offspring only 50% of his/her nuclear DNA inherited from his/her parents. Which DNA is passed to one's offspring depends largely on how it was divided up during the production of gametes. With 23 chromosomes in each gamete, each one comprising a large number of genes, the number of variations among male or female gametes is rather high. Crossover or exchange of genetic material between paired chromosomes during meiosis increases the variety of DNA that can be passed on. This makes it possible for each child to have a different genetic makeup from that of his/her siblings while sharing much of the inherited genetic material. [vi]
Over time, minute changes or mutations occur in the nucleotide chains, often by substitution of one base for another. [vii] This results in inherited genetic material from a common ancestor having a different chemical composition in individuals descended from that ancestor. Thus, corresponding loci (called alleles) on the nucleotide chain can differ between individuals even when the alleles in question came from the same source. This is called polymorphism, which in effect denotes a variety of alleles descended from a common source.
Human beings have 23 pairs of chromosomes in the nucleus of each cell, except when it comes to the gametes (ova and sperm), which are cells used for reproduction. The gametes are haploid, containing just one set of 23 chromosomes, while all the other cells in the body are diploid. Each female diploid cell includes a pair of chromosomes designated X, while each male diploid cell has one X chromosome paired with a Y chromosome. [viii]
When the male and female gametes merge during fertilization to produce a zygote, the chromosomes from the father match up with their female counterparts and the process of replication begins and continues, in humans, for about nine months. Consequently, each of us has received half of his/her nuclear genetic material from his/her mother and half from the father. If the sperm that fertilizes the ovum (egg) has an X chromosome, it pairs with an X chromosome from the mother and produces a girl. If the sperm has a Y chromosome, it similarly pairs with the X from the mother and produces a boy. [ix]
Most DNA is found in the chromosomes located in the nucleus of the cell and is hence called nuclear DNA (nDNA). However, small structures outside the nucleus, called mitochondria (singular mitochondrion), also have DNA strands called mitochondrial DNA (mtDNA). Unlike nDNA, mtDNA is not recombinant, meaning that it does not contain the genome code that enables cells to replicate and, in the case of gametes, to merge the maternal and paternal DNA. Rather, its function is to enable the cell to use the energy provided by nutrients coming via the bloodstream. In addition, mtDNA contains only 37 genes, compared with the tens of thousands in nDNA, and the mtDNA genome represents about .0005% of one's entire genome. Because sperm cells generally lose their mitochondria during the fertilization process, the mtDNA in each human being is inherited only from the mother. [x] 
Examining the DNA of an individual and comparing it with the DNA of close relatives can establish the origin of specific genetic markers in the parents, grandparents, or other shared ancestors. Because of the complexity of nDNA, its recombination in each generation, and occasional mutations, it is much more difficult to trace one's genealogy over many generations. [xi] While all of one's distant ancestors have the potential of contributing to one's DNA, in practical terms it doesn't work that way. After many generations of recombination in both maternal and paternal ancestors, some of the nDNA simply is not passed on to the next generation. Indeed, in each generation, each parent passes on only 50% of his/her nuclear DNA inherited from his/her parents, because there are a finite number of positions to fill in each succeeding generation. [xii]
The task is greatly simplified when it comes to determining strict male and female ancestral lines. Since the Y chromosome is passed from father to son, it is possible to determine common paternal ancestry (patrilineage) shared by two or more individuals, especially if they are closely related. Most changes to the genetic makeup of the Y chromosome are due to mutations, though there are occasional gene transfers from other chromosomes (usually the X chromosome with which the Y is paired). Each time a man fathers a daughter, his Y chromosome is lost to that line, unless one of her descendants marries a male who picked it up from her brother or another male relative (e.g., an uncle, a cousin, or a grandfather) of the same patrilineage. [xiii]
Similarly, since only daughters pass their mtDNA to their offspring, one can determine common maternal ancestry (matrilineage) as well. [xiv] In both cases, one must take into account that mutations occur in the DNA so that there are minute changes over time. Thus, while the paternal (Y-chromosome) and maternal (mtDNA) markers passed down through the generations will be similar, there will be individual differences caused by mutation and other factors. It is possible for these paternal and maternal markers to be discernible thousands of years later in descendants whose nuclear DNA no longer resembles that of the ancestor. This is because nDNA, like radioactive elements, has a half-life. In each generation, it loses half of its substance during gamete production and that half combines with the nuclear DNA from the other parent to produce offspring. After many generations, the nDNA inherited from a specific ancestor may be so minute in a descendant as to be undetectable or may have disappeared altogether, either through mutation or the recombination process that occurs during fertilization of the ovum.
For Native American studies, geneticists have concentrated mostly on mitochondrial DNA (mtDNA, inherited from one's mother), though some studies of the Y chromosome (inherited by males from the father) have also been published. While there is some disagreement on the actual numbers, most geneticists believe that mutation in mtDNA occurs at a steady rate, making it possible to determine how long ago a given haplogroup entered the New World. Most mtDNA studies have concentrated on living populations from whose samples ancestral mtDNA has been postulated. Thus, if certain mtDNA markers are found in contemporary Asian and Native American populations, it is assumed that these came from a common female ancestor.
Most tests of mtDNA sequence a small portion (400, 2.4%) of the 16,569 base pairs in the mtDNA molecule, looking for specific "markers" of matrilineal ancestry. Malhi and Eshleman wrote that, "For both mtDNA and Y chromosome, haplogroups are usually defined by a single nucleotide polymorphism (or SNP) which is a single change or mutation in the DNA sequence. For example, all individuals in mtDNA haplogroup A share a mutation at nucleotide position 663 in the mitochondrial genome." [xv] This does not take into account that other ancestral lines may have developed the same mutation over time. If none of the markers are found, the sample is classified as "other" and, in the case of Native American mtDNA, is routinely assumed to derive from post-Conquest Europeans. The history of genetics research has demonstrated that this explanation is not always correct.
Other mtDNA Haplogroups
Clearly, the mtDNA evidence suggests an Asian origin for the four major Native American haplogroups or matrilineages, designated A, B, C, and D (and perhaps X, which will be discussed later). What Book of Mormon critics fail to note is that other, less important haplogroups have also been found in the New World, which means that none of the research actually excludes ancient immigrations from other parts of the world. Some researchers dismiss these other haplogroups as later admixture from Old World immigrants since the time of Columbus, but studies of this matter are insufficient to establish that there were no other migrations in ancient times. A report issued in 2003 declares that "haplogroup frequencies alone cannot distinguish between admixture and common ancestry." [xvi] The authors also note,
However, it is important to remember that mtDNA is but one marker, and one that is solely maternally inherited, and is unlikely to answer all questions regarding the origins of Native Americans ... Like mtDNA, Y-chromosome data have not on their own conclusively answered questions regarding either source populations within Asia or the number of migrations out of Asia into the New World. Clearly, nuclear markers from more populations should be examined to provide additional data relevant to these controversies, even though it is unlikely that additional data will significantly simplify what is a convoluted and complex scenario of migrations and postmigrational evolutionary forces. [xvii]
Continuing, they write that:
In almost all studies of ancient Native American populations [from skeletal remains], individuals have been discovered who do not appear to belong to one of the five founding lineages. In many cases, this is undoubtedly a result of external contamination of samples lacking DNA or in which the DNA is inhibited from amplifying using the polymerase chain reaction. Nonetheless, the possibility remains that additional haplogroups may be discovered by studies of ancient DNA in the Americas. Such a lineage may have either become extinct or be a yet-undiscovered lineage persisting at low levels in modern populations. [xviii]
The authors of the report note that, "Early studies of Na-Dene populations [of North America] suggested that they possessed high frequencies of haplogroup A but lacked haplogroup B and exhibited only low frequencies of haplogroups C and D, whereas Eskimo-Aleut populations appeared to have high frequencies of haplogroups A and D but lacked haplogroups B and C. However, on closer inspection of a large number of samples, Merriwether, Rothhammer, and Ferrell demonstrated that groups traditionally classified as Eskimo and Na-Dene had measurable frequencies of all four haplogroups when larger samples were assayed." [xix] The lesson to be learned from this is that undersampling cannot give us the whole picture.
