This is an interesting article that uses simulated data to show graphically the difference between being genetically related vs. being genealogically related to a particular ancestor on your tree. From these simulations based on the inheritance property of autosomal DNA, you can observe that just within a few generations, the DNA of many of our ancestors is not represented in our current genome. Ancestors that were not able to pass autosomal DNA down to the present generation are represented by white blocks in the two graphs displayed. This phenomenon is pretty simple to explain. Each of us received basically 50% of our parents DNA. This immediately implies that the other half is lost unless they have more children and therefore a greater chance to pass additional segments of their DNA to the next generation. As we go back one more generation, that of our grandparents, randomness becomes a player in the equation and although statistically we average 25% of each of our grandparents DNA, the reality can show as much as 50% and as little as zero of a single grandparent's DNA. Mom and dad received 50% from each of their parents and therefore, they could have given us more DNA from one and less from the other. Going back a few more generations and more and more of your ancestors will not be represented genetically in your genome, although they were real people that are part of your family tree. These charts are based on simulations going back 11 generations. As the author explains it, just 20 generations ago, you would have had over one million ancestors. I want to add that 30 generations ago, approximately 750 years ago, or around the year 1250AD, each person alive today would have had more than one billion potential ancestors. If we think about Book of Mormon genetics and genealogy, Lehi and his family arriving to the American double continent 2600 years ago, or approximately 100 generations ago, would most likely be on every Native American pedigree chart and therefore be genealogically related to all those who have American pre-Columbian roots, but what is the likelihood that some of these individuals DNA would have survived until today?

Last year I received an invite to attend the Paleoamerican Odyssey conference that was held last week in Santa Fe, New Mexico. I declined knowing that it would have been difficult to find the necessary funding for yet another trip across the ocean this year. However, my good friend and colleague Dr. Alessandro Achilli from the University of Perugia (Italy) was able to go and wrote me immediately after attending the presentation where these results were shared. Now I really wished I would have gone!

The study that will come out in the prestigious journal NATURE shortly (as of today it is in press), describes the genetic analysis of a 24,000 year old skeleton found in Siberia. The complete genome was sequenced, including the paternally inherited Y chromosome and the maternally inherited mitochondrial DNA. The results were not quite what was to be expected. The young boy DNA showed no relationship to Easter Asians, but 1/3 of the genome in common with Native American populations and the rest with Europeans. Even the Y chromosome and mitochondrial DNA look European as they belong to haplogroups R and U respectively. The report from SCIENCE included the following comment from the leading researcher:
"The finding suggests that about a third of the ancestry of today's Native Americans can be traced to western Eurasia, with the 
other two-thirds coming from eastern Asia, according to a talk at [the meeting "Paleoamerican Odyssey" in Santa Fe, NM on 16–20 October 2013] by ancient DNA expert Eske Willerslev of the University of Copenhagen. It also implies that traces of European ancestry previously detected in modern Native Americans do not come solely from mixing with European colonists, as most scientists had assumed, but have much deeper roots."

It is obvious that these data and findings will have major implications with regard to our understanding of Native American origins and colonization events. Moreover, it opens a lot more questions on a topic that for so many was already closed. For sure, there is so much more to learn about how and when the ancestors of Native Americans arrived to the Western Hemisphere. Although the DNA in this particular study refers to a very ancient specimen, the presence of European DNA in the Americas that predates the arrival of Europeans within the last 500 years poses some serious new consideration with regard to be able to discern any sort of Old World DNA in the Americas from the time of the first arrivals all the way through the millennia to our days. Can European DNA found in modern and ancient Native Americans be immediately dismissed as being for sure post-Columbian? Can we discern European DNA introgression in the America's gene pool from 20,000 years ago, 10,000 years ago, 3,000 years ago, or 1,000 years ago? 

Native American genetics got all of a sudden a lot more exciting! It will be interesting to see what the future will bring.

