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Thread: The genomic history of the Aegean palatial civilizations.

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    Any idea why these results seem to be different to the PCA and other results?



    Figure S4 Genetic affinities between BA Aegeans compared to other present-day Eurasian populations.

    For each case, we show the geographic distribution of f3 (warmer colors represent greater sharing between populations X and Y).

    Beside each map, we plot the f3 values for the 15 populations that are most closely related to each of the populations in Y.

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    Quote Originally Posted by real expert View Post
    I actually agree with most what you've said, but you sometimes misunderstand what I try to bring across. Why you, me and others here, are befuddled is the fact, that the skin color prediction doesn't match the accounts of Ancient Greeks about their coloration. Nobody here would be surprised about this result if the Ancient Greeks would claim they were as dark as the Ethiopians or compared themselves to them. Ancient Greeks saw super pale Northern Europeans, moderately dark Egyptians and extremely dark Ethiopians. Hence, they were well aware of all the shades and hues of all kinds of people. They took dark to very dark, and pale to very pale people as an example, to stress their intermediate complexion. Plus, the Greeks talked about their females and Barbarians being pale/white. So, I'm discussing with you and others here because I try to connect the dots, thus make sense out the fact, that there is a discrepancy between the self-description of the Ancient Greeks in terms of their complexion and the result from this study.
    I agree, although if you go and look at the Hirisplex examples of their skin shade system, dark is not very dark.

    Still, as I said, I agree.


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    Quote Originally Posted by Philjames100 View Post
    Any idea why these results seem to be different to the PCA and other results?



    Figure S4 Genetic affinities between BA Aegeans compared to other present-day Eurasian populations.

    For each case, we show the geographic distribution of f3 (warmer colors represent greater sharing between populations X and Y).

    Beside each map, we plot the f3 values for the 15 populations that are most closely related to each of the populations in Y.
    This is an F3 analysis, not admixture. I provided a link which explains the differences between F3, F4 etc. Given that Log 4 is about 50% steppe, someplace like England or Germany or Norway does make more sense to me.

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    2 members found this post helpful.
    Quote Originally Posted by Cato View Post
    Why is the word *** censored? "***mentation"

    Inviato dal mio POT-LX1T utilizzando Tapatalk
    Because the woke idiots have taken control of google and most platforms. Good luck trying to find a paper on population genetics with regard to ***mentation on google. They're censored.

    I've switched to Bing, but who knows how long they'll remain sane.

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    Quote Originally Posted by Angela View Post
    This is an F3 analysis, not admixture. I provided a link which explains the differences between F3, F4 etc. Given that Log 4 is about 50% steppe, someplace like England or Germany or Norway does make more sense to me.
    So do you think f3 is more accurate in this case?


    'Outgroup F3 statistics are a measure of how closely two populations are related with each other... It is thus a similarity measure: The higher the statistic, the more genetically similar A and B are to one another.'

    https://compvar-workshop.readthedocs...s/f3stats.html

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    Quote Originally Posted by Philjames100 View Post
    Any idea why these results seem to be different to the PCA and other results?



    Figure S4 Genetic affinities between BA Aegeans compared to other present-day Eurasian populations.

    For each case, we show the geographic distribution of f3 (warmer colors represent greater sharing between populations X and Y).

    Beside each map, we plot the f3 values for the 15 populations that are most closely related to each of the populations in Y.
    Here is their genetic distance, which does seem very far.

    Distance to: MBA_Helladic_Logkas:Log04
    26.07227071 Scottish
    43.55175427 Lithuanian

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    Quote Originally Posted by Angela View Post
    Because the woke idiots have taken control of google and most platforms. Good luck trying to find a paper on population genetics with regard to ***mentation on google. They're censored.

    I've switched to Bing, but who knows how long they'll remain sane.
    Thanks

    Inviato dal mio POT-LX1T utilizzando Tapatalk

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    Quote Originally Posted by Jovialis View Post
    Here is their genetic distance, which does seem very far.