A 1991 study of the Nuu-Chah-Nulth tribe of the Pacific Northwest revealed some 28 haplotypes, of which 19 clustered in the four maternal DNA haplogroups (A, B, C, and D), while 9 did not. [xx] Because of DNA changes over time due to mutation and other factors, a given haplogroup typically includes various haplotypes or individual lineage markers that descend from a common source. No explanation was given for the other 9 haplotypes.
Mayan Samples
The authors of a 2001 study of skeletal remains from precolumbian Maya burials recovered from the Late Classsic/Postclassic site of Xcaret in the Mexican province of Quintana Roo noted that "Many analyses of mtDNA haplotypes in New World contemporary and ancient populations have shown the presence of a small number of individuals possessing none of the markers defining the four founding lineages." [xxi]
In 1998, 102 DNA samples were taken from skeletal remains at the Norris Farms Oneota prehistoric (700 years old) cemetery, with successful extraction of mtDNA from 50 of them. All four of the American haplogroups were found, along with one individual with a haplogroup not previously attested in contemporary Native Americans and designated as N. The researchers wrote, "This new mtDNA lineage might be present in contemporary Amerindian populations but not yet sampled, or it might belong to a lineage that is no longer present in contemporary populations. Alternatively, this new mtDNA lineage might actually be one of the four lineages, but a mutation or reversion has occurred at the relevant diagnostic marker, thereby obscuring the affiliation of this mtDNA type. Another possibility is that this sample was contaminated by modern DNA of non-Amerindian origin." [xxii] In 1998, the researchers summarized a study of mtDNA from skeletal remains of 108 individuals from the same site, of which 6 fell outside the four Asian haplogroups and were lumped together as "other." They noted that "data indicate that the lineages from haplogroups A, B, C, and D are the most common among Native Americans but they were not the only lineages brought into the New World from Asia. The mtDNA evidence . . . suggests a single 'wave' of people with considerable mtDNA diversity." [xxiii]
The variety of findings from mtDNA research was summed up in a 1998 article, [xxiv] in which the authors wrote that
Some of the hypotheses based on the interpretation of mitochondrial haplotypes are conflicting. Mitochondrial analysis has been invoked to support a multiwave-founder colonization of America, whereas, on the other hand, mtDNA markers have also been interpreted as supporting a monophyletic colonization from Asia. Archaeological studies seem to indicate an antiquity in the range of 11,000-33,000 years before the present (YBP) for the first settlements in Beringia and the New World, whereas different laboratories working with mitochondrial polymorphisms have proposed times in the range of 14,000-55,000 YBP for this event. Founder maternal Amerindian lineages initially had been estimated as being four. Now it is assumed that there are > 10-13 such lineages, although there is no agreement on the molecular typification of some of these founder haplogroups. [xxv]
The disagreement over the migration of the four major mtDNA lineages (whether one or more migrations) is further complicated by the fact that geneticists are not in agreement concerning the other mtDNA haplotypes found in Native American samples. Torroni and colleagues believe that only one haplotype from each of the four founding lineages arrived in the New World via migration and that all the additional variation arose in the New World, with other types being attributed to later Caucasian admixture. On the other hand, Merriwether and Ferrell believe that "multiple variants of each lineage entered the New World, and that additional unrelated lineages also entered." They illustrate this by two additional lineages they call X6 and X7, found throughout the New World, Siberia, and Asia, providing "strong evidence that at least nine different founding lineage haplotypes entered the New World," and that "these distributions among Native Americans best fit a single wave of migration into the New World." [xxvi]
Most researchers have tended to dismiss the minor haplogroups detected among Native Americans as admixture following the arrival of Europeans in the New World or to ignore them completely. From the data collected thus far, the critics find it easy to ignore the possibility that Book of Mormon peoples imported any of these haplogroups. When Latter-day Saints point out the inconsistencies, they respond that only the major haplogroups count, since all Native Americans are supposedly descended from Lehi. This information comes not from the text of the Book of Mormon, but from the interpretation some have erroneously placed on the text. [xxvii]
When geneticists examine Native American DNA, they use procedures to screen for each of the four (now five) "Native American" haplogroups. If, after screening a sample without a successful identification, the sample is labeled "other." Ultimately, some of these "others" are found to be related to samples tested from other settlements or archaeological sites, and can then be classified as a new haplogroup. This is what happened with haplogroup X.
Haplogroup X
A brackish pond (bog) at Windover, adjacent to Titusville, Florida, has preserved the largest North American collection of human skeletal remains and fabric for its time, along with the largest tool collection. Brain tissue was preserved in nearly a hundred of the skeletons and was extracted for DNA analysis. None of the common Native American mtDNA haplogroups (A, B, C, and D) were present, but haplogroup X, known mostly from Europe, was plentiful, suggesting that these ancient remains are of people of European ancestry. [xxviii] Later research concluded that there was a persistence of both nuclear and mitochondrial haplotypes at Windover throughout its entire period of use. "Analysis of the mtDNA sequences suggests that some mitochondrial types are clearly related to extant Amerind types, whereas others, more distantly related, may reflect genetically distinct origins." [xxix]
A study reported in 2000 examined DNA samples drawn from human remains ranging from 300-6,000 years in age, from the Aleut, eastern Utah Fremont, Southwestern Anasazi, Pyramid Lake (Nevada), Stillwater Marsh (Nevada), and Oneota (western Illinois), which were then compared with 41 samples from contemporary North American populations. The report admits that "Haplogroup X is an additional ancestral Amerindian mtDNA lineage and is evident upon screening with additional markers and through sequence analysis. Because most of the samples available for analysis have not been screened for these additional markers, it is not possible to identify haplogroup X in all these data." The researchers also noted that "although haplogroup assignment is straightforward in modern samples, it is not always so easy for ancient samples." [xxx]
A 1999 study examined 70 samples of Native American mtDNA, most of which did not evidence any of the four haplogroups (A-D). Of these, 32 were found to belong to haplogroup X. The researchers concluded that
the wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestral descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups. [xxxi]
The authors also note that, "Haplotypes that are not members of A, B, C, or D and that are characterized by specific mutations have been reported in modern (presumably unmixed) Native Americans and in prehistoric individuals, suggesting that founding haplogroups other than A, B, C, and D were once present in the New World, whether or not they have survived," [xxxii] adding that "it is of interest to determine whether or not additional founding haplogroups were once present, but have since become extinct, in the New World." [xxxiii] They cite a 1996 study by Lorenz and Smith, who worked with mtDNA samples from 829 Native North Americans and classified 50 of them as "other" than the four haplotypes (A-D). Revisiting the data, the new study was able to rescreen mtDNA from 25 of the 50, they found that seven had been mistyped and were reassigned to haplogroups A and C (2 each) and D (3), with some of the others assigned to haplogroup X. [xxxiv]
Initial mtDNA studies suggested that there were four haplogroups (A-D) found among Native Americans that are also attested mostly in Asia, though they are not the dominant haplogroups in Asia. Indeed, the earliest studies did not detect haplogroup B in Siberia. [xxxv] The discovery of a fifth haplogroup, X, led to suggestions that it may be due to a migration from Europe, since X had not yet been attested in Asia but was found in DNA samples from Finland, Italy, and Israel, with possible connections to samples from Spain, Bulgaria, and Turkey. [xxxvi] As it turns out, haplogroup X was later identified at a low frequency (3.5%) among the Altaians of Siberia. [xxxvii] While the critics believe that this seals the fate of the Book of Mormon, it really demonstrates that all of the evidence is not yet in and that new discoveries are the norm. If, following further research, a haplogroup not attested in Asia was found in some Asian populations, could not the same thing happen in the New World as the DNA sampling increases the size of the database?