A couple of weeks ago I had the great honor to be invited to spend a week in the beautiful country of Panama together with my long time friend and colleague Dr. Alessandro Achilli. Together, we recently published a paper on the mitochondrial DNA landscape of Panama (Perego, et al. PLoS ONE 2012) and we were asked to share our findings at the annex of the upcoming Biodiversity Museum in Panama City and at the Annual Panamanian Congress of Science and Technology at the City of Knowledge (Ciudad del Saber) next to the Panama Canal.
In addition to the two of us, other invited speakers included Nobel Prize winner Yuan T. Lee (Chemistry, 1986) and the current director of the National Human Genome Research Institute, Dr. Eric Green. The highlight of our trip was a special VIP dinner at the home of the Taiwanese Ambassador to Panama with other special guests, mostly scientists involved with the local science institutions. I had some of the best Chinese food in years! That is one thing I miss for sure about living in the States. This was my third time to Panama, but I have the feeling that it won't be the last. There are few ideas about possible future projects and I am excited about continuing this collaboration.

Recently, the National Geographic's Genographic Project launched a new DNA test kit called GENO 2.0. It is an autosomal DNA test that covers very specific nuclear SNPs providing information about the history of our genes including a survey of our paternal line (Y chromosome), maternal line (mitochondrial DNA), and the deep ancestry written in the autosomes. It will link our DNA to the history of humankind as it started in Africa tens of thousands of years ago, all the way to the present time. I just ordered my own test, even though they won't be shipped until the end of October. This test will also compare genes between humans and apes, and even Neandertals, looking for surviving rare genetic links between our species and our closest relatives in the evolutionary tree.

National Geographic has a strong pro-evolution agenda, which continues to stimulates all sort of interesting thoughts in religious arenas about harmonizing the biblical creation account with evidence (particular genetic evidence) from science pointing to evolution (something that I have also speculated about in the past). Interestingly, just today, someone in a forum that does not like LDS beliefs mentioned me in a dissatisfied manner stating that "an LDS scientist speculates if those in the past were even human." Believe it or not, I don't think I am the first one that postulated that there were hominids more than 6,000 years ago, but I am flattered if someone would think so.

Here is a video by the Genographic Project introducing the new test.

I recently published on the FAIR Blog a post called Misquoting Science with the objective of clarifying a statement that appeared in the June 2012 issue of Sunstone magazine. In a nutshell, the poorly formulated quote was yet another attempt to demonstrate how DNA science is the ultimate proof against the historicity of the Book of Mormon since no Israelite DNA could be detected in the Americas. I have addressed this issue in great length before here and spoke a little more about it at the recent FAIR conference (a full transcript will be available some time in September). However, I have been made aware of a comment posted on a forum not particularly fond of LDS beliefs, which reads:

"A full transcript of his presentation is not available yet but he has posted some of his words on the FAIR blog.

One of things I read in his blog concerned me. He said "I personally find it a very complex task to identify and clearly discern any non-Asian-like genetic signals in the New World that would have resulted from migrations that took place in the last couple thousands of years."

How does he square this statement with the fact that his Italian mentor Dr. Antonio Torroni and colleagues were able to determine a Near Eastern origin of the Etruscans?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852723/pdf/AJHGv80p759.pdf

'The origin of the Etruscan people has been a source of major controversy for the past 2,500 years, and several hypotheses have been proposed to explain their language and sophisticated culture, including an Aegean/Anatolian origin.'

'These findings support a direct and rather recent genetic input from the Near East—a scenario in agreement with the Lydian origin of Etruscans. Such a genetic contribution has been extensively diluted by admixture, but it appears that there are still locations in Tuscany, such as Murlo, where traces of its arrival are easily detectable.'

Dr. Perego would do well to explain why science works in Italy but not in America."

I have wondered why it took so long for anyone to bring this up. I am very familiar with the study my colleagues at the University of Pavia did on Etruscan DNA and I was surprised no one had yet correlated that study with the search for Near Eastern mitochondrial DNA lineages in the Americas. "Bravo" to the individual that has finally come up with this question and,  since this person was "concerned" about my statement and also calls for an explanation on "why science works in Italy but not in America," I am happy to write a couple of lines on my own blog with the hope that it will be a good educational opportunity to others, particularly to those that also commented on the above post.