    Distance to: MBA_Helladic_Logkas:Log04
    26.07227071 Scottish
    43.55175427 Lithuanian
    Eurogenes K13 shows similar results:

    Distance to: Log04_Helladic-Logkas-MBA
    30.98066655 Scottish
    42.89642992 Lithuanian

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    2 members found this post helpful.
    Here is Log04 using the Ancient Ethnicities Analyzer sample sets for Dodecad K12b. I have omitted EMBA_Greece, since it is a average with the sample in and of itself in it. I also only used samples prior to the Bronze Age:

    Distance to: MBA_Helladic_Logkas:Log04
    4.05551446 49.20% Minoan_Greece_(n=10) + 50.80% Western_Corded_Ware_(n=17)
    4.32742922 30.80% Chalcolithic_Anatolia_(n=35) + 69.20% Bell_Beaker_Bavaria/Saxony_(n=20)
    4.35235309 28.20% Chalcolithic_Anatolia_(n=35) + 71.80% Bell_Beaker_Poland_(n=6)
    4.42282822 57.80% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 42.20% Chalcolithic_Northwest_Caucasus_(n=3)
    4.79227742 55.60% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 44.40% Kura-Araxes_culture_(n=8)
    4.83485120 49.60% Early_Neolithic_Anatolia_(n=7) + 50.40% Western_Corded_Ware_(n=17)
    4.84387292 55.60% Minoan_Greece_(n=10) + 44.40% Eastern_Corded_Ware_(n=8)
    4.87434178 49.40% Early_Neolithic_Greece_(n=3) + 50.60% Western_Corded_Ware_(n=17)
    5.14965055 34.20% Chalcolithic_Anatolia_(n=35) + 65.80% Bell_Beaker_Czechia_(n=15)
    5.19833457 55.80% Early_Neolithic_Greece_(n=3) + 44.20% Eastern_Corded_Ware_(n=8)
    5.46720224 20.40% Chalcolithic_Anatolia_(n=35) + 79.60% Bell_Beaker_Hungary_(n=6)
    5.71054814 47.40% Minoan_Greece_(n=10) + 52.60% Battle-Axe_culture_(n=3)
    5.71379690 56.00% Early_Neolithic_Anatolia_(n=7) + 44.00% Eastern_Corded_Ware_(n=8)
    5.78136591 31.60% Chalcolithic_North_Levant_(n=6) + 68.40% Bell_Beaker_Bavaria/Saxony_(n=20)
    5.79376873 32.60% Chalcolithic_Anatolia_(n=35) + 67.40% Bell_Beaker_Gaul_(n=13)
    5.96151263 17.80% Chalcolithic_Northwest_Caucasus_(n=3) + 82.20% Bell_Beaker_Hungary_(n=6)
    6.00558714 27.40% Chalcolithic_Azerbaijan_(n=4) + 72.60% Bell_Beaker_Poland_(n=6)
    6.02101976 63.80% Pre-Pottery_Neolithic_Anatolia_(n=8) + 36.20% Khvalynsk_culture_(n=3)
    6.04999866 35.20% Chalcolithic_North_Levant_(n=6) + 64.80% Bell_Beaker_Czechia_(n=15)
    6.38082750 81.00% Bell_Beaker_Hungary_(n=6) + 19.00% Kura-Araxes_culture_(n=8)
    6.38690853 34.00% Mesolithic_Volga-Ural_(n=2) + 66.00% Pre-Pottery_Neolithic_Anatolia_(n=8)
    6.39897383 59.40% Pre-Pottery_Neolithic_Anatolia_(n=8) + 40.60% Yamna_culture_(n=16)
    6.54373606 48.00% Early_Neolithic_Anatolia_(n=7) + 52.00% Battle-Axe_culture_(n=3)
    6.55968204 19.40% Chalcolithic_Azerbaijan_(n=4) + 80.60% Bell_Beaker_Hungary_(n=6)
    6.60249184 53.60% Bell_Beaker_Netherlands_(n=7) + 46.40% Minoan_Greece_(n=10)

