Native American DNA News

It’s a good DNA day for Native American DNA research.

Yesterday, I was talking to Bennett Greenspan at Family Tree DNA.  He knows of my interest in Native heritage.  Our conversation turned to the new Geno 2.0 chip, now called the GenoChip, and the expected ethnicity results relative to Native heritage.

It turns out that Bennett and Spencer Wells had just been talking about the same thing.  Spencer said that the GenoChip is exceptionally good at picking up Native American ancestry and that it’s one of the key features built into the autosomal SNPs they chose and the resulting admixture analyses.  Spencer says that as long as the admixture is above 2%, we’ll see it.

Two percent equates to between 5 and 6 generations.

I can’t wait to compare Geno 2.0 results of people who previously tested at 23andMe and with Family Tree DNA’s Family Finder, and especially those who showed the Middle Eastern percentage with the Family Finder test.

This information dovetails nicely with a new paper to be published in the American Journal of Human Genetics, the February 10th edition.

In this new paper, Dr. Theodore Schurr has used Y and mitochondrial DNA evidence collected from 500 Siberian people living in remote villages and more than 2500 Native Americans from Canada, the US and Mexico.  The paper confirms the homeland of the Native people in the Americans was originally the Altay Mountains in Siberia (photo above).  This isn’t new news, but it’s nice to have confirmation and it will be interesting to see the details in the paper.

In an article published this week by the National Geographic Society titled “Is this Russian Landscape the Birthplace of Native Americans?”, they mention that there is one marker in a male Y-line that mutated about 18,000 years ago and is still carried by Native men today.

http://news.nationalgeographic.com/news/2012/01/120203-native-americans-siberia-genes-dna-science/

I know that many recently discovered Y-line SNPs were included for haplogroup Q on the new GenoChip.  I’m very hopeful that the DNA of the Siberian people was vetted for new autosomal SNPs and included as well.  It’s likely, as Dr. Schurr, in addition to his work at the University of Pennsylvania is also the North American Director for the Genographic Project.

36 thoughts on “Native American DNA News

  1. In addition, here is the abstract for another scientific study, presented this week at ASHG annual meeting, which uses the Genochip for the same purpose:

    “3329W
    Genetic ancestry and admixture analysis in a Bermudian population
    reveals evidence of Native American origins consistent with oral histories
    and genealogies. J.B. Gaieski1, E. Elhaik2, 3, A.C. Owings1, M.G.
    Vilar1, A.T. Walia1, D.F. Gaieski4, R.S. Wells5, T.G. Schurr1, The Genographic
    Consortium. 1) Anthropology, University of Pennsylvania, Philadelphia,
    PA; 2) Department of Mental Health, Johns Hopkins University
    Bloomberg School of Public Health, Baltimore, MD; 3) McKusick-Nathans
    Institute of Genetic Medicine, Johns Hopkins University School of Medicine,
    Baltimore, MD; 4) Department of Emergency Medicine, Hospital of the University
    of Pennsylvania, Philadelphia, PA; 5) Mission Programs, National
    Geographic Society, Washington, D.C.
    Background: Shortly after its colonization in the early 17th century, Bermuda
    became the first English speaking dependency to forcibly import its
    labor by trafficking in enslaved Africans, European ethnic minorities, and
    indigenous Americans. Unlike the many ethnic groups that now call the
    island home, Bermuda’s St. David’s Islanders claim to be linked to Native
    American ancestors. In particular, their use of oral traditions and complex
    genealogies helps to reinforce their Native American identity. To elucidate
    the influence of historical events on genetic ancestry and native cultural
    identity among St. David’s Islanders, we examined mtDNA and Y-chromosomal
    variation in over 100 individuals. We found that the majority of their
    mtDNA and Y-chromosome haplotypes (greater than 98%) were African
    and West Eurasian in origin. However, due to the limitations of this approach
    in reconstructing the genetic history of admixed populations, and because
    most participants were interested in learning more about their genetic
    genealogies, we expanded our analysis to include autosomal markers using
    a novel genotyping platform. Methods: To identify genetic contributions of
    putative indigenous American ancestors among the St. David’s Islanders,
    we used the GenoChip to genotype Bermudians along with 200 samples
    from ~20 worldwide populations. Developed by Genographic Project scientists,
    the GenoChip is a SNP array ascertained from over 450 worldwide
    populations, and is dedicated to enhancing our knowledge of genetic anthropology.
    Results: Principal component analysis of the autosomal SNP data
    separated our participants into three discrete clusters. An admixture analysis
    identified up to 9% ancestry associated with Native Americans overall. The
    two largest clusters overlapped with African Americans and Puerto Ricans,
    and distributed evenly amongst the two main clusters (mean of 3% each).
    Samples from the third cluster averaged an unusually high Native American
    ancestry (mean of 6%). Conclusions: The GenoChip enabled us to detect
    otherwise elusory Native American ancestry among the Bermudians of St.
    David’s Island. We speculate that the uneven distribution of this ancestry
    is due to admixture of Africans, Europeans, and Native Americans in varying
    degrees in the different source populations for modern-day St. David’s
    Islanders. Application of this novel genotyping platform has provided new
    insights into the complex history of the Bermudian population.”

