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Clovis-Anzick-1 Amerindian ancient DNA have matches with living people.

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  • #46
    Originally posted by Armando View Post
    Nice. Thank you.

    I guess for starters Mal’ta boy MA-1 http://www.nature.com/nature/journal...ture12736.html and Mesolithic La Braña http://www.nature.com/nature/journal...ture12960.html

    I know those are available I just don't know where the files can be downloaded from.
    I had processed the Malta boy and it is available here. I also uploaded to GEDMatch as Kit# F999914. (The kit it tokenized but batch processing is pending). I also wrote a blog on what I found in MA-1, Mal’ta MA-1 Ancient DNA Analysis.

    The kit also has 4.5% of "South Indian" which is very interesting.

    Comment


    • #47
      Originally posted by felix View Post
      I had processed the Malta boy and it is available here. I also uploaded to GEDMatch as Kit# F999914. (The kit it tokenized but batch processing is pending). I also wrote a blog on what I found in MA-1, Mal’ta MA-1 Ancient DNA Analysis.

      The kit also has 4.5% of "South Indian" which is very interesting.
      If you are stating that Mal'ta boy was in the Y-Haplogroup is R, but also positive for R1b1a2a1a2c1b4 (or R-CTS3087) then it was contaminated.

      Comment


      • #48
        Originally posted by felix View Post
        I had processed the Malta boy and it is available here. I also uploaded to GEDMatch as Kit# F999914. (The kit it tokenized but batch processing is pending). I also wrote a blog on what I found in MA-1, Mal’ta MA-1 Ancient DNA Analysis.

        The kit also has 4.5% of "South Indian" which is very interesting.
        Thank you Felix.

        I knew Mal’ta didn't have East Asian and I thought I had read about the South Asian before but I can't find the post at the moment.

        Haplogroup P, the parent of R, is from southeast Asia according to Dr. Michael Hammer. http://dna-explained.com/2013/11/12/...ference-day-2/

        For R-CTS3087 to be valid he should also be positive for other SNP markers between R-CTS3087 and R-M269. Otherwise it is happenstance or contamination as 1798 stated.

        Comment


        • #49
          Originally posted by felix View Post
          The genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana is converted into familiar formats which I made available here.

          I also uploaded it to GEDMatch# F999912 (with FTDNA SNPs) and you might be surprised to hear this 11,000 year old infant has some 3rd cousins living today . Interestingly, most of the Y-haplogroup for the first 15 matches to kit F999912 is Q1a3a* and the haplogroup of the infact child is also Q-L54 (which is Q1a3a).

          GEDMatch Screenshot:


          Please leave your comments and possible questions for this mystery of 11,000 year old ancient DNA matching living people today either here or at my blog ...

          Link: http://www.fc.id.au/2014/09/clovis-a...ng-people.html
          This is what our matches look like, for me, close to this, but for my mom, just higher totals but the largest segment is about the same as what you see in this image.

          https://www.dropbox.com/s/2vpvmrruz4...60914.png?dl=0

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          • #50
            Originally posted by Armando View Post
            Thank you Felix.

            I knew Mal’ta didn't have East Asian and I thought I had read about the South Asian before but I can't find the post at the moment.

            Haplogroup P, the parent of R, is from southeast Asia according to Dr. Michael Hammer. http://dna-explained.com/2013/11/12/...ference-day-2/

            For R-CTS3087 to be valid he should also be positive for other SNP markers between R-CTS3087 and R-M269. Otherwise it is happenstance or contamination as 1798 stated.
            I rushed through this last post and I need to correct what I wrote. If Mal’ta boy does not have other markers between R-CTS3087 and R-M269 then it is coincidence that he has the R-CTS3087 SNP marker. If Mal’ta boy does have other markers between R-CTS3087 and R-M269 then it is from contamination. Contamination isn't very likely based on the Admixture (heritage) calculators at Gedmatch.

            Comment


            • #51
              Felix,

              Your thought logs continually mention doubt about the age of multiple ancient specimens and as to whether or not they are contaminated. The specimens have been radiocarbon dated. The dates shouldn't be doubted. You are putting more faith in a computer program that is allowing errors than you are into a time tested science based on nature. You are also showing that the specimens are different than living humans based on the MLDP K23b Calculator but yet you think that they are contaminated. I disagree with your conclusions.

