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  • rs1426654 AA

    Wikipedia
    "SLC24A5 appears to have played a key role in the evolution of light skin in humans of European ancestry. The gene's function in pigmentation was discovered in zebrafish as a result of the positional cloning of the gene responsible for the "golden" variety of this common pet store fish. Evidence in the International HapMap Project database of genetic variation in human populations showed that Europeans, represented by the "CEU" population, had two primary alleles differing by only one nucleotide, changing the 111th amino acid from alanine to threonine, abbreviated "A111T".[1][8][9]

    The derived threonine allele (Ala111Thr; also known as A111T or Thr111) represented 98.7 to 100% of the alleles in European samples, while the ancestral or alanine form was found in 93 to 100% of samples of Sub-Saharan Africans, East Asians and Indigenous Americans. The variation is a SNP polymorphism rs1426654, which had been previously shown to be second among 3011 tabulated SNPs ranked as ancestry-informative markers. This single change in SLC24A5 explains between 25 and 38% of the difference in skin melanin index between peoples of West African vs. European Ancestry.

    Furthermore, the European mutation is associated with the largest region of diminished genetic variation in the CEU HapMap population, suggesting the possibility that the A111T mutation may be the subject of the single largest degree of selection in human populations of European ancestry.[1] It is theorised that selection for the derived allele is based on the need for sunlight to produce the essential nutrient vitamin D. In northerly latitudes, where there is less sun, greater requirement for body coverage due to colder climate, and frequently, diets poor in vitamin D, making lighter skin more suitable for survival.[10] Tests for this variation have obvious application to forensic science.

    It has been estimated that the threonine allele became predominant among Europeans 11,000 to 19,000 years ago."

  • #2
    Two SNPs that were posted at anthrogenica were rs2402130 A/G and rs1291382 C/C that are linked to ancient dna. These are the alleles for these SNPs that I have.There is another one
    rs11755393 A/G. Does anyone know anything about these?

    Comment


    • #3
      A11172R

      Originally posted by 1798 View Post
      Wikipedia
      "SLC24A5 appears to have played a key role in the evolution of light skin in humans of European ancestry. The gene's function in pigmentation was discovered in zebrafish as a result of the positional cloning of the gene responsible for the "golden" variety of this common pet store fish. Evidence in the International HapMap Project database of genetic variation in human populations showed that Europeans, represented by the "CEU" population, had two primary alleles differing by only one nucleotide, changing the 111th amino acid from alanine to threonine, abbreviated "A111T".[1][8][9]

      The derived threonine allele (Ala111Thr; also known as A111T or Thr111) represented 98.7 to 100% of the alleles in European samples, while the ancestral or alanine form was found in 93 to 100% of samples of Sub-Saharan Africans, East Asians and Indigenous Americans. The variation is a SNP polymorphism rs1426654, which had been previously shown to be second among 3011 tabulated SNPs ranked as ancestry-informative markers. This single change in SLC24A5 explains between 25 and 38% of the difference in skin melanin index between peoples of West African vs. European Ancestry.

      Furthermore, the European mutation is associated with the largest region of diminished genetic variation in the CEU HapMap population, suggesting the possibility that the A111T mutation may be the subject of the single largest degree of selection in human populations of European ancestry.[1] It is theorised that selection for the derived allele is based on the need for sunlight to produce the essential nutrient vitamin D. In northerly latitudes, where there is less sun, greater requirement for body coverage due to colder climate, and frequently, diets poor in vitamin D, making lighter skin more suitable for survival.[10] Tests for this variation have obvious application to forensic science.

      It has been estimated that the threonine allele became predominant among Europeans 11,000 to 19,000 years ago."
      I have a heteroplasmy A11172R, wonder if this mutation is related to the A111T that you have researched?

      Best regards, Douglas W. Fisher, kit#122883

      Paternal: U106+Z18+Z14+Z372+
      Maternal: V19a1

      Comment


      • #4
        Originally posted by DWFlineage View Post
        I have a heteroplasmy A11172R, wonder if this mutation is related to the A111T that you have researched?

        Best regards, Douglas W. Fisher, kit#122883

        Paternal: U106+Z18+Z14+Z372+
        Maternal: V19a1
        I don't know but rs1426654 AA and rs1291382 CC are the alleles I have and this is Motala12 rs1426654 AA and rs1291382 GG.

        Comment


        • #5
          Okay

          Originally posted by 1798 View Post
          I don't know but rs1426654 AA and rs1291382 CC are the alleles I have and this is Motala12 rs1426654 AA and rs1291382 GG.
          I will have to research further, because I think my heteroplasmy A11172R must be related to A111T, maybe skin pigmentation?

          Best regards, Douglas W. Fisher, kit#122883

          Paternal: U106+Z18+Z14+Z372+
          Maternal: V19a1

          Comment


          • #6
            Originally posted by DWFlineage View Post
            I will have to research further, because I think my heteroplasmy A11172R must be related to A111T, maybe skin pigmentation?

            Best regards, Douglas W. Fisher, kit#122883

            Paternal: U106+Z18+Z14+Z372+
            Maternal: V19a1
            The SNP rs1426654 AA was found in the Swedish Mesolithic remains. It is a SNP for pale skin gene found in Europeans.

            "The Motala12 forager, like the Stuttgart farmer, carries at least one copy of the derived rs1426654 pigmentation-lightening allele, and may thus have had lighter skin pigmentation than the Loschbour forager.*We typed the three ancient modern humans at 7 SNPs forming three short haplotypes associated with eye color in present-day worldwide populations (Table S8.3)26.*The observed reads in the Motala12 forager, like the Loschbour forager match the blue-eye-associated allele at all 7 SNPs. However, this includes two SNPs (rs7495174 and rs1291382) at only 1× coverage. Motala12 carries the blue-eye haplotype at the two BEH3 SNPs, which are in LD with the causal SNP, rs1291382, in present-day Europeans (but not outside of Europe)26.*However, the Stuttgart farmer is also homozygous for the two blue-associated BEH3 SNPs, despite being homozygous for the ancestral allele at rs1291382.*Stronger support for the inference of non-brown eyes for Motala12 is the observation of the derived allele at rs1129038, a site at almost complete LD with rs1291382 in present-day populations26."