    • “The two largest clusters overlapped with African Americans and Puerto Ricans,
      and distributed evenly amongst the two main clusters (mean of 3% each).”
      Please tell me the GenoChip does not use “Puerto Ricans” as a representative sample. I understand the 1000 Genomes Project attached this descriptor because one of the members of its sampling committee is a professor at the University of Puerto Rico. There are no native Puerto Ricans, Carib or Arawak, remaining. Puerto Rico is populated by a mix of mostly Spanish and sub-Saharan Africans, with a minority of more recent ethnic groups, including Jewish, none native. So it is very reasonable for there to exist an overlap with African Americans.

      IMHO, admixture (autosomal) analysis is still in its infancy, and many of the conclusions reached by researchers should be viewed with a grain of salt.

      • Mark, I have personally spoke with the lead researcher (a PhD) on this Bermuda research project.

        She’s presenting out in San Francisco today at the ASHG meeting.

        She personally administered over 100 of the new NatGeo GenoChip 2.0 tests to participants in Bermuda and reports that the GenoChip 2.0 results are fantastic and beneficially accurate (not in an infancy state as you said). Specially when it came to distilling out enslaved Native American admixture which took place in the 1600s.

        This is literally the 1st significant study with this new multi-array GenoChip 2.0. This is indeed important news for those into Deep Ancestry and Population Genetics.

        I plan on using the GenoChip 2.0 in a Wales study seeking out more information about Ancient Britons and Neolithic R1b migrations in from the Iberian Peninsula. I can tell you this, I bet the POBI researchers wish they had this lowcost GenoChip 2.0 DNA test for their research project before taking over 5000 samples.

        There is more to BioInformatics than Admixture and BGA analysis. FastIBD analysis to determine pairwise SNP cohorts, 3D PCA analysis, Autosomal aging analysis via ADLER and other methods, and more.

        I think Roberta is wrong in implying her 2% (5 to 6 generation) rule and just limiting things to IBD states on cM lengths from about 2cM to 4cM when one sample is involved

        That doesn’t apply when you have multiple comparative samples and can look at things at an individual refined SNP level vs a broader Centimorgan length which most Citizen Genetic Genealogists are accustomed to.

        So Mark, I think you are completely in the minority in claiming her Bermuda research conclusions along with others in her team should be “viewed with a grain of salt.” Heck, you have not even read the FULL Research Report, only a Partial Abstract, nor taken the time to talk with the researchers and you raising yourself up as an expert professional in this area versus taking a more constrained approach consistent with the amateur your appear to be.

      • Roberta,

        I am not in SF at the meeting … but know a couple people there.

        What are you looking for? I will try to forward your inquiries to them if you email me,

        Thanks for clarifying the IBD 2%. (5 – 6 Generations) part.

        Which “I” think is about 2cM to 4cM of IBD DNA based on my experience and this academic paper: http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0034267

        I think some want us to believe that Autosomal Analysis “has to be always” limited to a 5 or 6 generations time frame and to me that simply is poor advice.

