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Thread: New DNA Papers - General Discussion Thread

  1. #2181
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    Quote Originally Posted by parasar View Post
    Y
    n=166
    H1a-M82 9
    J-M304 1
    J2a-M172 19
    R1a-M17 63
    R2a-M124 74

    Y-R 82.53%
    FTDNA: IN41220
    YFull: YF62636

    FATHER:

    Y-DNA (ISOGG 2019): R2a2b1b2a1a1-Y1383* (Y154917-)
    Y-DNA path: M207 > M479 > M124 > P267 > Y12100 > Y8763 > Y8766 > V3714 > SK2142 > Y1377 > Y1379 > Z29271 > Y1383 x Y154917


    mtDNA: M5a1a1-G9064A


    MATERNAL UNCLE:

    Y-DNA (ISOGG 2019): R1b1a1b1b3a-Z2109
    Y-DNA path: M207 > M173 > M343 > L754 > L388 > P297 > M269 > L23 > Z2103 > Z2106 > Z2109

    mtDNA: U7a3a12-C15433T

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  3. #2182
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    Poland England Ireland Munster

    A Genetic Difference between Farmers and Hunter-Gatherers

    Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism
    CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retained the paralogous CLTC gene encoding CHC17 clathrin, which mediates endocytosis. For vertebrates retaining CLTCL1, strong evidence for purifying selection supports CHC22 functionality. All human populations maintained two high frequency CLTCL1 allelic variants, encoding either methionine or valine at position 1316. Functional studies indicated that CHC22-V1316, which is more frequent in farming populations than in hunter-gatherers, has different cellular dynamics than M1316-CHC22 and is less effective at controlling GLUT4 membrane traffic, attenuating its insulin-regulated response. These analyses suggest that ancestral human dietary change influenced selection of allotypes that affect CHC22's role in metabolism and have potential to differentially influence the human insulin response.
    ...
    The derived allele arose in ancient humans and is more frequent in farming populations when compared to hunter-gatherers.
    ...
    We found that the V1316 amino acid is present in Pleistocene hunter-gatherers and Neolithic farmers but not in other Neanderthals or Holocene hunter-gatherers in this limited data set
    ...
    Statistical analysis comparing early farmer and hunter-gatherer populations shows an apparent increase of the V1316 variant, suggesting a correlation with regular consumption of digestible carbohydrate. Notably, the SNP distinguishing these alleles is human-specific and likely arose 550-50 KYA (i.e. post-Neanderthal, pre-Neolithic).
    ...
    One plausible explanation of the high genetic diversity and frequency of the two major alleles of CLTCL1 that occur in all modern human populations is balancing selection. Such a distribution of allele frequency was confirmed using a different data set of more than 50 sampled human populations (Figure 4-figure supplement 2). In several populations, we also observed an apparent excess of heterozygosity at SNP rs1061325, compatible with heterozygote advantage (overdominance) for the two encoded allotypes differing at residue 1316. Specifically, all European populations show a ratio of observed versus expected (assuming Hardy-Weinberg equilibrium) heterozygosity greater than 1, with the highest value of 1.24 (chi-squared test nominal p-value 0.047) for Iberic Spanish (IBS) . Selective pressures that might be acting on CLTCL1, irrespective of population distribution, could be changes in human diet, a number of which have been inferred over the last 2.6 million years (Hardy et al., 2015). Perhaps the best known of these dietary transitions are the introduction of cooking ~450 KYA, development of farming ~12,500 YA, and more recently industrialized food processing, which gradually and then dramatically increased carbohydrate availability and consumption by humans.

    rs1061325 was the main SNP discussed in the paper. It was present in both my 23andMe and Ancestry DNA tests. I was mixed (CT) for rs1061325. If I interpreted the paper correctly C should be the allele associated with farmers and T is the allele associated with hunter-gatherers. I tried to figure that out by looking at dbSNP https://www.ncbi.nlm.nih.gov/snp/rs1061325. It would would be great if anyone would be kind enough to confirm that. Anyone else willing to share their test results for rs1061325?
    Last edited by pmokeefe; 05-16-2019 at 07:49 AM.
    YFull: YF14620 (Dante Labs 2018)

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  5. #2183
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    23andMe v3 result for an East Asian: rs1061325 CC
    Last edited by cpan0256; Yesterday at 03:07 PM. Reason: add the SNP number to my reply

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  7. #2184
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    Quote Originally Posted by pmokeefe View Post
    Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism
    CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retained the paralogous CLTC gene encoding CHC17 clathrin, which mediates endocytosis. For vertebrates retaining CLTCL1, strong evidence for purifying selection supports CHC22 functionality. All human populations maintained two high frequency CLTCL1 allelic variants, encoding either methionine or valine at position 1316. Functional studies indicated that CHC22-V1316, which is more frequent in farming populations than in hunter-gatherers, has different cellular dynamics than M1316-CHC22 and is less effective at controlling GLUT4 membrane traffic, attenuating its insulin-regulated response. These analyses suggest that ancestral human dietary change influenced selection of allotypes that affect CHC22's role in metabolism and have potential to differentially influence the human insulin response.
    ...
    The derived allele arose in ancient humans and is more frequent in farming populations when compared to hunter-gatherers.
    ...
    We found that the V1316 amino acid is present in Pleistocene hunter-gatherers and Neolithic farmers but not in other Neanderthals or Holocene hunter-gatherers in this limited data set
    ...
    Statistical analysis comparing early farmer and hunter-gatherer populations shows an apparent increase of the V1316 variant, suggesting a correlation with regular consumption of digestible carbohydrate. Notably, the SNP distinguishing these alleles is human-specific and likely arose 550-50 KYA (i.e. post-Neanderthal, pre-Neolithic).
    ...
    One plausible explanation of the high genetic diversity and frequency of the two major alleles of CLTCL1 that occur in all modern human populations is balancing selection. Such a distribution of allele frequency was confirmed using a different data set of more than 50 sampled human populations (Figure 4-figure supplement 2). In several populations, we also observed an apparent excess of heterozygosity at SNP rs1061325, compatible with heterozygote advantage (overdominance) for the two encoded allotypes differing at residue 1316. Specifically, all European populations show a ratio of observed versus expected (assuming Hardy-Weinberg equilibrium) heterozygosity greater than 1, with the highest value of 1.24 (chi-squared test nominal p-value 0.047) for Iberic Spanish (IBS) . Selective pressures that might be acting on CLTCL1, irrespective of population distribution, could be changes in human diet, a number of which have been inferred over the last 2.6 million years (Hardy et al., 2015). Perhaps the best known of these dietary transitions are the introduction of cooking ~450 KYA, development of farming ~12,500 YA, and more recently industrialized food processing, which gradually and then dramatically increased carbohydrate availability and consumption by humans.

    rs1061325 was the main SNP discussed in the paper. It was present in both my 23andMe and Ancestry DNA tests. I was mixed (CT) for rs1061325. If I interpreted the paper correctly C should be the allele associated with farmers and T is the allele associated with hunter-gatherers. I tried to figure that out by looking at dbSNP https://www.ncbi.nlm.nih.gov/snp/rs1061325. It would would be great if anyone would be kind enough to confirm that. Anyone else willing to share their test results for rs1061325?
    Interestingly I have CC and my grandmother TT, and in most calculators my gm have a slightly greater proportion of Neolithic farmer

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