            Also http://www.snpedia.com/index.php/Rs1426654

            Comment


            • #7
              Blue eyes

              Originally posted by 1798 View Post
              The SNP rs1426654 AA was found in the Swedish Mesolithic remains. It is a SNP for pale skin gene found in Europeans.

              "The Motala12 forager, like the Stuttgart farmer, carries at least one copy of the derived rs1426654 pigmentation-lightening allele, and may thus have had lighter skin pigmentation than the Loschbour forager.*We typed the three ancient modern humans at 7 SNPs forming three short haplotypes associated with eye color in present-day worldwide populations (Table S8.3)26.*The observed reads in the Motala12 forager, like the Loschbour forager match the blue-eye-associated allele at all 7 SNPs. However, this includes two SNPs (rs7495174 and rs1291382) at only 1× coverage. Motala12 carries the blue-eye haplotype at the two BEH3 SNPs, which are in LD with the causal SNP, rs1291382, in present-day Europeans (but not outside of Europe)26.*However, the Stuttgart farmer is also homozygous for the two blue-associated BEH3 SNPs, despite being homozygous for the ancestral allele at rs1291382.*Stronger support for the inference of non-brown eyes for Motala12 is the observation of the derived allele at rs1129038, a site at almost complete LD with rs1291382 in present-day populations26."

              Also http://www.snpedia.com/index.php/Rs1426654
              I have blue eyes. I am an adoptee, and have figured out my paternal side, still figuring out my maternal side. So far my closest FMS matches seem to have ancestors from England, Scotland & Australia. Thanks for sharing this.

              Best regards, Douglas

              Comment


              • #8
                Originally posted by DWFlineage View Post
                I have blue eyes. I am an adoptee, and have figured out my paternal side, still figuring out my maternal side. So far my closest FMS matches seem to have ancestors from England, Scotland & Australia. Thanks for sharing this.

                Best regards, Douglas
                This SNP is Mesolithic in western Europe and it wasn't brought here by the farmers. It is hard to believe that I have a link to a Swedish man who died in the Mesolitic. He was in the Y group I2b and it is found mostly in the north east of Ireland.
                Last edited by 1798; 15 June 2014, 05:58 AM.

                Comment


                • #9
                  Interesting

                  Originally posted by 1798 View Post
                  This SNP is Mesolithic in western Europe and it wasn't brought here by the farmers. It is hard to believe that I have a link to a Swedish man who died in the Mesolitic. He was in the Y group I2b and it is found mostly in the north east of Ireland.
                  I could have this link to this Swedish man, since I carry a lot of common snps to Swedish men. I also have some northern Ireland matches on my maternal side.

                  Best regards, Douglas

                  Comment


                  • #10
                    Originally Posted by*Lazaridis.et.al.2013
                    "The Motala12 forager, like the Stuttgart farmer, carries at least one copy of the derived rs1426654 pigmentation-lightening allele, and may thus have had lighter skin pigmentation than the Loschbour forager.*We typed the three ancient modern humans at 7 SNPs forming three short haplotypes associated with eye color in present-day worldwide populations (Table S8.3)26.*The observed reads in the Motala12 forager, like the Loschbour forager match the blue-eye-associated allele at all 7 SNPs. However, this includes two SNPs (rs7495174 and rs1291382) at only 1× coverage. Motala12 carries the blue-eye haplotype at the two BEH3 SNPs, which are in LD with the causal SNP, rs1291382, in present-day Europeans (but not outside of Europe)26.*However, the Stuttgart farmer is also homozygous for the two blue-associated BEH3 SNPs, despite being homozygous for the ancestral allele at rs1291382.*Stronger support for the inference of non-brown eyes for Motala12 is the observation of the derived allele at rs1129038, a site at almost complete LD with rs1291382 in present-day populations26.
                    [...]

                    Examining the SLC24A5 region, we find that the Stuttgart farmer is homozygous for the C11 haplotype found in 97% of all modern carriers of the derived rs1426654 pigmentation-lightening allele27. The A111T mutation is estimated to have arisen at ~22-28 kya28, with the selective sweep favoring its rise beginning ~19kya (under a dominant model) or ~11kya (under an additive model)29. The Loschbour forager does not carry the derived rs1426654 allele.*The Motala12 forager, like the Stuttgart farmer, is homozygous for the C11 haplotype. Although three of the SNPs defining C11 were genotyped at 1× coverage in the Motala12 sample, C11 is the only haplotype matching the possible patterns of variation.Motala12 according to TableS8.1 Page 88 was typed at rs1426654 being derived A/A with a coverage of 3x, he was also typed at rs28777 being derived A/A with a coverage of 4x, and as I showed above this SNP is strongly(OR 4.31) linked to pale skin in Europeans. Also both Motala12(3x coverage) and Loschbour are derived T/T at rs12203592, another pigmentation lightening SNP found in Europeans. Add to it the derived G/G found at rs16891982 for StoraFörvar11, and the weight of evidence points to the obvious fact that the European Hunter Gatherers carried the mutations for light skin, what is clear, is that such mutations only became fixed, or attained majority frequency in the last 8000 years, unlike the blue eye mutation which seemed to have been nearly fixed in Hunter Gatherers, and reduced in frequency with the introduction of farming by the migration of brown eye farmers from the Middle East."

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