Outside of the nucleus, but still in the human cell, is something called mitochondrial DNA, or mtDNA for short. MtDNA contains only 16,569 pieces of genetic information. Perego said mtDNA is good for tracing populations because, unlike nuclear DNA, it doesn't recombine with other DNA every generation. However, every once in a while, a random mutation — a slight mistake in copying the mtDNA — will be passed on to the next generation.
Compare mtDNA to a 16,569-word book. Occasionally, a word or two might be changed by accident in an edition — such as "an" being changed to "a." That mistake will then be in every subsequent edition. Over time, in other editions, other changes happen. Some editions are printed in different areas with their own unique mistakes.
Now imagine a scholar gathering various editions of the book. All the cumulative mistakes leave a trail of when and where an edition was published and how it is related to other editions. Population geneticists do a similar thing when they look at the various mutations in mtDNA.
Large groups of people that share similar mtDNA mutations are called haplogroups. "A haplogroup is a group of genetic lineages sharing common characteristics. The reason they share this common characteristic is because they share a common origin or female ancestry," Perego said.
This "female ancestry" thing about mtDNA may seem strange. It only passes from a mother to her children. You have your mother's mtDNA. She has her mother's. And because changes in mtDNA are infrequent, it is likely that your mtDNA is nearly identical to your great-great-great-great-grandmother's mtDNA. There could be millions of people with similar mtDNA — and not a one of them got that mtDNA from a man. If a woman only had sons, her mtDNA ends with them. It goes no further.
Perego used the example of a family he knows in Italy. The father had five daughters. How many of those daughters have his mtDNA? None. Those daughters gave him 28 grandchildren. If that Italian father had married an African woman, all these grandchildren would be classified as African using their mtDNA.
The father in Perego's example was genealogically related to all his grandchildren but left no trace of his mtDNA in any of them. In fact, his grandchildren's mtDNA could have more in common with complete strangers from other centuries than with the father's mtDNA.
Perego points out the immediate way this information could affect looking at the Book of Mormon. "Let's say 20 people came with Lehi and 10 were men and 10 were women. The next generation you already lose 50 percent of the mitochondrial DNA just because all the men will not pass it on. Lehi's mitochondrial DNA is gone. Ishmael's mitochondrial DNA is gone. Zoram's mitochondrial DNA is gone. Period. That's just how it works."
This leaves two women to pass on mtDNA: Ishmael's wife and Lehi's wife, Sariah.
But wouldn't the women in Lehi's group have similar mtDNA to Lehi's? "That is a very wrong assumption to make," Perego said. "You can find in any population a great variety of mitochondrial DNA lineages. You would find a higher frequency of certain lineages and a lower frequency of other lineages, but in most populations you would find a very good variety."
Most of the studies done on Native Americans to date utilized only a small part of the mtDNA. In the book edition analogy, this is like looking for changes in only the first 300 to 500 words in our 16,569-word book.
Perego calls studies that look at only a small portion of mtDNA "low resolution." A complete sequence of a person's entire mtDNA is "high resolution" and can give greater information. But so far, these complete sequences are rare — and expensive. According to Perego, in the entire world, there have been about 6,000 complete sequences of mtDNA samples — and less than 300 on Native Americans.
Part 3
DNA science can't tell us if Book of Mormon prophet Lehi and his small group came to the Americas 2,600 years ago. But Lehi's intrepid group of seafaring Israelites is a great example for understanding how a small group can enter a land, flourish and then leave no identifiable genetic trace.
Among the many principles of population genetics are three that are essential to understanding what may have happened to Lehi's DNA: Genetic drift, founder effect and population bottleneck. "If people dismiss these three principles … they show that they do not understand population genetics," said Ugo Perego, senior researcher at Sorenson Molecular Genealogy Foundation.
These three principles apply whether you are talking about people in Indiana or Iceland. Lehi's group is a good hypothetical to look at these principles ?— whether you believe he existed or not.
Genetic drift
Genetic drift explains how a lineage, also called a "haplogroup," can disappear by random genetic interaction. "If you start with a population of 10 or 20 lineages, after many generations you might only have two or three of these lineages represented," Perego said.
Perego used an well-known analogy: Imagine a jar has 10 red marbles and 10 blue. Pick one marble at random — let's say red. Put the marble back in the jar and put a new red marble in a second jar. The new marble carries on that particular "red" haplogroup or lineage.
Keep picking random marbles until the second jar has 20 new marbles, perhaps six red and 14 blue. Now pick random marbles from the second jar to determine a third jar's contents, perhaps three red and 17 blue. By the fourth or fifth jar, it is possible to have only blue marbles. Blue is fixed. The sixth, seventh, or even 3,500th jar will all be blue. Red is gone forever.
Population geneticists trace groups by using mitochondrial DNA (mtDNA), which only passes from mothers. In Lehi's group this leaves two possible sources of mtDNA: Lehi's wife Sariah and Ishmael's wife. Imagine that Ishmael's wife's mtDNA became fixed and Sariah's disappeared through genetic drift.
If the continent was heavily populated when Lehi arrived, inevitable intermarriage and genetic drift could make Ishmael's wife's mtDNA disappear like a red marble in a sea of blue.
The founder effect
In the founder effect, a rare lineage will remain rare in a large population. If a small group that has that rare lineage founds an isolated colony, that rare lineage can become the dominant lineage. If the colony came to a populated area, founder effect would have less impact than genetic drift.
If Sariah or Ishmael's wife had a rare lineage, then the descendants of Lehi's group would also have that rare lineage — that is, until it was lost in the genetic drift of a larger population. Population bottleneck
A large population can become small very quickly in the case of disease or disaster. After the event, the population may build up again, but many lineages may not have survived that disaster — that "bottleneck."
