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Tuesday, 2 February 2016

Response to the claim 1/3 of Native American DNA came from the Middle East - now that would be a Great Surprise



Some Mormons have been claiming that a recently published human genomics research paper offers support for the belief that Native Americans have Jewish ancestors. The paper causing the excitement was published in the Jan 2013 issue of Natureone of the most prestigious scientific journals. The article in question was written by Raghavan et al. and entitled “Upper Palaeolithic Siberian Genome Reveals Dual Ancestry of Native Americans.”  The paper would have gone unnoticed by Mormons had a National Geographic journalist not sensationalised it with the following hyperbole.


"Great Surprise"—Native Americans Have West Eurasian Origins.

Oldest human genome reveals less of an East Asian ancestry than thought.
Nearly one-third of Native American genes come from west Eurasian people linked to the
 Middle East and Europe, rather than entirely from East Asians as previously thought, according to a newly sequenced genome.


Many Mormons reading these headlines have seized upon this research as conclusive proof that Native Americans have Middle Eastern, and thus potentially Jewish, DNA (1234). Even President Newsroom cited Raghavan's research in the Church's official "Book of Mormon and DNA Studies" essay, claiming it challenges previous conclusions and proves the picture isn't clear. But the conclusions being challenged have nothing to do with recent Hebrew migrations. The Raghaven study is focussed on a 25,000-year-old paleolithic DNA sample which tells us something about major human migration events that took place over 20,000 years ago. There is nothing in the Raghavan research that supports the Book of Mormon or challenges the mainstream scientific views about the colonization of the New World. Native Americans are still all descended from ancient Asian ancestors.

The Context of the Research 


Raghavan's research adds another detail to a broad scientific understanding of the timing and route our ancestors took as they colonised the globe. The common ancestors of all humans lived in sub-Saharan Africa. They began migrating "out of Africa" about 80,000 years ago and by about 50,000 years ago had colonized Western Asia, India and Southeast Asia and Australia (Fig.1). Eastern Asia was colonised by people derived from this southern migration event. By about 40,000 years ago people arrived in Europe and Central Asia via a northern route, finally reaching the Americas between 15 and 25,000 years ago.

Fig.1.   Major routes and timing of human colonisation of the world 
(Wellcome Trust, www.sanger.ac.uk

Scientists have found no evidence that we all descend from a single man and women (Adam and Eve) who lived on the earth about 6,000 years ago. This is simply not what happened. The volumes of evidence in support of the mainstream scientific views are vast and span numerous disciplines. It is the truth and Mormons should face it. When the individual Raghavan's team studied was alive, humans had not even reached the Americas so it is difficult to comprehend how it tells us anything about mythical Jewish migrations in the last few thousand years. 

Fig. 2.  The extent of human colonization of the world 25,000 years ago 
and the location of Raghavan's Siberian sample.


The 2014 Raghavan Study 

Raghavan's team isolated DNA from the bones of a 24,000-year-old individual and sequenced its entire genome. They then examined 156,000 DNA markers (SNPs) to reveal how closely related this individual is to hundreds of other people from contemporary populations (Fig. 3). The more DNA markers two individuals share the more closely related they are. 


Fig. 3.  Heat map of relatedness between the Siberian (MA-1) and individuals from numerous 
geographical locations around the world. The graded heat key on the left indicates the 
degree of relatedness with red indicating high relationship and black low relationship. 
(See Raghavan et al. 2014)

The major finding of the study is that the Siberian individual (MA-1) is not closely related to other Central and Eastern Asians (dark blue dots) and much more closely related to Native Americans (red dots). In addition, this Siberian appears to be related to people now living in Europe and Western Asia (yellow, light blue-green dots). This suggests that this Siberian individual's ancestors had migrated from Western Eurasia into Siberia, but when they arrived they did not mix very much with Asian populations living further east. Consequently, when some of this Siberian's descendants migrated on to the Americas, they didn't carry many DNA markers found in East Asian populations.