First, I find it humorous (and I cannot resist, but have to write something here about it) that the original comment from Sunstone magazine did not receive a single note of criticism by those that are bringing up issues with my own comments. As long as someone having absolutely no credentials in the field of science is willing to openly criticize the Book of Mormon, he/she is immediately welcome by all those that share similar feelings toward that volume of scriptures. However, how dare I say anything on this very subject, having a PhD in population genetics (with a dissertation on Native American DNA), and having researched extensively about the origin of Native Americans through DNA, publishing the results with international collaborators in a peer-reviewed journal with a considerable high impact factor! But this is not all. Dr. Torroni and Dr. Achilli, the main authors on the Etruscan DNA study mentioned in the comment above, are among those that read and provided feedback to my own essay on DNA and Book of Mormon published in No Weapon Shall Prosper last year (see note at the end of the article).

Here is the problem, for anyone honestly interested in understanding how population genetics work: the study on Etruscan DNA proposes a genetic link (mitochondrial DNA only) between the population of modern-day Turkey (ancient Lydia) and a few villages in Tuscany, Italy (where Etruscans lived prior to their assimilation by the Roman Empire). This movement of people took place about 2500 years ago, which is about the same time when the Book of Mormon voyage of Lehi and his family took place toward the Americas. Why then can science work for the Etruscans and not for Book of Mormon people? Here are a few points that should help clarify the matter.

First of all, the Near Eastern origin of Etruscans is a theory, not a fact. Just like some individuals claim that Old World DNA in the Americas is a legacy of Book of Mormon migrants, not everyone agrees with that hypothesis. It is an idea that needs further investigation and does not provide conclusive evidence. So it is with the genetic origin of the Etruscans. The 2007 study by Achilli et al. stands on solid foundations and I strongly support their conclusions, but not everyone in the field of population genetics agrees with them. A more recent study (2009) using both modern and ancient mtDNA reached different conclusions, stating that "So far, the study of mtDNA has not substantially contributed to addressing the most debated question concerning the Etruscans, their origin." People disagree on conclusions drawn using genetic data to reconstruct ancient population migrations all the time. It is OK to have a preferred opinion or a favorite publication, but we must also acknowledge that there are others that don't see it the way we do.

If the genetic evidence is correct (based on the study by Achilli et al. 2007), we must then consider the next two points.

According to one tradition, the king of Anatolia sent half of his population to settle another area due to the fact that there was a severe famine in the land and not enough resources to sustain everyone. If this is the case, the number of people that left the ancient Near East and settled in Italy was not small. In contrast, when talking about Lehi and his family, we have a nucleus of about 15-20 people settling in a continent where tens of millions of indigenous Amerindians already lived. As I explained in my blog post, one of the problems in ensuring the survival of genetic signals into future generations was the size of the Israelite group within the much dominant Amerindian genetic landscape. Additionally, there are records that show where the ancestors of Etruscans landed and settled (the Italian region Tuscany was named by the Romans after the Etruscans), while the geography of the Book of Mormon is still a matter of debate even among LDS scholars. 

Next, the Etruscan mtDNA paper is a study about frequency and geographic distribution, not necessarily about age coalescence (see Figure 3). The mtDNA lineages observed in the Near East are similar to those observed in Italy, but not in other parts of Western and Eastern Eurasia. Thus the link about the ancient migration of the ancestors of Etruscans was proposed. In the Americas we also find a large number of Old World mtDNA lineages that are found in many parts of Europe and the Middle East. If we would apply the same criteria used in the Etruscan paper, we would also conclude that many individuals in the Americas have Old World origins. However, scientists feel more comfortable in assigning these lineages to post-Columbian introgression, thus excluding a priori any migration (or genetic evidence) to the Americas that took place within the last couple of millennia. And this is OK with me, because:

I still think that the primary reason why DNA cannot be used to test for the presence of Book of Mormon migrants arriving to the Americas in 600BC lies in the fact that it quickly disappeared due to genetic drift and the small size of the migrant group (and this is also the reason why it has not been detected in the few ancient DNA samples recovered and analyzed to date), as well as the obvious reason that we don't have the genetic profile of those arriving with Lehi to the Americas. We know something about their genealogy and we assume that their DNA would be the most representative DNA from the Middle East. But this is another straw man assumption. No one would accept the "assumption" of a genetic lineage as evidence in any modern-day legal, paternity, or forensic case. So, why is the fact that we don't know Lehi's genetic profile "proof" that the Book of Mormon people never existed?