        When there are multiple samples (as I mentioned in another post here) much better triangulation and correlation can be done both with 1cM to 2cM IBD segments AND at the individual SNP level where one unique SNP mutation might be identified in atDNA (similar to as you mentioned here in the Shurr study with more stable and less recombination Y-DNA and atDNA samples) OR as I and have others have done in defining a set of unique and informative AISNPS (Ancestry Informative atDNA SNPs) and LISNPs (Lineage Informative atDNA DNA SNPs).

        I have done that back 12 Generations … twice as far as the 5 – 6 generations mentioned with the people you spoke with.

      • I’m not looking for anything specific at ASGH, just anything relevant to our search. Kathy Johnson is there too, and I’ll be seeing her at the conference, so hopefully she can fill us in. I agree that I’m very hopeful that with new tools we may be able to pick up more ancient admixture as opposed to more direct admixture. I think with individual ancestral informative markers, we can do a lot better than that, but it may take time and more study….but I know we’re progressing in that direction.

      • @Mark Deutsch
        “…Dr. Juan Carlos Martinez Cruzado, a geneticist from the University of Puerto Rico. In an island-wide genetic study, he found that at least 61.1% of those surveyed had mitochondrial DNA of indigenous origin.” the Taino/Arawak indians are not extinct their blood is alive and well in the Puerto Rican population. Please read the rest of the story here:

        http://www.cnn.com/2011/US/09/30/latino.native.american/index.html

  2. I guess I should get that test for my Dennis uncles or my Mother. The guys are Q1a3a. My uncle at Family Finder has some percentages coming out of Palestine, etc.

    • I show ancestry from Africa and Palestine with 92% Western Europe. My Paternal Haplogroup is E1b1a8a1. Paternal family from North Carolina and earlier Virginia.

      • Family oral history is that we are part Native American from Eastern North Carolina on my father’s family. My research has not identified a Native American ancestor. I have pictures of a few 1800’s paternal relatives who appear to have some Native American features. I have tested my DNA to Y-DNA67. Where do I go from here?

      • That’s very interesting. My dad has the same haplogroup. They are also from the North Carolina/Virginia border area. We also have rumors of Native American ancestry in our background. 23andme says that we do have a few traces of Native American DNA. We are mainly West African, but we have a TON more European DNA than we expected. My dad is almost half European. We did not know this. (All we ever knew is that his dad looked very European, but was “black”.) If you’re still around ,you can contact me at s.hunt.brown@gmail.com.

  3. Roberta, how can those of us who have Middle Eastern percentages at FTDNA use this information? Will we be able to compare matches with those who tested with Geno 2.0?

  4. I have a grandmother (father’s mother) who I suspect was part Native American by skin tone and family history. I have researched my father’s surname and no Native American rumored or in the family tree before my father. My Question Is; will this test give results that could verify if my grandmother was part Native American by me taking this test? Family Tree DNA tests taken are Y-DNA67, and Deep Clade-R. R1b1a2a1a1b4 L21+ P66- M37- M222-

    • Either the Family Finder Test or the Geno 2.0 test will return percentages of ethnicity. But they are different tests and test different markers. We don’t yet have results for the Geno 2.0 test so we don’t know how sensitive the test is as compared to Family Finder.

    • Ray, if its your father’s mother then researching your father’s name will not turn it up. You need to research your mothers maiden name. If you feel that you have Indian connection then follow the trail from where they ended up to where they started. Also look on sites like Rootsweb.com or Cyndislist to find your surname (for your grandmother’s maiden name) & for the states they are in. There are a lot of helpful people out there.

      • Alli, I have researched my father’s mother’s lineage.
        I have not been able to determine whether or not the family rumors of which grandmother was part Native American. The family members who would have known are long passed. If I did DNA and I had a percentage of Native American then at least I’d know I’m not chasing a false family story. My grandmother’s skin tone would indicate that the family story may be true. I’ve hit a brick wall on my grandmother’s lineages. Thank you for the suggestion but I’ve already done all of that research. I’ve worked on this for years.