Another way of illustrating the results of the study is shown in Fig. 4 below. All Eurasians and Native Americans descend from people who lived in West Asia (near modern day Afghanistan and Pakistan) about 50,000 years ago (see also Fig. 1.). These people carried with them large numbers of DNA markers that can be defined as West Asian. When the ancestors of the Siberians and Europeans/Middle Easterners migrated away from each other, both groups carried the same set of West Asian (blue) DNA markers with them. This is why the Siberian individual carried DNA markers also found in Europeans and Middle Easterners. They shared common ancestors about 15,000 years earlier (50,000 years ago).   

However, once they became separated from each other, each group began to accumulate DNA markers that were unique to each group. This is indicated by the green (Eur/ME) and purple (Siberian) shading on the tree (Fig. 4). Once the Siberian groups encountered East Asians some of their DNA lineages (red) also entered Siberian populations, and some of these DNA markers found their way to the Americas.


Fig. 4.  Origin of DNA markers in Native Americans and some Eurasian populations 
and the approximate timing of their occurrence 

Summary

Virtually all Eurasian and New World populations descend from populations that migrated out of Africa and colonised West Asia about 50,000 years ago. Eastern Asia is likely to have been first colonised by populations that split away from a southern migration through India that ended in Australia. The Raghavan study tells us that Siberians are mostly derived from people who migrated into Central Asia via a northern route that resulted in little admixture with Eastern Asian populations. The research paper is focussed on very ancient migrations and tells us nothing about the likelihood or occurrence of recent Jewish migrations to the pre-Columbian New World.

22 comments:

  1. Simon,

    While browsing the internet I came across a pro-Mormon page that claims (bullet #3):

    "Another separate study demonstrates that DNA that was present as recent as 500 years ago on the American continent could be completely lost in today’s indigenous inhabitants."

    http://debunking-cesletter.com/?page_id=169

    The study cited is from April 2016:

    http://advances.sciencemag.org/content/2/4/e1501385.full

    I read the study and, while I did see a few caveats, it does seem to say that many pre-Columbian south american haplotypes have disappeared. I re-read some of your blog posts, but I'm unable to determine if this means "Lamanite" DNA could just disappear. I would appreciate your input.

    ReplyDelete
  2. Hi Kris,

    Thanks for your question. Below is my response to this apologist claim

    "Another separate study demonstrates that DNA that was present as recent as 500 years ago on the American continent could be completely lost in today’s indigenous inhabitants."

    The study in question compared the whole mitochondrial genomes of 92 ancient samples with modern Native American mitochondrial genomes. There were no matches, which is hardly surprising and the authors explain why. The database of modern Native American entire mitochondrial genomes is quite small (probably a few hundred) and most of them are derived from people living great distances from where the ancient samples were collected. If we had tens of thousands of whole mitochondrial genomes from across the continents I am sure we would see some matches. It has already been shown that if you compare the mitochondrial DNA of ancient and modern samples from the same geographical area, you do find identical mitochondrial DNA sequences.

    This URL takes you to a study in Patagonia. I can’t find the reference but I know they have found identical lineages in ancient and modern individuals in Native American tribes from the Pacific Northwest. http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22815/abstract;jsessionid=AB3A4B9A6FC3B41F7BE496E2F60606D7.f02t04?userIsAuthenticated=false&deniedAccessCustomisedMessage=

    I’m not saying that individual lineages cannot go extinct. They can and they do. However, mitochondrial DNA studies are typically used to track populations rather than individuals. While individual lineages can go extinct, major haplogroups rarely go extinct. In their haste to find excuses for why we can’t find Lamanite DNA, the apologists overlook the fact that ALL 92 of the ancient lineages in the earlier study fell into either the A2, B2, C1b, C1c, C1d, and D1 lineage families or haplogroups. All of these are Asian lineages. Not a single ancient sample has ever been found that didn’t originate in Asia.

    The apologetic arguments assume the Lamanites were a tiny group who inhabited an unknown corner of the Americas and their DNA has been diluted away to undetectable levels. If you can believe that then the DNA evidence is largely irrelevant.

