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

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  • #61
    Originally posted by felix View Post
    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
    Now you understand the premise of my request. Thank you so much for uploading the file.

    If we can get random files whose admixture results look more like those of living people I think we will be able to get an even better understanding. That was the reason of trying to get a random file of only Native American SNPs.

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    • #62
      Originally posted by Armando View Post
      If we can get random files whose admixture results look more like those of living people I think we will be able to get an even better understanding.
      Hell no! Those don't look like living people. No matter how many random files you create, the admixture will always be same/similar for a particular calculator because of the properties of entropy. What you see as admixture results is the percentage of SNPs for each population used in order to create that calculator itself and nothing to do with the random file itself. So, basically you can find the percentage of SNPs assigned to each population used in calculating admixture results using these random files.

      I just updated the post, IBS Noise Kit at GEDMatch to be much clearer.
      Last edited by felix; 13th October 2014, 12:14 AM.

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      • #63
        Originally posted by felix View Post
        Hell no! Those don't look like living people. No matter how many random files you create, the admixture will always be same/similar for a particular calculator because of the properties of entropy. What you see as admixture results is the percentage of SNPs for each population used in order to create that calculator itself and nothing to do with the random file itself. So, basically you can find the percentage of SNPs assigned to each population used in calculating admixture results using these random files.

        I just updated the post, IBS Noise Kit at GEDMatch to be much clearer.
        You completely misunderstood my statement. I never said that it looks like a real person and I never inferred that. Please reread my statement.

        Certain SNPs should be able to be selected from certain populations then from those SNPs a artificial person should be able to be created. That is what my statement "If we can get random files whose admixture results look more like those of living people" meant.

        If you don't want to do that it's fine. I just wanted you to understand what my statement did and didn't mean.

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        • #64
          Originally posted by Armando View Post
          You completely misunderstood my statement. I never said that it looks like a real person and I never inferred that. Please reread my statement.

          Certain SNPs should be able to be selected from certain populations then from those SNPs a artificial person should be able to be created. That is what my statement "If we can get random files whose admixture results look more like those of living people" meant.

          If you don't want to do that it's fine. I just wanted you to understand what my statement did and didn't mean.
          Sure, no problem. Btw, the batch processing for random genotype GEDMatch kit #F999901 is complete and there are no matches at any level.

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          • #65
            Felix
            Can you explain this to me please?
            1.93 cM matching SNPs 4,700
            14.6 cM matching SNPs 2,791
            These are on chromosome 4.
            Why is the larger cM with less SNPs more significant than the smaller cM with the larger amount of SNPs?

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            • #66
              Originally posted by 1798 View Post
              Felix
              Can you explain this to me please?
              1.93 cM matching SNPs 4,700
              14.6 cM matching SNPs 2,791
              These are on chromosome 4.
              Why is the larger cM with less SNPs more significant than the smaller cM with the larger amount of SNPs?
              1 cM can have a million base-pairs to more than 5 million base-pairs depending on where it occurs on the chromosome because it is a probablistic measure. So, you have varying SNP counts. SNP count also varies depending on number of SNPs each person match or don't match and number of no calls allowed as matching. Consecutive matching SNPs which is referred as SNP count is used to identify if single stand segment match on both DNA are same. The reason why it is used as a measure is because consecutive matching SNPs don't occur accidentally to match beyond a limit.

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              • #67
                Originally posted by felix View Post
                1 cM can have a million base-pairs to more than 5 million base-pairs depending on where it occurs on the chromosome because it is a probablistic measure. So, you have varying SNP counts. SNP count also varies depending on number of SNPs each person match or don't match and number of no calls allowed as matching. Consecutive matching SNPs which is referred as SNP count is used to identify if single stand segment match on both DNA are same. The reason why it is used as a measure is because consecutive matching SNPs don't occur accidentally to match beyond a limit.
                Thanks felix.

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                • #68
                  Wow...this is all very interesting....I hope this conversation continues. I am very interested in this topic.

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                  • #69
                    I noticed the Gedmatch now has a page for Archaic DNA matches. This utility compares your kit with various ancient and archaic samples uploaded to GEDmatch by Felix Jeyareuben Chandrakumar.

                    http://v2.gedmatch.com/archaic1.php

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                    • #70
                      I compared the raw base file for kit F999902 to my FTDNA raw data:

                      OldGuy 999902 vs Me 255515

                      SNPs 942293 vs. 708092

                      heterozygosity 1.5% vs 30.6%

                      no-calls ZERO vs 4017

                      I learned that:
                      "Heterozygosity is of major interest to students of genetic variation in natural populations. It is often one of the first "parameters" that one presents in a data set. It can tell us a great deal about the structure and even history of a population. Just for example, very low heterozygosities for allozyme loci in cheetahs and black-footed ferrets indicate severe effects of small population sizes (population bottlenecks or metapopulation dynamics that severely reduced the level of genetic variation relative to that expected or found in comparable mammals). High heterozygosity means lots of genetic variability. Low heterozygosity means little genetic variability. Often, we will compare the observed level of heterozygosity to what we expect under Hardy-Weinberg equilibrium (HWE). If the observed heterozygosity is lower than expected, we seek to attribute the discrepancy to forces such as inbreeding. If heterozygosity is higher than expected, we might suspect an isolate-breaking effect (the mixing of two previously isolated populations). "

                      Another way of looking at it, if 98.5% of your base pairs are homozygous, crossover [in meiosis] doesn't seem to be very productive... You won't see but a small fraction of them...

                      Doesn't it make sense that a lot of the diversity that differentiates us today didn't yet exist back then?

                      Haven't we chosen the SNPs we use today based on current known variation being in a band [not too large yet not too small MAFs]? Who says it was always that way for those base-pairs?

                      Seems like there is more likely more to learn here; our whole concept of using SNPs and cMs is challenged by the homozygosity of this data [if correct and true]

                      Just my thoughts.

                      Bob

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                      • #71
                        I compared the raw base file for kit F999913 to my FTDNA raw data:

                        OldGuy 999913 vs Me 255515

                        SNPs 441662 vs. 708092

                        heterozygosity 25% vs 30.6%

                        no-calls ZERO vs 4017

                        It looks like only around 40-50% of the SNPs even line up...

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                        • #72
                          Originally posted by hansonrf View Post
                          I compared the raw base file for kit F999913 to my FTDNA raw data:

                          OldGuy 999913 vs Me 255515

                          SNPs 441662 vs. 708092

                          heterozygosity 25% vs 30.6%

                          no-calls ZERO vs 4017

                          It looks like only around 40-50% of the SNPs even line up...
                          How can you get an accurate result when they don't line up? It would be like comparing apples and oranges.

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                          • #73
                            Originally posted by 1798 View Post
                            How can you get an accurate result when they don't line up? It would be like comparing apples and oranges.
                            The GEDmatch algorithm only compares SNPs that exist in both kits being compared. You are correct - It DOES affect accuracy. When only 40% of the SNPs line up, it will be less accurate than when 100% of the SNPs are present. Of course, using 1cM thresholds is also less accurate than using 10cM thresholds.

                            John

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                            • #74
                              none of the kit numbers work

                              I get this error when I try to use any of the kit numbers listed
                              (1486) ERROR: Kit F999913 not found.

                              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

                              Comment


                              • #75
                                Originally posted by 435237 View Post
                                I get this error when I try to use any of the kit numbers listed
                                (1486) ERROR: Kit F999913 not found.
                                Felix added 23andme and AncestryDNA SNPs to the Clovis Anzick-1 file then re-uploaded it with a new kit number of F999919.

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