Critics have suggested that even though mtDNA haplogroup X is represented in the Near East, the time-depth for its arrival in the New World is too great to be attributable to Lehi's group. But the existence of this haplogroup in the New World at the time of Lehi's arrival does not a priori mean that it did not exist among the Lehites. If Sariah and her daughters or the wife of Ishmael and her daughters carried haplogroup X into the New World, it would be different from the X haplogroup found among Native Americans because it would have a different mutational history. But since the same haplogroup is different in various Native Americans because of genetic drift following their separation from other New World inhabitants, none of them are precisely like those of such other inhabitants, nor are they identical to the haplogroup X found in Siberia.
The debate about the origin of haplogroup X continues to this day. Because it is attested in higher percentages among Europeans sampled than Asians and because the Native American X shares affinities with the European X not found in the Asian, [xxxviii] some researchers have suggested that it was brought to the New World from Europe across the north Atlantic by people hunting seals. Archaeologists have demonstrated that the earliest spear points found in the Americas are identical in design and method of production to the Solutrean points found in western Europe (notably France and Spain) for the same time period, and that these points are ancestral to the Clovis points previously thought to be the earliest use of flaked stone tools in the New World.
Dennis Stanford of the Smithsonian Institution, an archaeologist who drew attention to the Solutrean connection, said, "The way the tools are made, the whole tool kit, bone artifacts and some artistic expressions are similar, and burial practices are similar." [xxxix] Stanford noted that "There are so many matching steps in how they made their tools: bifacial flaking, heat treatment, similar ceremonial items, the presence of red ochre. There must be fifty or sixty points of comparison. It can't be chance." [xl] Among the more important New World prehistoric sites with suspected ties to the Solutrean culture of Europe are Meadowcroft Rock Shelter, near Pittsburgh, Pennsylvania, and Cactus Hill, Virginia. [xli]
Significantly, both the Solutrean points and mtDNA haplogroup X are attested in a geographical region most likely to have been affected by a migration from Europe. Haplogroup X is found principally among the Algonquian-speaking peoples of the Great Lakes region, including the Ojibwa, but has also been found among the Nuu-Chah-Nulth and Yakima tribes of the northwest. It is known in about a fourth of Ojibwa natives tested and in lesser amounts among members of the Sioux and Navajo. [xlii] It has also been found in skeletal remains of two individuals found in a fourteenth-century burial in Illinois, demonstrating that it was in North America prior to the time of Columbus.
Despite these evidences, other researchers have suggested that haplogroup X came from Europe or Central Asia across Beringia to the New World, leaving very little trace in Siberia. Ripan S. Malhi and David Glenn Smith noted that the Altai of Siberia "are the only known modern ethnic group whose membership represents all five Native American haplogroups and, assuming the New World was colonized by a single migration, constitute a possible origin of the founders of Native America." This leads them to reject the hypothesis of a European migration of haplogroup X to the New World and discount the suggestion that there are similarities between Clovis and Solutrean cultural artifacts. Because it is found among ancient samples from the Norris Farms, Windover, and Vantage sites and the Amazon Basin, they consider haplogroup X to be "a founding Native American lineage" and reject the idea that it resulted from Viking or more recent European admixture. They note that three Algonquian-speaking Native Americans "exhibit both the haplogroup X with the transition at np 16,213 and the rare Albumin marker Albumin*Naskapi," both of which are found only among North American natives." [xliii]
The haplogroup X saga clearly indicates that there is no consensus on matters relating to migrations from the Old World to the New. Perhaps related to the haplogroup X question is that of the "Red Paint People" of ca. 4000 B.P., whose cultural remains have been excavated mostly in Labrador and Maine. The name given them by modern archaeologists resulted from the fact that they added brilliant red iron oxide to their graves. It now seems clear that they sailed across the Atlantic, for similar graves are found in France, England, and Denmark. [xliv]
The authors of a 2003 study wrote, "we have completely sequenced a haplogroup X mtDNA from the Ojibwa ... A comparison of this sequence with those haplogroup X mtDNA sequences of European ancestry that were published by Finnilä et al. (2001) and by Herrnstadt et al. (2002) shows that this Native American mtDNA carries all of the mutations that define haplogroup X." [xlv] A 2003 study makes it clear that haplogroup X originated in the Near East and the version found in Asia was recently introduced from Europe and is more distantly related to that found among Native Americans.
A maximum parsimony tree of 21 complete mitochondrial DNA (mtDNA) sequences belonging to haplogroup X and the survey of the haplogroup-associated polymorphisms in 13,589 mtDNAs from Eurasia and Africa revealed that haplogroup X is subdivided into two major branches, here defined as "X1" and "X2." The first is restricted to the populations of North and East Africa and the Near East, whereas X2 encompasses all X mtDNAs from Europe, western and Central Asia, Siberia, and the great majority of the Near East, as well as some North African samples. Subhaplogroup X1 diversity indicates an early coalescence time, whereas X2 has apparently undergone a more recent population expansion in Eurasia, most likely around or after the last glacial maximum. It is notable that X2 includes the two complete Native American X sequences that constitute the distinctive X2a clade, a clade that lacks close relatives in the entire Old World, including Siberia. The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East. [xlvi]
In 2000, geneticist Theodore Schurr noted that "Recent claims ... that European stock may have been present in pre-Columbian America do not deny the overwhelming contribution of Asiatic peoples to the ancestry of modern Amerindians." [xlvii] The same could be said of Book of Mormon peoples, i.e., that most of the mtDNA makeup of Native Americans can be Asian even if some of their ancestors came from the Near East.
[i] I am indebted to Matthew Roper for bringing some of the articles mentioned herein to my attention.
[ii] Some of the articles listed in the appendix deal with these issues.
[iii] For a discussion, see John L. Sorenson, "The Problematic Role of DNA Testing in Unraveling
Human History," Journal of Book of Mormon Studies 9/2 (2000): 66-74.
[iv] For a good explanation of how DNA can be used in population studies, see D. Andrew Merriwether, David M. Reed, and Robert E. Ferrell, "Ancient and Contemporary Mitochondrial DNA Variation in the Maya," in Nancy P. Dutro, ed., Bones of the Maya: Studies of Ancient Skeletons (Washington and London: Smithsonian Institution Press, 1997), 208-17. For general information about how DNA works, see the following web sites:
http://www.accessexcellence.org/RC/AB/BA/dnaintro/index.html
[v] It is actually a little more complicated than that, involving RNA and other processes, but the explanation given here is sufficient to understand what is going on.
[vi] Identical twins are an exception because they develop from the same fertilized egg.