    ReplyDelete
  3. Simon,

    Thank you for replying. After reading your response I re-read the article and it's becoming clearer to me. I can now see I used some terms improperly in my original question. It's been a long time since college biology, plus genetics has advanced a lot since then.

    Let me see if I have this right: The 92 pre-Columbian samples had 84 distinct haplotypes which didn't match any modern native Americans because:
    1) the haplotype database of modern native Americans is small and only covers a few geographic locations.
    2) haplotypes are usually concentrated in a geographic region and the regions of the pre-Columbian and modern samples don't overlap, or overlap only slightly.
    3) new haplotypes (mutations) occur over time so it's not surprising that modern native Americans have different haplotypes than pre-Columbians.

    Haplotypes often share similarities that allow them to be pooled into haplogroups, and both the pre-Columbian and modern native Americans have the same haplogroups, thus indicating they are related farther back in time.

    When you say an individual lineage can go extinct, is that another way of saying a haplotype can die out? The paper talks about a lack of genetic diversity, is that because the contact with Europeans (disease, war) killed a lot of native Americans and thus some of the haplotypes probably died out? But the main haplogroups survived.

    Moving on to the issue of Lamanites, I agree with you that it would take a very implausible set of conditions to prevent "Hebrew" DNA from being found today - conditions which contradict the Book of Mormon itself (millions of nephites and lamanites, spread over the land, built many cities, etc.). And citing this paper does nothing to support the BoM position, upon careful reading. It really only says that if you are looking for particular haplotypes, you need samples from that same time period and geographic location. Otherwise the main haplogroups are still an effective marker for tracing populations through time and geography, and no "Hebrew" haplogroup(s) have been found in the Americas.

    ReplyDelete
  4. Hi Kris,

    Yes, when I refer to an individual lineage I am referring to a haplotype, which is the more technically correct term. And haplogroups are collections of related haplotypes. I often use the term lineage families for haplogroup.

    War and disease will definitely have reduced diversity in the haplogroups, however, all of the major haplogroups we see today are present in ancient samples. The apologists frequently cite a paper on Icelandic populations where they observed "extinction" of many haplotypes over a 200 year period due to disease, famine and large scale emigration. However, ALL of the haplogroups present in Iceland 200 years ago can be found in living individuals. Thus the haplogroups are very useful for tracking population movements.

    ReplyDelete
  5. Thank you for the confirmation. Initially I wasn't picking up the finer points and distinctions. The difference between halpotypes and haplogroups is important, and now I know this after having gone through this exercise.

    Thank you for all the information you have shared here. It's been useful and helpful to me.

    ReplyDelete
  6. michele@mail.postmanllc.net

    ReplyDelete
  7. what are your views on the recent discovery of the Ark of the Covenant in Panama? There are over 20 Jewish archaeologists involved into the excavation. The tomb was found by a local Panamanian Indian digging a well and found the ancient tomb. The video is quite impressive it seems to prove Jews migrated to Panama 2600 years ago. Tell me what you think of the documentary video @ https://www.youtube.com/watch?v=ijIp4bXb2C4

    ReplyDelete
    Replies
    1. It is a scam.
      http://www.mormondialogue.org/topic/67774-the-ark-of-the-covenant-discovered-in-panama/?page=1

      Delete
  8. Dr. Southerton,

    Have you or do you know of someone who has responded to the other points in the gospel essay "Book of Mormon and DNA Studies?" It references the "founder effect" and "population bottleneck and genetic drift." The essay essentially argues that DNA studies cannot adequately address these and other issues surrounding population migration. The essay seems to cite some peer reviewed evidence that calls into question the DNA studies and certainty about Native American origins. The conclusion of the essay says the evidence is simply inconclusive. Would you consider doing a critique of the major truth claims in the essay on DNA? I see major logical errors in the front end of the essay, but once it gets to the "Understanding Genetic Evidence" it gets a bit tricky. Thanks.

