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Palaeo-Eskimo 2000 BC DNA

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  • Palaeo-Eskimo 2000 BC DNA

    The Saqqaq Genome Project generated 20x sequence coverage over the genome of an individual from the Extinct Palaeo-Eskimo Saqqaq culture. The project was a large collaboration between many Centres across the world, coordinated by Professor Eske Willerslev from the Centre for GeoGenetics at University of Copenhagen, Denmark. Full details of authors and the cooperation can be obtained from the Feb 2010 article referenced below.

    I converted the available raw data of the extinct Palaeo-Eskimo Genome to a raw data download file if FTDNA (or) 23andMe did the test. So, basically, I am just extracting the SNPs from the full Genome and constructing the autosomal raw data file. The source files are taken from Data for the Saqqaq genome project.

    Download Link: http://www.y-str.org/tools/palaeo-eskimo-2000-bc-dna/

    GEDMatch:
    I already uploaded it to GEDMatch #F999905. The uploaded kit is tokenized for one to one comparision, but have not completed batch processing for one to many.

    Reference:
    Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo
    Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E
    Nature 463, 757-762 (11 February 2010)

    (Note: Feel free to correct me if I had done any mistakes in parsing the data)

  • #2
    Population Admixture for Palaeo-Eskimo 2000 BC in GEDMatch







    Attached Files

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    • #3
      Eye Color for Palaeo-Eskimo 2000 BC

      Attached Files

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      • #4
        Originally posted by felix View Post






        Any explanation for the African component

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        • #5
          Thank you for these posts. I am always interested in anything related to Arctic peoples so I'll be following this thread closely. I too noticed the African component.

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          • #6
            Originally posted by josh w. View Post
            Any explanation for the African component
            Originally posted by mixedkid View Post
            Thank you for these posts. I am always interested in anything related to Arctic peoples so I'll be following this thread closely. I too noticed the African component.
            The authors of the paper concluded no European component in the Saqqaq genome and seems to have focused their research on Asia and Americas but ignored Africa.

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            • #7
              How is the admixture composition of present day eskimos?

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              • #8
                Felix, that's mind-boggling. Although I do have to wonder about the predicted eye-color algorithms-- they haven't been too accurate for the mostly-European-ancestors kits I administer.

                ps. Found your blog, I think. As stated before, you do fascinating work!

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                • #9
                  Originally posted by MerryB View Post
                  Felix, that's mind-boggling. Although I do have to wonder about the predicted eye-color algorithms-- they haven't been too accurate for the mostly-European-ancestors kits I administer.

                  ps. Found your blog, I think. As stated before, you do fascinating work!
                  Yes though I love Gedmatch, their eye color predictions are way off for my kit and my Mom's. I tested her at 23andme, and myself here. I get a weird yellow color, my eyes are so dark almost black. And my Mom's kit gets a green/yellow hue, and her eyes are brown.

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                  • #10
                    The eye colour is based on few FTDNA SNPs. I have most of the SNPs in full genome in the download link but uploaded only FTDNA SNPs in GEDMatch for size reasons.

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                    • #11
                      Originally posted by felix View Post
                      The eye colour is based on few FTDNA SNPs. I have most of the SNPs in full genome in the download link but uploaded only FTDNA SNPs in GEDMatch for size reasons.
                      I had heard that the 23andme data was more accurate on Gedmatch for the eye color prediction. However for my Mom it was clearly wrong. 23andme had accurately predicated that my Mom's eye color is brown.

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                      • #12
                        GEDmatch eye color predictions

                        23andMe V3 DNA files are more accurate with the GEDmatch eye color predictor, because they contain more of the SNPs used in the prediction algorithm. FTDNA and Ancestry.Com DNA results produce less accurate results for the GEDmatch prediction algorithm.

                        Brown eyes have been surprisingly hard for me to predict accurately. The reason is that there are many SNPs that can produce brown eyes. I have not discovered all of them, and many more simply aren't tested by either company. When the prediction algorithm does not detect these "brown" SNPs, it often falls back on a lighter color that would in reality be hidden by the darker brown.

                        While it is intriguing to imagine what Neanderthal, Denisovian or even Palaeo-Eskimo eyes might have looked like, their eye color would have almost certainly been determined by a different set of SNPs than modern humans.
                        Last edited by JOlson; 28th December 2013, 01:28 AM.

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                        • #13
                          Originally posted by JOlson View Post
                          While it is intriguing to imagine what Neanderthal, Denisovian or even Palaeo-Eskimo eyes might have looked like, their eye color would have almost certainly been determined by a different set of SNPs than modern humans.
                          John, I think this Eskimo is a modern human.

                          Also the parents are cousins feature (RoH) is not working in GEDMatch. Does the kit must be batch processed to use that feature?

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                          • #14
                            Originally posted by felix View Post
                            John, I think this Eskimo is a modern human.
                            Yeah, I hesitated to add that to the list. I really have no idea what color eyes Eskimos have. Still only 6 SNPs were included in the evaluation, so I would take that prediction with a grain of salt. Maybe a V3 version of the file would produce different results?
                            Also the parents are cousins feature (RoH) is not working in GEDMatch. Does the kit must be batch processed to use that feature?
                            It doesn't require batch processing. More likely, after the recent database changeover it is still pointed at the old database and doesn't see recent uploads. There's still a couple of other utilities that have the same problem. It just takes time...

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                            • #15
                              Originally posted by josh w. View Post
                              Any explanation for the African component
                              I don't think that these Admix calculator's are made for this kind of data. Probably neither of them is. In ten or even five years the situation might be improved.

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