If anyone wants to embrace genetic evidence for population migrations, he/she must also be willing to consider all the research that is available and the limitations proposed by the different authors, and not pick only what best suits their preconceived notions. Of course, when it comes to the Book of Mormon and anything that is considered "secular evidence," it is nearly impossible to be completely unbiased and that is why the final test is what the book call for itself (Moroni 10:3-5). 

No Weapon Shall Prosper: New Light on Sensitive Issues is a recently published volume (2011) by Brigham Young University Religious Studies Center, and edited by Dr. Robert Millet, former Dean of Religious Education at the same university. It is a collection of articles written by scholars from diverse fields and addressing topics that have been used by critics of The Church of Jesus Christ of Latter-day Saints to attack the Church, its history, or doctrines. I was asked to write an essay on the issue of DNA claims with regard to the historicity of The Book of Mormon, which during the past decade has been used both against and in favor of such argument. In one sentence, my conclusions could be summarized with a simple: "You cannot use genetic evidence to conclusively support whether The Book of Mormon was historical in nature, or not." What I mean with "conclusively" is that you cannot state that genetic evidence is sufficient to close the matter once and for all, one way or the other.

I recently found an online review for No Weapon Shall Prosper by Richard Packham, which included a section about my essay "The Book of Mormon and the Origin of Native Americans from a Maternally Inherited DNA Standpoint." (An earlier version of this article was published in FARMS Review in 2010).I have posted the full text of the review pertaining to what I wrote below, with the objective of addressing Mr. Packham comments, section by section.

PACKHAM: Ugo Perego, a geneticist at BYU, authored the article on how DNA research impacts the message of the Book of Mormon. Perego frankly admits that current DNA research on the origin of Native Americans cannot confirm the Book of Mormon by showing Israelite ancestry for them (p 182). He confirms the view generally held by authorities in the field that DNA research shows an origin for them in the area of Mongolia, and that they began to migrate to the Americas thousands of years before Book of Mormon times. Perego acknowledges that the entire human race is descended from a single woman who lived in Africa about 200,000 years ago (p 170).
PEREGO: For the record, I am not a geneticist at BYU. I received a BS and MS at Brigham Young University, but I have never been part of their faculty. I received a PhD in Genetics and Biomolecular Sciences, with an emphasis on population genetics, at the University of Pavia (Italy) under the mentorship of Professor Antonio Torroni. I have worked for the past decade in the private industry for the non-profit Sorenson Molecular Genealogy Foundation and taught Human Biology at the Salt Lake Community College as an adjunct faculty (both institutions located in Utah). A simple internet search would have provided this information. 
The purpose of my treatise in No Weapon Shall Prosper  was not to discuss the impact of DNA research on the message of The Book of Mormon, as stated by Mr. Packham, but on the misuse of genetic data in linking the origin of Native Americans with the historicity of The Book of Mormon, two topics that in my mind have to be addressed separately and with proper understanding of fundamental population genetics principles. Mr. Packham is obviously familiar with the topic, but he is definitely not an expert in the field of population migrations and genetics. He makes a couple of common misstatements at the beginning of his review that are often spelled out by those that have a superficial understanding of this topic: 1. A large subset of Native American lineages share a common ancient ancestry with Asian populations, which is substantially different from stating that they originated from Central Asia. In my article, I also explain that the currently accepted molecular clock for mitochondrial DNA allows for the splitting of deep lineages (i.e. ancient migrations that took place tens of thousand of years ago), but this instrument is often not adequate to successfully detect migrations that occurred in a relatively recent past (i.e. the last couple of millennia). Such a research as not yet been designed with the objective of studying lineages with no Asian affinity in the Americas, although there have been several instances in which additional, more recent pre-Columbian migrations to the Americas, including interesting DNA markers that could have a non-Asian origin, have been reported in the past. 2. Mitochondrial DNA evidence does not claim that all humanity descends from a single woman, but that all mtDNA lineages eventually coalesce in a single female ancestor. This is just one of the many ancestors modern humans have. Both of these points are extensively discussed in my essay, but have been ignored in Mr. Packham's review.
On a shorter note, Mr. Packham, as many critics of The Book of Mormon, enjoys dwelling on the fact that I have openly admitted the lack of Israelite DNA in the Americas. At the same time, he purposely neglects that in other parts of my essay I emphasized that we don't have a reference to be used when searching for Lehi's party DNA in the Americas and the many reasons why it would be nearly impossible to detect such a genetic signal even if we knew what we were looking for.