Perego said that Native Americans hit a considerable population bottleneck when the Europeans came to the Americas. A study showed gene pools were reduced to between one-third and 1/25th of their former size. "What we have today represents the survivors of the European arrival. It does not represent (all the lineages of) the people who arrived here 2,000 years ago, 2,600 years ago or 10,000 years ago," Perego said.
This becomes important when you are looking for remnant lineages from a small family that colonized in a populated area."You had a lot of (genetic) variation before the Europeans came," Perego said. "Then came the destruction, the killing, the disease, the slavery. … Some villages were wiped out completely — especially if you look at the East Coast. There are Native American groups for which there are no survivors."
The "deCODE Project" in Iceland is a good example of how these principles work. Researchers had DNA samples of people born in Iceland after 1972. They were also able to trace their genealogies back to 1742. They discovered that the vast majority of the people alive today in Iceland are the descendants of a very small percentage of the people who lived in 1742.
"Many people who were living in 1742 have no living descendants or do not have any genetic lineages represented … in the modern population," Perego said. "Why? Because lineages just disappear. We don't normally realize how much they do, but here we have a tremendous discrepancy between who lived 300 years ago and who live now. Think about 2,600 years ago (when Lehi came), how much that would have an effect. This is a powerful example."
Some people may counter that Iceland was a special case because it had migrations and volcanic eruptions. "But the same thing happened to America," Perego said, "There were Europeans coming and disease."
Genetic drift, population bottleneck and founder effect can eliminate genetic lineages through time — making it possible that mtDNA from Lehi's group went the way of the red marble.
Part 4
A, B, C, D.
These four letters represented the first DNA classifications of Native Americans into similar lineages, or haplogroups.
Things were simpler then — and so were the conclusions.
Because A, B, C and D appear to be Asian in origin, some said this proved the Book of Mormon false. But even then, a simple understanding of DNA showed that it would have been possible, or even probable, that we wouldn't find traceable DNA evidence from a small group of Israelites coming to a largely populated continent.
Enter X.
A few years later, the story became more complicated. A fifth haplogroup was found in Native Americans. Ironically, the letter chosen to identify the new haplogroup was the mysterious letter X. "Studies confirmed the presence of X in the Americas," said Ugo Perego, senior researcher at Sorenson Molecular Genealogy Foundation, "particularly in the Great Lake regions of northern North America — but also in other areas to a lesser extent such as Texas, New Mexico and Arizona."
X was an enigma. Unlike A, B, C and D, it was rare in the world. X lineages were found in West Eurasia — an area that stretches from Scandinavia down to the Middle East.
It was also found in Asia.
The gauntlet was thrown down. Was the X found among Native Americans from the Middle East or Asia? Did it have anything to do with the Book of Mormon?
"Some people believe that haplogroup X is of Near Eastern origins and (they said) the fact that you find it in the Americas … proves the Book of Mormon to be historically correct and true and the people existed," Perego said.
Others took an opposite view.
"Other people, both from the LDS background and the critics, argued that haplogroup X is of Asian origins, just like the other Native American lineages, and arrived to America through Beringia (through the Bering Straits ancient land bridge), more than 10,000 years ago. Therefore it has nothing to do with the Book of Mormon people," Perego said.
Studies from 2001 indicated that the X haplogroup of American Indians came from Middle East or European lineages via Asia. A group in Asia, the Altaians in upper Mongolia, have the X haplogroup lineage, and so were thought to show the Asian source of the Native American X lineage.
These studies, however, were low resolution. They only analyzed a small portion of the mitochondrial DNA (mtDNA). It was like looking at an area code. Soon, technology advanced and geneticists started looking at full sequences of mtDNA — like looking at a whole phone number. It didn't change the general information, but the details made a difference.
As higher resolution studies progressed, the Native American haplogroup classifications were made more specific with the addition of numbers: A2, B2, C1, D1 and X2a.
In 2003, high-resolution data from complete sequences of mtDNA gave a different story. It appeared that the Native American X (X2a) did not have any close match anywhere in the Old World. It also did not match and was an older lineage than the Asian X of the Altaians.
Current published data indicates that Native Americans belonged to a branch of X that split from the other X lineages near the beginning of X's spread out from the Middle East. It was old, but it wasn't Asian.
Last year a study suggested that the Druze religious minority of northern Israel represented a surviving population of the source of X lineages.
But just because X came originally from the Middle East doesn't mean it is connected with the Book of Mormon. Dating mtDNA is done by looking at the number of mutations in a haplogroup. The more mutations, the older the haplogroup. The currently accepted dating for X2a, based on its unique mutations, predates Book of Mormon times. "If X2a is only found (in America) we assume it has been there for 12,000 years," Perego said. "But if you can find it in another part of the world and prove that it has been there for a long time, then the 12,000 years would include that lineage, too."
In other words, for now it appears that X2a "aged" in the Americas for 12,000 years. If X2a is found somewhere else in the world, that may mean it aged there first before it came to the Americas. One verified match in the Old World and the date of X2a in America could drop from 12,000 years to, say, 4,000 years or even Book of Mormon time periods.
According to currently published studies, the closest match to X2a outside of the Americas was found in Iran. But even if X2a matched a Middle Eastern genetic signature perfectly, Perego says there is no way to know for sure the X2a in America came from Lehi's group.
"In my mind it's a lot more comfortable, the idea that DNA is not the ultimate proof against or in favor of the Book of Mormon," Perego said. "There are too many (other factors) regarding the Book of Mormon's historicity that cannot be verified with DNA."
But this won't stop some from trying to use DNA to prove or disprove the LDS Church's unique scripture.
"People don't like the unknown," Perego said.