[vii] There are actually four kinds of changes: 1) indels, which are insertions into or deletions of the DNA at particular locations on the chromosome, 2) snips, which are single nucleotide polymorphisms in which a particular nucleotide (A, C, G, or T) is changed into another, 3) microsatellite changes, which are short sequences (10-60) of nucleotides that are repeated a variable number of times in succession along the nucleotide chain, and 4) minisatellite changes, in which the repeated sequences are short (usually up to 3-4 nucleotides).
[viii] While this is essentially the case, there are very rare occasions where a human being has two X chromosome and one Y or even three X.
[ix] During meiosis, only 1% of the Y chromosome recombines with the X chromosome, the rest evidently constituting what one could call "maleness."
[x] An exception is noted later in this paper.
[xi] The task is not totally impossible, provided one has access to a supercomputer that can perform billions of calculations per second, and provided one also takes into account any mutations over time.
[xii] I acknowledge that it is more complicated than this, but most readers will not want to know more than the basics.
[xiii] For an informative discussion of Y chromosomes, see Neil Bradman and Mark G. Thomas, "Why Y? The Y Chromosome in the Study of Human Evolution, Migration and Prehistory," Science Spectra 14 (1998): 32-37, posted http://www.ucl.ac.uk/tcga/ScienceSpectra-pages/SciSpect-14-98.html.
[xiv] Barring mutations, all offspring of a woman have identical mtDNA, regardless of how many men may have fathered her children.
[xv] Ripan S. Malhi and Jason A. Eshleman, "The Uses and Limitations of DNA Based Ancestry Tests for Native Americans," 11, Trace Genetics web site, http://www.tracegenetics.com/nativeamericandna.pdf.
[xvi] Jason A. Eshleman, Ripan S. Malhi, and David Glenn Smith, "Mitochondrial DNA Studies of Native Americans: Conceptions and Misconceptions of the Population Prehistory of the Americas," Evolutionary Anthropology 12 (2003), 8.
[xvii] Ibid., 15-16.
[xviii] Ibid., 13; emphasis added.
[xix] Ibid., 8.
[xx] R. H. Ward et al., "Extensive Mitochondrial Diversity Within a Single Amerindian Tribe," Proceedings of the National Academy of Science USA 88 (1991): 8720-24.
[xxi] Angelica Gonzalez-Oliver et al., "Founding Amerindian Mitochondrial DNA Lineages in Ancient Maya from Xcaret, Quintana Roo," American Journal of Physical Anthropology 116 (2001): 230.
[xxii] Anne C. Stone and Mark Stoneking, "Ancient DNA from a Pre-Columbian Amerindian Population," American Journal of Physical Anthropology 92/4 (1993): 466.
[xxiii] 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 (1998): 1153.
[xxiv] I have omitted the parenthetical references from the text cited here so readers will not be distracted from the flow of the paragraph. Some of those references will be cited later.
[xxv] Néstor O. Bianchi et al., "Characterization of Ancestral and Derived Y-Chromosome Haplotypes of New World Native Populations," American Journal of Human Genetics 63 (1998): 1862.
[xxvi] D. Andrew Merriwether and Robert E. Ferrell, "The Four Founding Lineage Hypothesis for the New World: A Critical Reevaluation," Molecular Phylogenetics and Evolution 5 (February 1996): 241.
[xxvii] This has been dealt with elsewhere; see the appendix to this article.
[xxviii] Glenn H. Doran et al., "Anatomical, Cellular and Molecular Analysis of 8,000-year-old Human Brain Tissue from the Windover Archaeological Site," Nature 323 [6091] (1986): 803-6. In 2002, the University of Florida Press published a book edited by Doran, Multidisciplinary Investigations of an Early Archaic Florida Cemetery, which includes the following articles: W. Hauswirth and C. Dickel, "Investigations of DNA Isolated from Windover Brain Tissue: Methods and Implications"; David Glenn Smith et al., "Serum Albumin Phenotypes and a Preliminary Study of the Windover mtDNA Haplogroups and Their Anthropological Significance"; D. C. Hyland and T. R. Anderson, "Biomolecular Analysis of CollagenousTissue."
[xxix] W. W. Hauswirth et al., "Inter- and Intrapopulation Studies of Ancient Humans," Experientia 50/6 (1994): 585.
[xxx] Dennis H. O'Rourke et al., "Spatial and Temporal Stability of mtDNA Haplogroup Frequencies in Native North America," Human Biology 72/1 (February 2000): 17.
[xxxi] David Glenn Smith et al., "Distribution of mtDNA Haplogroup X among Native North Americans," American Journal of Physical Anthropology 110/3 (November 1999): 271.
[xxxii] Ibid., 272. To facilitate reading for the nonspecialist, I have omitted the parenthetical references to other articles, some of which are included in this present survey.
[xxxiii] Ibid., 275.
[xxxiv] Ibid., 276, 278-9. The earlier study to which they refer was Joseph G. Lorenz and David Glenn Smith, "Distribution of Four Founding mtDNA Haplogroups Among Native North Americans," American Journal of Physical Anthropology 101/3 (November 1996): 307-23.
[xxxv] Antonio Torroni et al., "mtDNA Variation of Aboriginal Siberians Reveals Distinct Genetic Affinities with Native Americans," American Journal of Human Genetics 53/3 (September 1993): 591-608.
[xxxvi] Virginia Morell, "Genes May Link Ancient Eurasians, Native Americans," Science 280 (24 April 1998), 520; 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 (December 1998): 1852-61.
Part 1 of 3 - Unwarranted Assumptions
During the past few years, a number of anti-Mormon writers and groups have been pushing the idea that DNA Studies of Native Americans prove that the Book of Mormon is false. They claim that these studies prove that all Native Americans have Asian ancestry. When Latter-day Saint scholars have shown that this does not contradict the Book of Mormon, the critics have sought to discount scholarly research that suggests that the peoples mentioned in the Book of Mormon were not alone in the New World and that events depicted in that volume took place in Mesoamerica. In doing this, they have relied on popular opinions about these people and events rather than on the text itself. [ii]
While generally not questioning the results of the DNA studies, I find serious problems in the interpretation placed on these results by critics of the Book of Mormon. For example, the original studies do not claim that the results exclude the possibility that Lehi (or even other groups) migrated to the Americas; the critics added that claim. Indeed, one non-Latter-day Saint scientist, looking at the DNA studies, has concluded that there is, indeed evidence for migration to the New World by various groups, including people from the ancient Near East. We shall return to this later.
A Priori Assumption
All DNA studies begin with the a priori assumption that the New World was populated from Asia via a land bridge called Beringia, thought to have connected Siberia with Alaska during the last ice age. The idea originated in 1589 with José de Acosta, a Jesuit missionary from Spain.
Today, the Bering Strait separates the Asian and North American continents by a mere 53 miles. The water depth in this region is 98 to 164 feet, and there are numerous islands in the strait. During the time of the last ice age, so much of the sea water was frozen into glaciers that the sea level in this area dropped by about 300 feet, leaving a narrow land passage where water exists today.
This has led anthropologists to postulate man's arrival in the New World 13-14,000 years ago, when there was an ice-free corridor in the midst of the glacial masses leading from Beringia to the United States. This idea has archaeological support from Paleoindian sites. More recent DNA studies push the arrival of humans in the Americas back to at least 30,000 years B.P., leading to deep divisions in the ranks of archaeologists.