              Roberta Estes posted an interesting piece of information at http://dna-explained.com/2014/10/04/...or-comparison/

              In it a new program called Haploscore that will be presented soon is mentioned and they state "Exploiting known familial relationships, we identified a false positive rate over 67% for 2-4 centiMorgan (cM) segments, in sharp contrast with accuracies reported in simulated data at these sizes. We show that nearly all false positives arise due to allowing switch errors between haplotypes when detecting IBD, a necessity for retrieving long (> 6 cM) segments in the presence of imperfect phasing."

              It looks like the programs that are comparing individuals just aren't good enough right now and you have put too much faith in them.

              Comment


              • #52
                Originally posted by Armando View Post
                Felix,

                Your thought logs continually mention doubt about the age of multiple ancient specimens and as to whether or not they are contaminated. The specimens have been radiocarbon dated. The dates shouldn't be doubted. You are putting more faith in a computer program that is allowing errors than you are into a time tested science based on nature. You are also showing that the specimens are different than living humans based on the MLDP K23b Calculator but yet you think that they are contaminated. I disagree with your conclusions.

                Roberta Estes posted an interesting piece of information at http://dna-explained.com/2014/10/04/...or-comparison/

                In it a new program called Haploscore that will be presented soon is mentioned and they state "Exploiting known familial relationships, we identified a false positive rate over 67% for 2-4 centiMorgan (cM) segments, in sharp contrast with accuracies reported in simulated data at these sizes. We show that nearly all false positives arise due to allowing switch errors between haplotypes when detecting IBD, a necessity for retrieving long (> 6 cM) segments in the presence of imperfect phasing."

                It looks like the programs that are comparing individuals just aren't good enough right now and you have put too much faith in them.
                I just take the raw data files which the authors provided with their research paper/journal and I convert them to FTDNA format and upload to GEDMatch. I am not sure what you are referring to as faith in this process

                You can't call "faith in computer program that is allowing errors" when Clovis Anzick DNA Match: SNP by SNP Analysis shows no errors in the segment. This proves, there were no errors in SNPs (one tested by FTDNA and the other tested by another lab) which also means no mutations had occurred on the matching strand.

                The haploscore is for detecting IBD segments refers to segments that are not affected by cousin marriages or endogamy. But here, we are good with compound segments or IBS which are not noise. A 10 cM compound segment which is not IBD is for sure related within 500-1000 years and not 12500 years.

                It is not me who is casting doubt about ages of these ancient specimens but their matches in genetic genealogy with living people do cast doubt, which is a problem for authors who published the papers to deal with and explain how an ancient DNA as old as 12500 years can match living people like recent cousins in genealogical timeframe.

                Comment


                • #53
                  Originally posted by Armando View Post
                  [----] Roberta Estes posted an interesting piece of information at http://dna-explained.com/2014/10/04/...or-comparison/ [----]
                  Let me quote Roberta Estes:
                  The higher no-call rate in the autosomal files can contribute as well, but wouldn’t account for all matches.
                  I think she did not closely look at the numbers involved. With 20% of no-calls it is surprising that only so few matches appear.

                  Comment


                  • #54
                    Originally posted by felix View Post
                    I just take the raw data files which the authors provided with their research paper/journal and I convert them to FTDNA format and upload to GEDMatch. I am not sure what you are referring to as faith in this process

                    You can't call "faith in computer program that is allowing errors" when Clovis Anzick DNA Match: SNP by SNP Analysis shows no errors in the segment. This proves, there were no errors in SNPs (one tested by FTDNA and the other tested by another lab) which also means no mutations had occurred on the matching strand.

                    The haploscore is for detecting IBD segments refers to segments that are not affected by cousin marriages or endogamy. But here, we are good with compound segments or IBS which are not noise. A 10 cM compound segment which is not IBD is for sure related within 500-1000 years and not 12500 years.

                    It is not me who is casting doubt about ages of these ancient specimens but their matches in genetic genealogy with living people do cast doubt, which is a problem for authors who published the papers to deal with and explain how an ancient DNA as old as 12500 years can match living people like recent cousins in genealogical timeframe.
                    Why do you think that it is not possible? Some men at ysearch have the YDNA markers that were found in a cave in Lichtestein. Does that mean that they are related recently?

                    Comment


                    • #55
                      Originally posted by felix View Post
                      I just take the raw data files which the authors provided with their research paper/journal and I convert them to FTDNA format and upload to GEDMatch. I am not sure what you are referring to as faith in this process

                      You can't call "faith in computer program that is allowing errors" when Clovis Anzick DNA Match: SNP by SNP Analysis shows no errors in the segment. This proves, there were no errors in SNPs (one tested by FTDNA and the other tested by another lab) which also means no mutations had occurred on the matching strand.