PACKHAM: In defending the Book of Mormon against the implications of these facts, Perego makes some astonishing claims. He claims that the Book of Mormon says nothing about "whether other populations were already established in the land" (p 163). He appears to want to ignore what God said to Lehi (2 Nephi 1:9) that Lehi's people would go to a land where they would be "kept from all other nations." Or God's assurance to the brother of Jared (Ether 2: that the land they had been promised would be preserved for them alone, so long as they remained righteous.
PEREGO: My "astonishing" claims are quite simple to understand in the context I originally made them. First of all I explain the vastness of the American double-continent and how The Book of Mormon states to be just a summary of several records spanning a period of 1000 years. Therefore, I am not surprised that such a volume does not mention clearly and unequivocally about other populations. The rate of population growth though is somewhat surprising and the fact that the faction labelled as Lamanites is growing considerably faster in number than their counterparts, the Nephites (given an equal rate of reproduction for both groups) would imply that in one case there could be rapid admixture with surrounding native populations, while the latter group attempted to remain homogeneous and keep things within the "covenant". Extensive warfare between the two factions during the same generation of their arrival to the New world would also imply recruitment of indigenous populations. Perhaps one of the strongest argument in favor of local inhabitants is found in the very book of Jacob, when Sherem stated that he "sought much opportunity " to speak with the leader of the Nephites (Jacob 7:6). Or when Mormon feels the need to state that he is "a pure descendant of Lehi" (3 Nephi 5:20). These and other statements in The Book of Mormon leave the door open to the possibility that other groups might have been present in the land. As Mr. Packham acknowledges (but also ignores in his review), the concept of inheritance of the land was tied to the righteousness of the people, which neither the Jaredites nor the Nephites kept as a standard of living until the end. Additionally, the concept of land could be referred to a geographic area either small or large. I have no preference in the geographic setting of The Book of Mormon and I leave it to others to discuss about a limited or continental setting for the events narrated in such volume, however, being The Book of Mormon a summary of a 1000 year history in just few hundred pages and due to the size of the American continent, I have no problem in considering that the record keepers and the man that claimed to have made a summary of such records left out many details about the population dynamics of their and other possible groups in the land. It is also plausible to interpret that "the other nations" from which our protagonists would be kept from were those that were a treat to them (the story tells of the destruction of Jerusalem and the persecution of Lehi as a good reason to leave their hometown and for the Jaredites it was the unrighteousness that reigned in the land at the time of the building of the Tower of Babel). This is very much in line with what motivated the first pilgrims to leave Europe in search for a place where they could exercise religious freedom and avoid persecution "from other nations" (the European ones).

PACKHAM: Perego gives no explanation for the fact that the Book of Mormon text makes no mention of encounters with people already there. When the Mulekites are discovered (Omni 1:14) there is a great todo, and the encounter is recorded. But that's the only such encounter or mention of other peoples. Compare that with the Israelites, who also were led to a "promised land." Their history repeatedly mentions their neighboring peoples, their wars with them, their victories over them, their intermarriages with them. Why - if a similar situation really existed with the Book of Mormon peoples - is there nothing of that nature? Perego comments that the Book of Mormon is a "sacred and religious history," but so is the Old Testament.
PEREGO: In my treatise I explain that the distance from Alaska to Tierra del Fuego is greater than that from Portugal to Japan. Considering the fact that The Book of Mormon states to be an abridgment of the most important events, it seems normal to me that there are no too many details about other populations and that not all the people that could have lived during that time and over the entire Western Hemisphere landmass were the object of the Nephites' record keeping. It is the story of the glass half empty or half full. In my mind, the fact that a group is mentioned (the followers of Mulek and a Jaredite survivor) is proof that other people were there and so could have been others. The comparison with the Israelite biblical record is somewhat not proper since Israel is only 8,000 square miles in size (compared to the 16,428,260 square miles of the combined North, Central and South America continent). Israel could fit into Florida 8 times being only 263 miles long and between 9 and 71 miles wide. Also, the Old Testament text does not claim to be an summary of other records, but a full account. The Nephites would have had an impossible task to fill if they wanted to include all the events of the Americas in their records, more so in the abridgment that was made by a single individual.