  5. Hi Roberta, Thank you for a very interesting new’s letter. It encourages me to beleive that there may still be hope of finding a connection to the Native American heritage which I claim to have. I have taken the y @ FTDNA, also Family Finder, (Autosomal), also tested at 23 and me. I am still paying for for 23 and me and Family Finder. Since I have already done these test, I am wondering if the Genochip applies to the test I have taken. I believe that I have already emailed the details of my claims to you earlier. If this is available to for the test I have taken, what would your fee be to research this issue. I want to inform you that I sincerely appreciate your DNAeXplained postings, I learn from the post and look forward to continue receiving them, keep up the good work.

    Best Regards, Harley Warlick

    Harley Warlick hawarlickc@aol.com

    • Hi Harley,

      The Geno 2.0 test is completely separate from what you’ve taken before. If you want to take it, you can order it at http://www.genographic.com. I’m hopeful that it will be looking a new and different markers and will be able to pick things up that we couldn’t before, but time will tell.

      Also, thank you for the nice compliment. They go a long way:)

      Roberta

  6. Hi Roberta,
    I have Hancock Co., TN Melungeon ancestry and received an 8% “Middle Eastern” result from Family Finder with no identifiable Middle Eastern or Mediterranean ancestry in the last 250+ years. I’m anxious to see what Geno 2.0 will reveal as well.
    Regards,
    Randy Walker

    • I have not had any test done but have looked up a lot on Melungean. A lot of people have some of the ancestry down as Black Dutch. Some research shows their possible origin as coming from “jewish” people. An excellent book that will give a lot of people a beginning of where to look is Missing Links Discovered In Assyrian Tablets by E Raymond Capt. I purchased mine through Artisan Publishers out of Muskogee Oklahoma. I hope people can purchase this as part of an answer to middle eastern and European blood lines. Hope this helps.
      Mawana Buller

      • Thanks for your reply, Mawana. Genealogists have studied the origins of the Melungeon families and have shown that they are bi or tri-racials and are a blend of either two or all three of the following racial groups (all of which existed in Colonial America): European, African, and Native American, depending on the particular family in question. While some Jewish ancestry in the European component is a possibility, I don’t believe it is likely in most of the Melungeon families. I suspect that the Middle Eastern component identified by Family Finder will be replaced by African and Native American in the GENO 2.0 results due to the more expansive world populations sampled in the National Geneographic study. Time will tell.

        Regards,
        Randy

  7. So there is a noise range of 2%? So if an African American were to get a “1% Native American/East Asian” result than more likely than not they probably do not have true Native American or East Asian ancestry?

    • No, that doesn’t mean that. They wouldn’t have listed it if there wasn’t evidence for that category. What is does men, in general is that is the fudge factor for the entire autosomal process. So theoretically, could it mean that something as low as 1% could “go away”? Yes, but it’s unlikely because as I said, if there hasn’t been some evidence for it, they wouldn’t have picked up on it. It’s more likely that one of the larger amounts might be as much as 2% higher or lower.

    • You are comparing to different tests. 2% for Geno is not the same as 23andMe. 23 is actually more reliable and accurate. If an AA has 1% NA/EA, it’s probably real.

  8. I am curious. Could it be that instead of the Siberians coming to the New World that it was actually the other direction! That the original people in the new world went north west instead of the Siberians going east. How can that be disproved or proved? I would really like to see that.
    I just have a really hard time believing that the Siberians went east. To me there is not enough evidence to prove conclusively that the Siberians only went east and the the people of the America s did not go west.

  9. I too have paid hundreds of dlats for the FTDNA TESTS. SAYS 92percent Orcadian and ten percent middle eastern. How much for the new test. I did not expect the Middle East result. I did expect Native American please help

  10. Just to add my two cents in here —
    I’ve had autosomal testing done with FTDNA, 23andme, AncestryDNA, and Geno 2.0. Regarding the accuracy of my own NA results I’d have to say that the Geno 2.0 result was the closest to my known genealogy, with 23andme’s most recent version the second best analysis. FTDNA was the worst, failing to pick up my 2% or so overall NA ancestry. Many of the admixture analysis tools on Gedmatch.com also do a good job, in my opinion.

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