                      The haploscore is for detecting IBD segments refers to segments that are not affected by cousin marriages or endogamy. But here, we are good with compound segments or IBS which are not noise. A 10 cM compound segment which is not IBD is for sure related within 500-1000 years and not 12500 years.

                      It is not me who is casting doubt about ages of these ancient specimens but their matches in genetic genealogy with living people do cast doubt, which is a problem for authors who published the papers to deal with and explain how an ancient DNA as old as 12500 years can match living people like recent cousins in genealogical timeframe.
                      If you are constantly call into question the age of the specimens since there are compound segments matching that infers that there was a problem with the radiocarbon dating. That means you are putting more faith into a process that has never been put through the testing, that you are putting it through now, and you are putting very little faith into radiocarbon dating that has been around for decades and has been put through tests by multitudes of scientists. Since the radiocarbon dating is very unlikely to be wrong with multiple specimens from 4 different publications there is definitely something wrong with the process or the belief that a 10 cM compound segment has to be from someone related in the past 500-1000 years. This speaks volumes in your trust of professional scientists when it comes to the collection of the specimens and the radiocarbon dating.

                      Dr. Ann Turner has not voiced a belief that there could be something wrong with the radiocarbon dating or the collection and DNA testing of the specimens.

                      You have not addressed the conundrum of multiple specimens having been tested by multiple labs and the MDLP K23b Admixture analysis of the specimens being significantly different from all of the other ancient specimens that aren't part of the same culture or time period and also different from living humans with the exception of Clovis and living Native Americans. You need to do a MDLP K23b Admixture analysis of the matches of the ancient specimens to see what I mean about being different from living people. The La Braña, Motala12, and Loschbour Hunter-Gatherers do not have the MDLP K23b Caucasian that F999916 LBK Stuttgart Early European Farmer has. Nor do Mal'ta and Clovis. F999916 LBK Stuttgart Early European Farmer does not have Ancient_Altaic and South Central Asian that living Europeans have. Living Europeans have a mix of Ancestral_Altaic, South_Central_Asian, Caucasian, European_Early_Farmers, European_Hunters_Gatherers. If the specimens were more recent or had been contaminated enough to show a close match in the Gedmatch 'One-to-many' matches and 'One-to-one' compare then they would also show a significant amount of admixture found in living Europeans. If there was contamination it can't be one or the other. It has to be both the admixture showing a mix from a modern person and close matches. Since the ancient specimens do not have both modern admixture and close matches and the radiocarbon dating shows the specimens to be ancient and the specimens are significantly different from each other, except the Hunter-Gatherers, then there is obviously a problem with the assumption that "A 10 cM compound segment which is not IBD is for sure related within 500-1000 years and not 12500 years." otherwise we have to question the MDLP K23b Admixture analysis and the radiocarbon dating.

                      So that others can see a comprehensive spreadsheet of MDLP K23b Admixture analysis I made one at https://www.dropbox.com/s/3bmjv02e78...s%20.xlsx?dl=0

                      Plus a document of screenshots of the pie graphs. https://www.dropbox.com/s/zgti0c2grl...mens.docx?dl=0

                      Comment


                      • #56
                        Originally posted by dna View Post
                        Let me quote Roberta Estes:I think she did not closely look at the numbers involved. With 20% of no-calls it is surprising that only so few matches appear.
                        A new post by Felix shows that the no-calls aren't a factor.
                        http://www.fc.id.au/2014/10/clovis-a...np-by-snp.html

                        The Clovis Anzick individual is not the only one that matches living people. All of these specimens can't be due to erroneous radiocarbon dating or contamination. The La Braña does have matches in 'One-to-one' compare when compared with Latin Americans with significant Spanish ancestry.

                        Loschbour ancient DNA matches living people

                        Kit F999918

                        I am not sure what to make of these matches who match with a 8000 years old ancient DNA. Could the sample be contaminated? Is the sample really ancient? I don't know for sure.

                        http://www.fc.id.au/2014/10/loschbou...es-living.html

                        Linearbandkeramik (LBK) ancient DNA matches with living people!

                        Kit F999916
                        Ancient DNA are not supposed to match with living people as recent cousins. Just like Clovis-Anzick-1 ancient DNA, there are matches. I am not sure how to interpret these matches, but my rational tells me to incline towards the sample not being ancient.