Prior to the development of DNA research, anthropologists relied on phenotypical studies, noting facial similarities between Asiatics and Native Americans and the fact that newborns in both Asia and the Americas are born with a dark blue spot in the lower back, adjacent to the buttocks. For skeletal materials, the shape and measurements of skulls and teeth were used to determine genetic relationships. The frequency of the various blood types was also considered to be a marker of an Asian origin for Native Americans, despite the fact that all blood types are found on each of the world's continents. [iii]
DNA and Ancestry
It was a monk named Gregor Mendel (1823-1884) who first noted the principles underlying biological inheritance. Unrecognized in his own day, his groundbreaking discoveries led to the science of genetics. The discovery of chromosomes and the genes of which they are comprised narrowed the processes of procreation and regeneration down considerably. The presence of deoxyribonucleic acid, commonly called DNA, found in the nucleus of all cells, was believed to lie behind these processes and was the stuff of which genes are made. In the fall of 1951, James Watson and Francis Crick began unraveling the structure of DNA and eleven years later, in company with Maurice Wilkins, who had performed the initial X-ray crystallography studies of DNA, they received the Nobel Prize for Medicine.
Strands of nuclear DNA (nDNA) are long polymers built of millions of nucleotides that are linked together by what are termed bases, to form a double helix. Nuclear DNA controls heredity on the molecular level, storing the necessary information in a sequence of bases along the polynucleotide chain. These bases or nucleotide sequences are built of four organic substances, adenine (A), cytosine (C), guanine (G), and thymine (T), linked by phosphate and sugar molecules. The sequence of these bases is the underlying chemical mechanism that contains all of the information necessary for a fertilized egg to produce a biological form, including human beings. In that respect, it can be likened to a computer code. [iv]
In a process known as replication, the two halves of the nDNA helix separate and each reproduces its counterpart. This is possible because thymine always pairs with adenine and guanine always pairs with cytosine. On a larger level, the chromosomes (which can be seen via an optical microscope) double, then separate with two halves of the cell, in a process known as mitosis. When the missing bases are recreated, it leads to the production of two separate cells, each of which has the same genetic material as its twin. Thus, as some body cells die, they are replaced by others that result from mitosis. [v]
A similar process occurs in the production of gametes or reproductive cells (ova and spermatozoa) in the testes and ovaries. This process, known as meiosis, involves the division of cells as in mitosis, plus an additional division in which the chromosomes are not replicated. Consequently, each gamete has only one set of chromosomes rather than pairs of chromosomes. Because of this, each parent passes to his/her offspring only 50% of his/her nuclear DNA inherited from his/her parents. Which DNA is passed to one's offspring depends largely on how it was divided up during the production of gametes. With 23 chromosomes in each gamete, each one comprising a large number of genes, the number of variations among male or female gametes is rather high. Crossover or exchange of genetic material between paired chromosomes during meiosis increases the variety of DNA that can be passed on. This makes it possible for each child to have a different genetic makeup from that of his/her siblings while sharing much of the inherited genetic material. [vi]
Over time, minute changes or mutations occur in the nucleotide chains, often by substitution of one base for another. [vii] This results in inherited genetic material from a common ancestor having a different chemical composition in individuals descended from that ancestor. Thus, corresponding loci (called alleles) on the nucleotide chain can differ between individuals even when the alleles in question came from the same source. This is called polymorphism, which in effect denotes a variety of alleles descended from a common source.
Human beings have 23 pairs of chromosomes in the nucleus of each cell, except when it comes to the gametes (ova and sperm), which are cells used for reproduction. The gametes are haploid, containing just one set of 23 chromosomes, while all the other cells in the body are diploid. Each female diploid cell includes a pair of chromosomes designated X, while each male diploid cell has one X chromosome paired with a Y chromosome. [viii]
When the male and female gametes merge during fertilization to produce a zygote, the chromosomes from the father match up with their female counterparts and the process of replication begins and continues, in humans, for about nine months. Consequently, each of us has received half of his/her nuclear genetic material from his/her mother and half from the father. If the sperm that fertilizes the ovum (egg) has an X chromosome, it pairs with an X chromosome from the mother and produces a girl. If the sperm has a Y chromosome, it similarly pairs with the X from the mother and produces a boy. [ix]
Most DNA is found in the chromosomes located in the nucleus of the cell and is hence called nuclear DNA (nDNA). However, small structures outside the nucleus, called mitochondria (singular mitochondrion), also have DNA strands called mitochondrial DNA (mtDNA). Unlike nDNA, mtDNA is not recombinant, meaning that it does not contain the genome code that enables cells to replicate and, in the case of gametes, to merge the maternal and paternal DNA. Rather, its function is to enable the cell to use the energy provided by nutrients coming via the bloodstream. In addition, mtDNA contains only 37 genes, compared with the tens of thousands in nDNA, and the mtDNA genome represents about .0005% of one's entire genome. Because sperm cells generally lose their mitochondria during the fertilization process, the mtDNA in each human being is inherited only from the mother. [x]
Examining the DNA of an individual and comparing it with the DNA of close relatives can establish the origin of specific genetic markers in the parents, grandparents, or other shared ancestors. Because of the complexity of nDNA, its recombination in each generation, and occasional mutations, it is much more difficult to trace one's genealogy over many generations. [xi] While all of one's distant ancestors have the potential of contributing to one's DNA, in practical terms it doesn't work that way. After many generations of recombination in both maternal and paternal ancestors, some of the nDNA simply is not passed on to the next generation. Indeed, in each generation, each parent passes on only 50% of his/her nuclear DNA inherited from his/her parents, because there are a finite number of positions to fill in each succeeding generation. [xii]
The task is greatly simplified when it comes to determining strict male and female ancestral lines. Since the Y chromosome is passed from father to son, it is possible to determine common paternal ancestry (patrilineage) shared by two or more individuals, especially if they are closely related. Most changes to the genetic makeup of the Y chromosome are due to mutations, though there are occasional gene transfers from other chromosomes (usually the X chromosome with which the Y is paired). Each time a man fathers a daughter, his Y chromosome is lost to that line, unless one of her descendants marries a male who picked it up from her brother or another male relative (e.g., an uncle, a cousin, or a grandfather) of the same patrilineage. [xiii]
Similarly, since only daughters pass their mtDNA to their offspring, one can determine common maternal ancestry (matrilineage) as well. [xiv] In both cases, one must take into account that mutations occur in the DNA so that there are minute changes over time. Thus, while the paternal (Y-chromosome) and maternal (mtDNA) markers passed down through the generations will be similar, there will be individual differences caused by mutation and other factors. It is possible for these paternal and maternal markers to be discernible thousands of years later in descendants whose nuclear DNA no longer resembles that of the ancestor. This is because nDNA, like radioactive elements, has a half-life. In each generation, it loses half of its substance during gamete production and that half combines with the nuclear DNA from the other parent to produce offspring. After many generations, the nDNA inherited from a specific ancestor may be so minute in a descendant as to be undetectable or may have disappeared altogether, either through mutation or the recombination process that occurs during fertilization of the ovum.
For Native American studies, geneticists have concentrated mostly on mitochondrial DNA (mtDNA, inherited from one's mother), though some studies of the Y chromosome (inherited by males from the father) have also been published. While there is some disagreement on the actual numbers, most geneticists believe that mutation in mtDNA occurs at a steady rate, making it possible to determine how long ago a given haplogroup entered the New World. Most mtDNA studies have concentrated on living populations from whose samples ancestral mtDNA has been postulated. Thus, if certain mtDNA markers are found in contemporary Asian and Native American populations, it is assumed that these came from a common female ancestor.
