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Thread: The evolution of skin pigmentation-associated variation in West Eurasia.

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    Quote Originally Posted by matp View Post
    Yes C would represent the derived allele on the snipper, also rs13289 the derived allele you input C rather than G
    What I found more puzzling than the prediction of the Cheddar man being "dark dot black" was the phenotype analysis for the BA Aegeans. HIrisPLex predicted 1 BA Aegean individual to be in the "dark" category while the other two were predicted to be most likely "dark to black". These 3 individuals are AA on rs1426654 (SLC24A5) but CC and CG (overwhelmingly GG in contemporary Europeans) on rsrs16891982 (SLC45A2). With that being said, the two Aegeans that scored "dark to black" carried OCA2 which also contributes to pigmentation. How realistic do you find the phenotype analysis in terms of BA Greeks having dark to black skin tone?

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    Quote Originally Posted by real expert View Post
    What I found more puzzling than the prediction of the Cheddar man being "dark dot black" was the phenotype analysis for the BA Aegeans. HIrisPLex predicted 1 BA Aegean individual to be in the "dark" category while the other two were predicted to be most likely "dark to black". These 3 individuals are AA on rs1426654 (SLC24A5) but CC and CG (overwhelmingly GG in contemporary Europeans) on rsrs16891982 (SLC45A2). With that being said, the two Aegeans that scored "dark to black" carried OCA2 which also contributes to pigmentation. How realistic do you find the phenotype analysis in terms of BA Greeks having dark to black skin tone?
    Wow that is some interesting information. The AA alleles SNP rs1426654 has been shown to explain 25% to 38% of the variation in skin tone between Europeans and West Africans, etc. (I have the paper in my files somewhere). The rs16891982 SNP on SLC45A2 does impact skin tone, but I don't think as much as SLC24A5.

    The US Department of Justice (USDOJ) published a study on genetics and skin tone which showed that 3 single polymorphisms on SLC24A5, SLC45A2 and ASIP in a Multiple Regression analysis explain 45.6% of skin tone variation across populations. When they added an Interaction term (ASIP*SLC45A2) to the model, they get 49.6% of the skin tone variation.

    So it would be something like Y (Skin Tone) = Constant + B1 (SLC24A5) + B2 (SLC45A2) + B3 (ASIP) + B4 (SLC45A2*ASIP).....and other variables + error term.

    USDOJ Final Copy of Research Paper conducted by Academicians at the University of Arizona (USA).

    https://www.ojp.gov/pdffiles1/nij/grants/223980.pdf

    The 2 SNP's in ASIP that impact Skin tone are rs6058017 and rs2424984. Both were significant in an ANOVA approach but the rs2424984 gave a slightly better fit in the Multiple Linear Regression analysis

    From the USDOJ study (page 10):

    "Using MLR, we found that both SNPs rs1426654 (SLC24A5) and rs16891982 (SLC45A2) described much of the variation in skin pigmentation across populations. The third most significant genetic contributor in a three-SNP MLR model was SNP rs2424984 (ASIP). ASIP has been shown to be associated with skin pigmentation, namely for rs6058017 (BONILLA et al. 2005; KANETSKY et al. 2002). Although we found rs6058017 to be significant by ANOVA, we did not find it to be a better predictor in skin reflectance than rs2424984. For both a single SNP analysis and a three-SNP model, rs2424984 was a better predictor for skin reflectance."

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    ................
    Last edited by matp; 08-08-21 at 22:02.

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    Quote Originally Posted by real expert View Post
    What I found more puzzling than the prediction of the Cheddar man being "dark dot black" was the phenotype analysis for the BA Aegeans. HIrisPLex predicted 1 BA Aegean individual to be in the "dark" category while the other two were predicted to be most likely "dark to black". These 3 individuals are AA on rs1426654 (SLC24A5) but CC and CG (overwhelmingly GG in contemporary Europeans) on rsrs16891982 (SLC45A2). With that being said, the two Aegeans that scored "dark to black" carried OCA2 which also contributes to pigmentation. How realistic do you find the phenotype analysis in terms of BA Greeks having dark to black skin tone?
    looking at the frequencies of those genes in modern populations i would guess they were probably intermediate. but those are only very few genes. for example the derived allele of SLC24A5 is at more than 50% frequency in ethiopians and somalis but they aren't really light skinned. i imagine them to have had the skin complexion of modern day north african, levantine populations. those are also almost fixated for SLC24A5. Krause said somewhere that the farmers in europe had the complexion of modern populations from around the mediterranean so the same probably applies to bronze age aegeans.

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    Quote Originally Posted by Ailchu View Post
    looking at the frequencies of those genes in modern populations i would guess they were probably intermediate. but those are only very few genes. for example the derived allele of SLC24A5 is at more than 50% frequency in ethiopians and somalis but they aren't really light skinned. i imagine them to have had the skin complexion of modern day north african, levantine populations. those are also almost fixated for SLC24A5. Krause said somewhere that the farmers in europe had the complexion of modern populations from around the mediterranean so the same probably applies to bronze age aegeans.

    I agree with you that the BA Aegeans were likely intermediate/olive skinned and not "dark to black". However, the academic paper concluded the opposite. Besides, many Ethio-Semites from Eritrea and North Ethiopia are (when not over-exposed to the sun) often light brown, yellowish. Somalis and Ethiopians from the largest Ethiopian ethnicity, the Oromo, are darker than the Ethio-Semites, though. We have to take into consideration that Horners have varying degrees of Western Eurasian admixture. They have also inherited certain genes for extremely dark skin. For instance, the African component in Somalis/ Ethiopians is largely Dinka-like and the Dinkas are not seldom literally black. Thus, they must have genes that makes them extremely dark even for African standard. When the Egyptians were depicting Nubians with literally black skin, they were not exaggerating.


    Here a picture of a Dinka man who is literally black.





    One picture of an Ethio-Semitic female from the Tigrinya tribe(Eritrea) with light brown skin tone. The second pic shows an Ethio-Semite women from Ethiopia. Anyway, Ethio-Semites have some additional Arab/Southern Arabian admixture. Bottom line, SLC24A5 has definitely a significant lightening effect.



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