    ReplyDelete
    Replies
    1. While you wait for Simon to respond, here is an earlier post of his that addresses some of your questions.
      http://simonsoutherton.blogspot.com/2014/02/response-to-president-newsroom.html

      Delete
    2. Hi Don,

      Tapir Rider has kindly linked you through to my response to the DNA essay. The claim that DNA studies cannot reliably detect an early introduction of Middle Eastern DNA is a very weak argument. DNA is being used to unravel human migration all around the world. This "DNA limitation" argument relies on the assumption that the amount of Middle Eastern DNA that was present in the Americas was vanishingly small. That is, Lehi and his Hebrew descendants never had many descendants. But they somehow managed to lead sophisticated New World civilizations with massive populations. The apologetics surrounding this new Book of Mormon narrative are frankly pathetic.

      Delete
  9. Hello,my new friend,this blog gives me a lot surprise and I like it very much.If you are interested in the game, you can come to my site RS 2007 Gold

    ReplyDelete
  10. Recently I've seen this article pop up among LDS acquaintances: DNA scientists claim that Cherokees are from the Middle East.

    http://www.nativeamericanhere.com/uncategorized/dna-scientists-claim-that-cherokees-are-from-the-middle-east/

    It's the typical unsubstantiated, stringing together of tenuous links, just trust me I know it's true, screed. The only references is to na-stuff.com which has been down for days.

    This article (with citations and references, how novel!) does a good job pointing out the myriad holes in the assertions made by the Cherokee article:

    https://www.accessgenealogy.com/native/cherokee-dna.htm

    My take away: Those who claim be Cherokee cannot prove there was not admixture with Europeans after 1492 (post-colonization), and there are plenty of logical and historical indicators that make admixture the most likely source of the Middle Eastern and other markers. Also note that DNA Consultants, Inc. did the study AND makes money from Cherokee DNA testing (conflict of interest). Now if one or more Cherokee corpses from before 1492 were found and DNA sequenced, then you'd have my attention.

    And might as well get ahead of another paper that will surely be twisted by Mormons to make a case for the Book of Mormon:

    http://arstechnica.com/science/2016/08/time-to-scrap-the-idea-that-humans-arrived-in-the-americas-by-land-bridge/

    Even a casually careful reader will see that just because the first people to migrate to America took boats instead of walking across the Bering Land Bridge, they still came from Asia.

    ReplyDelete
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    The RPG-22 is a one-shot disposable rocket launcher designed for use against armoured vehicles and fortifications.bryce wilson melbourne
    Through the improvised modification displayed in this video, the RPG-22 can be modified to fire further than its 150-200 meter range.

    ReplyDelete
  12. Hi, Simon. A Mormon friend sent me this.

    http://www.theepochtimes.com/n3/831180-geneticist-traces-mysterious-origins-of-native-americans-to-middle-east-ancient-greece/

    Could you share me your thoughts on this?

    Thanks.

    ReplyDelete
  13. Dr Yates has a vested interest in detecting Jewish DNA in Native Americans. He owns a DNA testing company and firmly believes the Cherokee descend from the Jews. His conclusion that he has found Jewish DNA are not supported by any scientists who study Native American ancestry.

    ReplyDelete
  14. Hey Simon I love your work, but I had one quick question. One of the arguments that I have commonly heard from apologists Recently is that we do not know what Hebrew DNA looked like when Lehi in 600 B.C., so there is no way we don't know that the Native Americans have no Jewish ancestory. How would you respond to this?

    ReplyDelete
  15. Hi Brogan,

    The Hebrews are closely related to Arab, Palestinian, Druze, Bedouin and other Semitic populations found in the Middle East. These people have lived in the Middle East for many thousands of years, they share related languages and they share a common ancestry. They also share similar DNA. The contemporary DNA of Semitic people today is closely related to the DNA of Semitic people living thousands of years ago in the Middle East. Since we know Lehi was a Hebrew, we would expect his offspring to carry markers that are unique to Middle Eastern populations. We would not expect his ancestors to carry DNA markers found in Siberian populations.

    ReplyDelete