PACKHAM: Perego attributes the belief that the Book of Mormon should be seen as a history of the origin of ALL Native Americans to "a common sentiment" and "speculation" by both Mormons and non-Mormons. He seems to be unaware that the same "sentiment" was shared by the Angel Moroni and most Mormon prophets from Joseph Smith through Spencer W. Kimball. Did not Moroni say (JS-Hist 1:34) that the gold plates gave "an account of the former inhabitants of this continent and the source from whence they sprang"? Perego (and many other modern Mormon apologists) apparently read that as "an account of a tiny percentage of the former inhabitants of a little corner of this continent before they were swallowed up without a trace."
PEREGO: First of all, to be genealogically related is one thing and to carry the genes of our ancestors is another. I mention in my article (and it is an accepted principle in population genetics) that the genes of a colonizing groups have a close to zero chance of survival in future generations when competing with those of the hosting population. Additionally, it is also a matter of determining which groups survived, what happened to them after the end of keeping the records, and what dynamics were involved. The Book of Mormon is not a complete record when it comes to the history of these people and their genealogies. The Angel Moroni spoke of the "former" inhabitants, which means that they no longer exist. If they don't exist, then their DNA should not be easily detected in the modern native population. Apparently, this is a concept that Mr. Packham has a hard time accepting as it would not support his position.

PACKHAM: Perego concludes with the assertion that "Anyone using DNA to ascertain the accuracy of historical events of a religious nature - which require instead a component of faith - will be sorely disappointed." How is the origin of Native Americans a religious question? Only because the Mormons have made it so. Yes, if one wants to believe something which is unsupported by historical or scientific information, a large component of faith is required. Faith apparently always trumps science (a common theme in this collection). But DNA is used every day in criminal cases to determine the accuracy of facts.
PEREGO: The religious question is obviously not about the origin of Native Americans, but about the historicity of The Book of Mormon, which in my mind is not a record with the objective to provide a detailed and complete origin of these people. How is that science could support unequivocally the truthfulness of a religious volume? What kind of evidence would provide such proof as to convince those that cannot rely on faith, prayer or personal revelation (the common standards for most religious practices) that an an ancient record is divine in nature and not man-made? What type of DNA testing or research design would provide the accuracy of facts that are described in The Book of Mormon or in the Biblical text (or other religious records for that matter) from a DNA viewpoint? As a retired lawyer, Mr. Packham should know that in a criminal case, to reconstruct the accuracy of facts you would need both the DNA of the perpetrator and at the same time the DNA of a list of suspects in order to find a match. What was the DNA of the people in Lehi's party and how would we conclude that it is what we think it could be without a chance to actually test it? How could a case be closed if we are missing the very genetic evidence that we need to ascertain whether these people actually existed? Either Mr. Packham is oblivious about genetic testing for population studies, or he is so biased about Mormonism as to fail to accept the very principles that govern such science.

Today I read a couple of pieces in the news reporting a new study that will soon appear in the prestigious European Journal of Human Genetic journal. The running title for each story was quite sensational with a clear reference to Jewish DNA found in the Americas: "Israeli researchers: Group of Colorado Indians have genetic Jewish roots" and "Israeli researchers find American Indians with Jewish genetic markers". The title is comforting if you have desperately been waiting for someone trustworthy to report a genetic connection between the Old and New Worlds. I know few people that would jump all over this one. The study is interesting; no doubt about it. I can't wait to read the full paper in the journal when it will become available. The genetic link is also plausible, but be aware that according to the researchers, the dating of the BRCA1 gene (one of those associated with breast cancer) reported in the study is 600 years before present. The researchers concluded that these are conquistadores with Jewish blood that left Spain following the discovery of the Western Hemisphere by Christopher Columbus and immediately interbred with the local native population of Central and North America (as north as probably modern-day Colorado) thus leaving a genetic legacy of Jewish DNA in the modern indigenous population. While the distribution of the BRCA1 gene in Old and New World populations is pretty clear, the dating for such mutation and its arrival to the Americas leaves some room for debate.