                        http://www.fc.id.au/2014/10/linearba...cient-dna.html

                        Mal'ta MA-1 ancient DNA have matches with a few living people on X-Chromosome!

                        Kit F999914

                        I wasn't expecting any surprise matches but I was wrong again. Unlike the Clovis-Anzick-1 sample having matches on autosomal DNA, the Mal'ta MA-1 sample is having matches on X chromosome. My immediate thought was wow! These matches, although small deserves further investigation.

                        http://www.fc.id.au/2014/09/malta-ma...e-matches.html

                        Analyzing La Braña-Arintero Ancient DNA

                        Kit F999915

                        I did one-to-one with my DNA and nothing in common. May be you have something in common. Let me know what you think.

                        http://www.fc.id.au/2014/09/analyzin...cient-dna.html

                        Clovis-Anzick-1 ancient DNA have matches with living people!
                        Kit F999913

                        I uploaded a new kit filtered with SNPs used by most DNA companies: Uploaded New GEDMatch Kit for Clovis-Anzick-1. Please use GEDMatch kit# F999913 as I had deleted F999912 to avoid redundant kits. In spite of this change, there is not much difference in matches. After some conversation with GEDMatch, there seems to be no-calls and SNPs found in kit not tested by DNA companies and vice-versa. Hence, I am trying to process from BAM files provided by the authors to see if I can get more SNPs to get to the bottom of this mystery.

                        http://www.fc.id.au/2014/09/clovis-a...ng-people.html

                        Comment


                        • #57
                          New Clovis Anzick-1 kit in GEDMatch: F999919

                          Originally posted by Armando View Post
                          A new post by Felix shows that the no-calls aren't a factor.
                          http://www.fc.id.au/2014/10/clovis-a...np-by-snp.html
                          Thanks Armando. The new GEDMatch kit# for Clovis Anzick-1 is F999919 which has significantly more SNPs common with DNA testing companies and no-calls will not be an issue. I am also not removing the old kit# F999913 so that comparison can be made on how the segment matches appear or disappear. I did some basic comparison of results between the old and the new kit and mentioned in the blog post.

                          Post: New Clovis Anzick-1 kit in GEDMatch: F999919

                          One-to-many batch processing is not yet completed in GEDMatch and may take an another day, but 1-to-1 comparison can be performed. It is interesting to see how the matches are going to appear.. Fingers crossed.
                          Last edited by felix; 9th October 2014, 02:43 AM.

                          Comment


                          • #58
                            Felix, I saw your post about The true IBS noise range.
                            http://www.fc.id.au/2014/10/the-true...ise-range.html

                            Will you upload that file as a research file to see if anyone matches at a higher level?

                            You should also create a random file of Native American SNPs and upload it as a research sample to see how many matches it gets and at what level.

                            Comment


                            • #59
                              Originally posted by Armando View Post
                              Felix, I saw your post about The true IBS noise range.
                              http://www.fc.id.au/2014/10/the-true...ise-range.html

                              Will you upload that file as a research file to see if anyone matches at a higher level?

                              You should also create a random file of Native American SNPs and upload it as a research sample to see how many matches it gets and at what level.
                              No, I don't have any intentions to put a random file on GEDMatch to overload their servers. I just wanted to verify if IBS noise can occur above 2 cM / 200 SNPs and it seems it doesn't occur.

                              This is basically a IBS-noise vs IBS-compound segments. While it seems 150 consecutive SNPs cannot just occur randomly to match someone, I am sill not sure how far back such a compound segment around 200 SNPs/ 2 cM would go back in time. Can it go to the very founder population? I don't know.

                              I don't have Native American specific SNPs data but I remember John mentioning somewhere that people from same geographical area mostly match at 3 cM with each other. So, I would assume if we restrict to some group of people, the random file should match most from that geographical area around 3 cM.

                              Comment


                              • #60
                                Originally posted by Armando View Post
                                Felix, I saw your post about The true IBS noise range.
                                http://www.fc.id.au/2014/10/the-true...ise-range.html

                                Will you upload that file as a research file to see if anyone matches at a higher level?
                                As a second thought, why not? May be this helps to understand IBS noise and compound segments better. I had uploaded a kit with FTDNA SNPs having random genotypes found in populations using frequencies from OpenSNP as kit# F999901

                                Link: IBS Noise Kit at GEDMatch

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