Most tests of mtDNA sequence a small portion (400, 2.4%) of the 16,569 base pairs in the mtDNA molecule, looking for specific "markers" of matrilineal ancestry. Malhi and Eshleman wrote that, "For both mtDNA and Y chromosome, haplogroups are usually defined by a single nucleotide polymorphism (or SNP) which is a single change or mutation in the DNA sequence. For example, all individuals in mtDNA haplogroup A share a mutation at nucleotide position 663 in the mitochondrial genome." [xv] This does not take into account that other ancestral lines may have developed the same mutation over time. If none of the markers are found, the sample is classified as "other" and, in the case of Native American mtDNA, is routinely assumed to derive from post-Conquest Europeans. The history of genetics research has demonstrated that this explanation is not always correct.
Other mtDNA Haplogroups
Clearly, the mtDNA evidence suggests an Asian origin for the four major Native American haplogroups or matrilineages, designated A, B, C, and D (and perhaps X, which will be discussed later). What Book of Mormon critics fail to note is that other, less important haplogroups have also been found in the New World, which means that none of the research actually excludes ancient immigrations from other parts of the world. Some researchers dismiss these other haplogroups as later admixture from Old World immigrants since the time of Columbus, but studies of this matter are insufficient to establish that there were no other migrations in ancient times. A report issued in 2003 declares that "haplogroup frequencies alone cannot distinguish between admixture and common ancestry." [xvi] The authors also note,
However, it is important to remember that mtDNA is but one marker, and one that is solely maternally inherited, and is unlikely to answer all questions regarding the origins of Native Americans ... Like mtDNA, Y-chromosome data have not on their own conclusively answered questions regarding either source populations within Asia or the number of migrations out of Asia into the New World. Clearly, nuclear markers from more populations should be examined to provide additional data relevant to these controversies, even though it is unlikely that additional data will significantly simplify what is a convoluted and complex scenario of migrations and postmigrational evolutionary forces. [xvii]
Continuing, they write that:
In almost all studies of ancient Native American populations [from skeletal remains], individuals have been discovered who do not appear to belong to one of the five founding lineages. In many cases, this is undoubtedly a result of external contamination of samples lacking DNA or in which the DNA is inhibited from amplifying using the polymerase chain reaction. Nonetheless, the possibility remains that additional haplogroups may be discovered by studies of ancient DNA in the Americas. Such a lineage may have either become extinct or be a yet-undiscovered lineage persisting at low levels in modern populations. [xviii]
The authors of the report note that, "Early studies of Na-Dene populations [of North America] suggested that they possessed high frequencies of haplogroup A but lacked haplogroup B and exhibited only low frequencies of haplogroups C and D, whereas Eskimo-Aleut populations appeared to have high frequencies of haplogroups A and D but lacked haplogroups B and C. However, on closer inspection of a large number of samples, Merriwether, Rothhammer, and Ferrell demonstrated that groups traditionally classified as Eskimo and Na-Dene had measurable frequencies of all four haplogroups when larger samples were assayed." [xix] The lesson to be learned from this is that undersampling cannot give us the whole picture.
A 1991 study of the Nuu-Chah-Nulth tribe of the Pacific Northwest revealed some 28 haplotypes, of which 19 clustered in the four maternal DNA haplogroups (A, B, C, and D), while 9 did not. [xx] Because of DNA changes over time due to mutation and other factors, a given haplogroup typically includes various haplotypes or individual lineage markers that descend from a common source. No explanation was given for the other 9 haplotypes.
Mayan Samples
The authors of a 2001 study of skeletal remains from precolumbian Maya burials recovered from the Late Classsic/Postclassic site of Xcaret in the Mexican province of Quintana Roo noted that "Many analyses of mtDNA haplotypes in New World contemporary and ancient populations have shown the presence of a small number of individuals possessing none of the markers defining the four founding lineages." [xxi]
In 1998, 102 DNA samples were taken from skeletal remains at the Norris Farms Oneota prehistoric (700 years old) cemetery, with successful extraction of mtDNA from 50 of them. All four of the American haplogroups were found, along with one individual with a haplogroup not previously attested in contemporary Native Americans and designated as N. The researchers wrote, "This new mtDNA lineage might be present in contemporary Amerindian populations but not yet sampled, or it might belong to a lineage that is no longer present in contemporary populations. Alternatively, this new mtDNA lineage might actually be one of the four lineages, but a mutation or reversion has occurred at the relevant diagnostic marker, thereby obscuring the affiliation of this mtDNA type. Another possibility is that this sample was contaminated by modern DNA of non-Amerindian origin." [xxii] In 1998, the researchers summarized a study of mtDNA from skeletal remains of 108 individuals from the same site, of which 6 fell outside the four Asian haplogroups and were lumped together as "other." They noted that "data indicate that the lineages from haplogroups A, B, C, and D are the most common among Native Americans but they were not the only lineages brought into the New World from Asia. The mtDNA evidence . . . suggests a single 'wave' of people with considerable mtDNA diversity." [xxiii]
The variety of findings from mtDNA research was summed up in a 1998 article, [xxiv] in which the authors wrote that
Some of the hypotheses based on the interpretation of mitochondrial haplotypes are conflicting. Mitochondrial analysis has been invoked to support a multiwave-founder colonization of America, whereas, on the other hand, mtDNA markers have also been interpreted as supporting a monophyletic colonization from Asia. Archaeological studies seem to indicate an antiquity in the range of 11,000-33,000 years before the present (YBP) for the first settlements in Beringia and the New World, whereas different laboratories working with mitochondrial polymorphisms have proposed times in the range of 14,000-55,000 YBP for this event. Founder maternal Amerindian lineages initially had been estimated as being four. Now it is assumed that there are > 10-13 such lineages, although there is no agreement on the molecular typification of some of these founder haplogroups. [xxv]
The disagreement over the migration of the four major mtDNA lineages (whether one or more migrations) is further complicated by the fact that geneticists are not in agreement concerning the other mtDNA haplotypes found in Native American samples. Torroni and colleagues believe that only one haplotype from each of the four founding lineages arrived in the New World via migration and that all the additional variation arose in the New World, with other types being attributed to later Caucasian admixture. On the other hand, Merriwether and Ferrell believe that "multiple variants of each lineage entered the New World, and that additional unrelated lineages also entered." They illustrate this by two additional lineages they call X6 and X7, found throughout the New World, Siberia, and Asia, providing "strong evidence that at least nine different founding lineage haplotypes entered the New World," and that "these distributions among Native Americans best fit a single wave of migration into the New World." [xxvi]
Most researchers have tended to dismiss the minor haplogroups detected among Native Americans as admixture following the arrival of Europeans in the New World or to ignore them completely. From the data collected thus far, the critics find it easy to ignore the possibility that Book of Mormon peoples imported any of these haplogroups. When Latter-day Saints point out the inconsistencies, they respond that only the major haplogroups count, since all Native Americans are supposedly descended from Lehi. This information comes not from the text of the Book of Mormon, but from the interpretation some have erroneously placed on the text. [xxvii]
When geneticists examine Native American DNA, they use procedures to screen for each of the four (now five) "Native American" haplogroups. If, after screening a sample without a successful identification, the sample is labeled "other." Ultimately, some of these "others" are found to be related to samples tested from other settlements or archaeological sites, and can then be classified as a new haplogroup. This is what happened with haplogroup X.
Haplogroup X
A brackish pond (bog) at Windover, adjacent to Titusville, Florida, has preserved the largest North American collection of human skeletal remains and fabric for its time, along with the largest tool collection. Brain tissue was preserved in nearly a hundred of the skeletons and was extracted for DNA analysis. None of the common Native American mtDNA haplogroups (A, B, C, and D) were present, but haplogroup X, known mostly from Europe, was plentiful, suggesting that these ancient remains are of people of European ancestry. [xxviii] Later research concluded that there was a persistence of both nuclear and mitochondrial haplotypes at Windover throughout its entire period of use. "Analysis of the mtDNA sequences suggests that some mitochondrial types are clearly related to extant Amerind types, whereas others, more distantly related, may reflect genetically distinct origins." [xxix]
A study reported in 2000 examined DNA samples drawn from human remains ranging from 300-6,000 years in age, from the Aleut, eastern Utah Fremont, Southwestern Anasazi, Pyramid Lake (Nevada), Stillwater Marsh (Nevada), and Oneota (western Illinois), which were then compared with 41 samples from contemporary North American populations. The report admits that "Haplogroup X is an additional ancestral Amerindian mtDNA lineage and is evident upon screening with additional markers and through sequence analysis. Because most of the samples available for analysis have not been screened for these additional markers, it is not possible to identify haplogroup X in all these data." The researchers also noted that "although haplogroup assignment is straightforward in modern samples, it is not always so easy for ancient samples." [xxx]
A 1999 study examined 70 samples of Native American mtDNA, most of which did not evidence any of the four haplogroups (A-D). Of these, 32 were found to belong to haplogroup X. The researchers concluded that
the wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestral descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups. [xxxi]
The authors also note that, "Haplotypes that are not members of A, B, C, or D and that are characterized by specific mutations have been reported in modern (presumably unmixed) Native Americans and in prehistoric individuals, suggesting that founding haplogroups other than A, B, C, and D were once present in the New World, whether or not they have survived," [xxxii] adding that "it is of interest to determine whether or not additional founding haplogroups were once present, but have since become extinct, in the New World." [xxxiii] They cite a 1996 study by Lorenz and Smith, who worked with mtDNA samples from 829 Native North Americans and classified 50 of them as "other" than the four haplotypes (A-D). Revisiting the data, the new study was able to rescreen mtDNA from 25 of the 50, they found that seven had been mistyped and were reassigned to haplogroups A and C (2 each) and D (3), with some of the others assigned to haplogroup X. [xxxiv]
Initial mtDNA studies suggested that there were four haplogroups (A-D) found among Native Americans that are also attested mostly in Asia, though they are not the dominant haplogroups in Asia. Indeed, the earliest studies did not detect haplogroup B in Siberia. [xxxv] The discovery of a fifth haplogroup, X, led to suggestions that it may be due to a migration from Europe, since X had not yet been attested in Asia but was found in DNA samples from Finland, Italy, and Israel, with possible connections to samples from Spain, Bulgaria, and Turkey. [xxxvi] As it turns out, haplogroup X was later identified at a low frequency (3.5%) among the Altaians of Siberia. [xxxvii] While the critics believe that this seals the fate of the Book of Mormon, it really demonstrates that all of the evidence is not yet in and that new discoveries are the norm. If, following further research, a haplogroup not attested in Asia was found in some Asian populations, could not the same thing happen in the New World as the DNA sampling increases the size of the database?
Critics have suggested that even though mtDNA haplogroup X is represented in the Near East, the time-depth for its arrival in the New World is too great to be attributable to Lehi's group. But the existence of this haplogroup in the New World at the time of Lehi's arrival does not a priori mean that it did not exist among the Lehites. If Sariah and her daughters or the wife of Ishmael and her daughters carried haplogroup X into the New World, it would be different from the X haplogroup found among Native Americans because it would have a different mutational history. But since the same haplogroup is different in various Native Americans because of genetic drift following their separation from other New World inhabitants, none of them are precisely like those of such other inhabitants, nor are they identical to the haplogroup X found in Siberia.
The debate about the origin of haplogroup X continues to this day. Because it is attested in higher percentages among Europeans sampled than Asians and because the Native American X shares affinities with the European X not found in the Asian, [xxxviii] some researchers have suggested that it was brought to the New World from Europe across the north Atlantic by people hunting seals. Archaeologists have demonstrated that the earliest spear points found in the Americas are identical in design and method of production to the Solutrean points found in western Europe (notably France and Spain) for the same time period, and that these points are ancestral to the Clovis points previously thought to be the earliest use of flaked stone tools in the New World.
Dennis Stanford of the Smithsonian Institution, an archaeologist who drew attention to the Solutrean connection, said, "The way the tools are made, the whole tool kit, bone artifacts and some artistic expressions are similar, and burial practices are similar." [xxxix] Stanford noted that "There are so many matching steps in how they made their tools: bifacial flaking, heat treatment, similar ceremonial items, the presence of red ochre. There must be fifty or sixty points of comparison. It can't be chance." [xl] Among the more important New World prehistoric sites with suspected ties to the Solutrean culture of Europe are Meadowcroft Rock Shelter, near Pittsburgh, Pennsylvania, and Cactus Hill, Virginia. [xli]
Significantly, both the Solutrean points and mtDNA haplogroup X are attested in a geographical region most likely to have been affected by a migration from Europe. Haplogroup X is found principally among the Algonquian-speaking peoples of the Great Lakes region, including the Ojibwa, but has also been found among the Nuu-Chah-Nulth and Yakima tribes of the northwest. It is known in about a fourth of Ojibwa natives tested and in lesser amounts among members of the Sioux and Navajo. [xlii] It has also been found in skeletal remains of two individuals found in a fourteenth-century burial in Illinois, demonstrating that it was in North America prior to the time of Columbus.
Despite these evidences, other researchers have suggested that haplogroup X came from Europe or Central Asia across Beringia to the New World, leaving very little trace in Siberia. Ripan S. Malhi and David Glenn Smith noted that the Altai of Siberia "are the only known modern ethnic group whose membership represents all five Native American haplogroups and, assuming the New World was colonized by a single migration, constitute a possible origin of the founders of Native America." This leads them to reject the hypothesis of a European migration of haplogroup X to the New World and discount the suggestion that there are similarities between Clovis and Solutrean cultural artifacts. Because it is found among ancient samples from the Norris Farms, Windover, and Vantage sites and the Amazon Basin, they consider haplogroup X to be "a founding Native American lineage" and reject the idea that it resulted from Viking or more recent European admixture. They note that three Algonquian-speaking Native Americans "exhibit both the haplogroup X with the transition at np 16,213 and the rare Albumin marker Albumin*Naskapi," both of which are found only among North American natives." [xliii]
The haplogroup X saga clearly indicates that there is no consensus on matters relating to migrations from the Old World to the New. Perhaps related to the haplogroup X question is that of the "Red Paint People" of ca. 4000 B.P., whose cultural remains have been excavated mostly in Labrador and Maine. The name given them by modern archaeologists resulted from the fact that they added brilliant red iron oxide to their graves. It now seems clear that they sailed across the Atlantic, for similar graves are found in France, England, and Denmark. [xliv]
The authors of a 2003 study wrote, "we have completely sequenced a haplogroup X mtDNA from the Ojibwa ... A comparison of this sequence with those haplogroup X mtDNA sequences of European ancestry that were published by Finnilä et al. (2001) and by Herrnstadt et al. (2002) shows that this Native American mtDNA carries all of the mutations that define haplogroup X." [xlv] A 2003 study makes it clear that haplogroup X originated in the Near East and the version found in Asia was recently introduced from Europe and is more distantly related to that found among Native Americans.
A maximum parsimony tree of 21 complete mitochondrial DNA (mtDNA) sequences belonging to haplogroup X and the survey of the haplogroup-associated polymorphisms in 13,589 mtDNAs from Eurasia and Africa revealed that haplogroup X is subdivided into two major branches, here defined as "X1" and "X2." The first is restricted to the populations of North and East Africa and the Near East, whereas X2 encompasses all X mtDNAs from Europe, western and Central Asia, Siberia, and the great majority of the Near East, as well as some North African samples. Subhaplogroup X1 diversity indicates an early coalescence time, whereas X2 has apparently undergone a more recent population expansion in Eurasia, most likely around or after the last glacial maximum. It is notable that X2 includes the two complete Native American X sequences that constitute the distinctive X2a clade, a clade that lacks close relatives in the entire Old World, including Siberia. The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East. [xlvi]
In 2000, geneticist Theodore Schurr noted that "Recent claims ... that European stock may have been present in pre-Columbian America do not deny the overwhelming contribution of Asiatic peoples to the ancestry of modern Amerindians." [xlvii] The same could be said of Book of Mormon peoples, i.e., that most of the mtDNA makeup of Native Americans can be Asian even if some of their ancestors came from the Near East.
[i] I am indebted to Matthew Roper for bringing some of the articles mentioned herein to my attention.
[ii] Some of the articles listed in the appendix deal with these issues.
[iii] For a discussion, see John L. Sorenson, "The Problematic Role of DNA Testing in Unraveling
Human History," Journal of Book of Mormon Studies 9/2 (2000): 66-74.
[iv] For a good explanation of how DNA can be used in population studies, see D. Andrew Merriwether, David M. Reed, and Robert E. Ferrell, "Ancient and Contemporary Mitochondrial DNA Variation in the Maya," in Nancy P. Dutro, ed., Bones of the Maya: Studies of Ancient Skeletons (Washington and London: Smithsonian Institution Press, 1997), 208-17. For general information about how DNA works, see the following web sites:
http://www.accessexcellence.org/RC/AB/BA/dnaintro/index.html
[v] It is actually a little more complicated than that, involving RNA and other processes, but the explanation given here is sufficient to understand what is going on.
[vi] Identical twins are an exception because they develop from the same fertilized egg.
[vii] There are actually four kinds of changes: 1) indels, which are insertions into or deletions of the DNA at particular locations on the chromosome, 2) snips, which are single nucleotide polymorphisms in which a particular nucleotide (A, C, G, or T) is changed into another, 3) microsatellite changes, which are short sequences (10-60) of nucleotides that are repeated a variable number of times in succession along the nucleotide chain, and 4) minisatellite changes, in which the repeated sequences are short (usually up to 3-4 nucleotides).
[viii] While this is essentially the case, there are very rare occasions where a human being has two X chromosome and one Y or even three X.
[ix] During meiosis, only 1% of the Y chromosome recombines with the X chromosome, the rest evidently constituting what one could call "maleness."
[x] An exception is noted later in this paper.
[xi] The task is not totally impossible, provided one has access to a supercomputer that can perform billions of calculations per second, and provided one also takes into account any mutations over time.
[xii] I acknowledge that it is more complicated than this, but most readers will not want to know more than the basics.
[xiii] For an informative discussion of Y chromosomes, see Neil Bradman and Mark G. Thomas, "Why Y? The Y Chromosome in the Study of Human Evolution, Migration and Prehistory," Science Spectra 14 (1998): 32-37, posted http://www.ucl.ac.uk/tcga/ScienceSpectra-pages/SciSpect-14-98.html.
[xiv] Barring mutations, all offspring of a woman have identical mtDNA, regardless of how many men may have fathered her children.
[xv] Ripan S. Malhi and Jason A. Eshleman, "The Uses and Limitations of DNA Based Ancestry Tests for Native Americans," 11, Trace Genetics web site, http://www.tracegenetics.com/nativeamericandna.pdf.
[xvi] Jason A. Eshleman, Ripan S. Malhi, and David Glenn Smith, "Mitochondrial DNA Studies of Native Americans: Conceptions and Misconceptions of the Population Prehistory of the Americas," Evolutionary Anthropology 12 (2003), 8.
[xvii] Ibid., 15-16.
[xviii] Ibid., 13; emphasis added.
[xix] Ibid., 8.
[xx] R. H. Ward et al., "Extensive Mitochondrial Diversity Within a Single Amerindian Tribe," Proceedings of the National Academy of Science USA 88 (1991): 8720-24.
[xxi] Angelica Gonzalez-Oliver et al., "Founding Amerindian Mitochondrial DNA Lineages in Ancient Maya from Xcaret, Quintana Roo," American Journal of Physical Anthropology 116 (2001): 230.
[xxii] Anne C. Stone and Mark Stoneking, "Ancient DNA from a Pre-Columbian Amerindian Population," American Journal of Physical Anthropology 92/4 (1993): 466.
[xxiii] 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 (1998): 1153.
[xxiv] I have omitted the parenthetical references from the text cited here so readers will not be distracted from the flow of the paragraph. Some of those references will be cited later.
[xxv] Néstor O. Bianchi et al., "Characterization of Ancestral and Derived Y-Chromosome Haplotypes of New World Native Populations," American Journal of Human Genetics 63 (1998): 1862.
[xxvi] D. Andrew Merriwether and Robert E. Ferrell, "The Four Founding Lineage Hypothesis for the New World: A Critical Reevaluation," Molecular Phylogenetics and Evolution 5 (February 1996): 241.
[xxvii] This has been dealt with elsewhere; see the appendix to this article.
[xxviii] Glenn H. Doran et al., "Anatomical, Cellular and Molecular Analysis of 8,000-year-old Human Brain Tissue from the Windover Archaeological Site," Nature 323 [6091] (1986): 803-6. In 2002, the University of Florida Press published a book edited by Doran, Multidisciplinary Investigations of an Early Archaic Florida Cemetery, which includes the following articles: W. Hauswirth and C. Dickel, "Investigations of DNA Isolated from Windover Brain Tissue: Methods and Implications"; David Glenn Smith et al., "Serum Albumin Phenotypes and a Preliminary Study of the Windover mtDNA Haplogroups and Their Anthropological Significance"; D. C. Hyland and T. R. Anderson, "Biomolecular Analysis of CollagenousTissue."
[xxix] W. W. Hauswirth et al., "Inter- and Intrapopulation Studies of Ancient Humans," Experientia 50/6 (1994): 585.
[xxx] Dennis H. O'Rourke et al., "Spatial and Temporal Stability of mtDNA Haplogroup Frequencies in Native North America," Human Biology 72/1 (February 2000): 17.
[xxxi] David Glenn Smith et al., "Distribution of mtDNA Haplogroup X among Native North Americans," American Journal of Physical Anthropology 110/3 (November 1999): 271.
[xxxii] Ibid., 272. To facilitate reading for the nonspecialist, I have omitted the parenthetical references to other articles, some of which are included in this present survey.
[xxxiii] Ibid., 275.
[xxxiv] Ibid., 276, 278-9. The earlier study to which they refer was Joseph G. Lorenz and David Glenn Smith, "Distribution of Four Founding mtDNA Haplogroups Among Native North Americans," American Journal of Physical Anthropology 101/3 (November 1996): 307-23.
[xxxv] Antonio Torroni et al., "mtDNA Variation of Aboriginal Siberians Reveals Distinct Genetic Affinities with Native Americans," American Journal of Human Genetics 53/3 (September 1993): 591-608.
[xxxvi] Virginia Morell, "Genes May Link Ancient Eurasians, Native Americans," Science 280 (24 April 1998), 520; 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 (December 1998): 1852-61.
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