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    1 members found this post helpful.
    Here is Log02 using the same parameters:

    Distance to: MBA_Helladic_Logkas:Log02
    2.48578595 28.60% Neolithic_Ukraine_(n=12) + 71.40% Minoan_Greece_(n=10)
    2.54935225 29.60% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.40% Minoan_Greece_(n=10)
    2.67591254 28.40% Mesolithic_Ukraine_(n=7) + 71.60% Minoan_Greece_(n=10)
    3.14827590 30.20% Neolithic_Latvia_(n=4) + 69.80% Minoan_Greece_(n=10)
    3.37486853 30.20% Neolithic_Lithuania_Narva_culture_(n=4) + 69.80% Minoan_Greece_(n=10)
    3.99730565 32.00% Mesolithic_Balkans_HG_(n=43) + 68.00% Minoan_Greece_(n=10)
    4.12687861 27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Early_Neolithic_Greece_(n=3)
    4.22228530 27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Minoan_Greece_(n=10)
    4.27831093 28.20% Mesolithic_Ukraine_(n=7) + 71.80% Early_Neolithic_Greece_(n=3)
    4.46740777 72.00% Early_Neolithic_Anatolia_(n=7) + 28.00% Neolithic_Ukraine_(n=12)
    4.51630287 29.00% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 71.00% Early_Neolithic_Anatolia_(n=7)
    4.54172493 27.80% Mesolithic_Ukraine_(n=7) + 72.20% Early_Neolithic_Anatolia_(n=7)
    4.57468244 71.40% Early_Neolithic_Greece_(n=3) + 28.60% Neolithic_Ukraine_(n=12)
    4.79669019 27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Early_Neolithic_Greece_(n=3)
    4.96434435 70.40% Early_Neolithic_Anatolia_(n=7) + 29.60% Neolithic_Lithuania_Narva_culture_(n=4)
    5.13790525 29.40% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.60% Early_Neolithic_Greece_(n=3)
    5.26229683 27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Minoan_Greece_(n=10)
    5.35003628 26.80% Mesolithic_Northwest_Russia_(n=4) + 73.20% Early_Neolithic_Anatolia_(n=7)
    5.37347791 66.20% Minoan_Greece_(n=10) + 33.80% Eastern_Corded_Ware_(n=8)
    5.38487045 70.60% Early_Neolithic_Anatolia_(n=7) + 29.40% Neolithic_Latvia_(n=4)
    5.42140579 48.80% Chalcolithic_North_Levant_(n=6) + 51.20% Bell_Beaker_Czechia_(n=15)
    5.48576804 70.00% Early_Neolithic_Greece_(n=3) + 30.00% Neolithic_Latvia_(n=4)
    5.57399731 31.40% Mesolithic_Balkans_HG_(n=43) + 68.60% Early_Neolithic_Anatolia_(n=7)
    5.60900699 46.80% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 53.20% Chalcolithic_Anatolia_(n=35)
    5.67090951 61.40% Minoan_Greece_(n=10) + 38.60% Western_Corded_Ware_(n=17)

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    1 members found this post helpful.
    Finally, here is the Early Bronze Age Helladic:

    Distance to: EBA_Helladic_Manika:Mik15
    1.61010098 92.40% Early_Neolithic_Anatolia_(n=7) + 7.60% Chalcolithic_Iberia_(n=62)
    1.62160649 91.20% Early_Neolithic_Anatolia_(n=7) + 8.80% Megalithic_Europe_(n=24)
    1.63866104 90.00% Early_Neolithic_Anatolia_(n=7) + 10.00% Chalcolithic_BB_Sardinia_(n=10)
    1.65156217 92.00% Early_Neolithic_Anatolia_(n=7) + 8.00% Neolithic_Britain_(n=62)
    1.65234286 92.60% Early_Neolithic_Anatolia_(n=7) + 7.40% Bell_Beaker_Iberia_(n=11)
    1.67178106 91.00% Early_Neolithic_Anatolia_(n=7) + 9.00% Late_Neolithic_Switzerland_(n=58)
    1.72194235 92.00% Early_Neolithic_Anatolia_(n=7) + 8.00% Middle_Late_Neolithic_Spain_(n=12)
    1.73119949 90.20% Early_Neolithic_Anatolia_(n=7) + 9.80% Middle_Neolithic_France_(n=19)
    1.78939834 92.40% Early_Neolithic_Anatolia_(n=7) + 7.60% Globular_Amphora_culture_(n=6)
    1.85073255 85.40% Early_Neolithic_Anatolia_(n=7) + 14.60% Late_Chalcolithic_Baden_culture_(n=14)
    1.87866617 4.00% Epipaleolithic_Magreb_(Iberomaurusians)_(n=5) + 96.00% Early_Neolithic_Greece_(n=3)
    1.88288829 92.20% Early_Neolithic_Anatolia_(n=7) + 7.80% CA_Remedello_culture_(n=3)
    2.02275718 91.20% Early_Neolithic_Anatolia_(n=7) + 8.80% Middle_Neolithic_Sardinia_(n=10)
    2.03488753 80.60% Early_Neolithic_Anatolia_(n=7) + 19.40% Early_Neolithic_Starcevo_culture_(n=8)
    2.04197772 84.60% Early_Neolithic_Anatolia_(n=7) + 15.40% EN_Alfold_Linear_Pottery_culture_(n=20)
    2.04488044 80.00% Early_Neolithic_Anatolia_(n=7) + 20.00% LN_Lengyel_culture_(n=8)
    2.05656394 84.60% Early_Neolithic_Anatolia_(n=7) + 15.40% Middle_Neolithic_Sicily_(n=10)
    2.05715270 89.40% Early_Neolithic_Anatolia_(n=7) + 10.60% Cucuteni-Trypillian_culture_(n=4)
    2.09633678 84.40% Early_Neolithic_Anatolia_(n=7) + 15.60% Middle_Chalcolithic_Hungary_(n=9)
    2.10271711 77.80% Early_Neolithic_Anatolia_(n=7) + 22.20% Chalcolithic_Bulgaria_(n=9)
    2.13077473 92.00% Early_Neolithic_Anatolia_(n=7) + 8.00% Early_Neolithic_Spain_(n=10)
    2.19451927 21.80% Pre-Pottery_Neolithic_Anatolia_(n=8) + 78.20% Early_Neolithic_Anatolia_(n=7)
    2.27480436 83.80% Early_Neolithic_Anatolia_(n=7) + 16.20% Early_Neolithic_Italy_(n=10)
    2.28583847 95.00% Early_Neolithic_Anatolia_(n=7) + 5.00% MN_Westphalia_(Megalithic_Wartberg)_(n=6)
    2.31740703 83.40% Early_Neolithic_Anatolia_(n=7) + 16.60% LN_Tisza-Sopot_culture_(n=11)

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    Quote Originally Posted by Jovialis View Post
    Here is Log02 using the same parameters:

    Distance to: MBA_Helladic_Logkas:Log02
    2.48578595 28.60% Neolithic_Ukraine_(n=12) + 71.40% Minoan_Greece_(n=10)
    2.54935225 29.60% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.40% Minoan_Greece_(n=10)
    2.67591254 28.40% Mesolithic_Ukraine_(n=7) + 71.60% Minoan_Greece_(n=10)
    3.14827590 30.20% Neolithic_Latvia_(n=4) + 69.80% Minoan_Greece_(n=10)
    3.37486853 30.20% Neolithic_Lithuania_Narva_culture_(n=4) + 69.80% Minoan_Greece_(n=10)
    3.99730565 32.00% Mesolithic_Balkans_HG_(n=43) + 68.00% Minoan_Greece_(n=10)
    4.12687861 27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Early_Neolithic_Greece_(n=3)
    4.22228530 27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Minoan_Greece_(n=10)
    4.27831093 28.20% Mesolithic_Ukraine_(n=7) + 71.80% Early_Neolithic_Greece_(n=3)
    4.46740777 72.00% Early_Neolithic_Anatolia_(n=7) + 28.00% Neolithic_Ukraine_(n=12)
    4.51630287 29.00% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 71.00% Early_Neolithic_Anatolia_(n=7)
    4.54172493 27.80% Mesolithic_Ukraine_(n=7) + 72.20% Early_Neolithic_Anatolia_(n=7)
    4.57468244 71.40% Early_Neolithic_Greece_(n=3) + 28.60% Neolithic_Ukraine_(n=12)
    4.79669019 27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Early_Neolithic_Greece_(n=3)
    4.96434435 70.40% Early_Neolithic_Anatolia_(n=7) + 29.60% Neolithic_Lithuania_Narva_culture_(n=4)
    5.13790525 29.40% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.60% Early_Neolithic_Greece_(n=3)
    5.26229683 27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Minoan_Greece_(n=10)
    5.35003628 26.80% Mesolithic_Northwest_Russia_(n=4) + 73.20% Early_Neolithic_Anatolia_(n=7)
    5.37347791 66.20% Minoan_Greece_(n=10) + 33.80% Eastern_Corded_Ware_(n=8)
    5.38487045 70.60% Early_Neolithic_Anatolia_(n=7) + 29.40% Neolithic_Latvia_(n=4)
    5.42140579 48.80% Chalcolithic_North_Levant_(n=6) + 51.20% Bell_Beaker_Czechia_(n=15)
    5.48576804 70.00% Early_Neolithic_Greece_(n=3) + 30.00% Neolithic_Latvia_(n=4)
    5.57399731 31.40% Mesolithic_Balkans_HG_(n=43) + 68.60% Early_Neolithic_Anatolia_(n=7)
    5.60900699 46.80% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 53.20% Chalcolithic_Anatolia_(n=35)
    5.67090951 61.40% Minoan_Greece_(n=10) + 38.60% Western_Corded_Ware_(n=17)

    This might be a dumb question. But does Neolithic Ukraine have any steppe in it?
    “Man cannot live without a permanent trust in something indestructible in himself, and at the same time that indestructible something as well as his trust in it may remain permanently concealed from him.”

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    Quote Originally Posted by real expert View Post
    That's because modern Greeks are not that swarthy as people pretend them to be. The same goes for Italians or Spaniards. That said, if the phenotype prediction from this study is 100% correct, that would make BA Greeks a lot darker than regular Middle Easterners or North Africans. If I remember correctly there was a phenotype prediction for individuals from the Roman paper here, and they turned out not be particularly swarthy.
    it would be a lot clearer if we had the genotypes. looked through the supplements but couldn't find them. if they were not homozygous for 45A2 their ***mentation probably was darker than regular modern people from near east.

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    Quote Originally Posted by Archetype0ne View Post
    This might be a dumb question. But does Neolithic Ukraine have any steppe in it?
    Not a dumb question,

    They fall between, EHG and WHG.

    Steppe has a lot more CHG:



    The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers - ScienceDirect

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    Quote Originally Posted by Jovialis View Post
    Eurogenes K13 shows similar results:

    Distance to: Log04_Helladic-Logkas-MBA
    30.98066655 Scottish
    42.89642992 Lithuanian

    What do you think the reason is for the difference between these results and the f3 statistics in the paper?

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    It's there:

    Attachment 12675

    Click to enlarge.

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    Quote Originally Posted by Philjames100 View Post
    What do you think the reason is for the difference between these results and the f3 statistics in the paper?
    TBH, I am not familiar with that tool. It could be worth e-mailing the author to inquire.

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    Quote Originally Posted by Angela View Post
    It's there:

    Attachment 12675

    Click to enlarge.

    Attachment doesn't work.

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    Quote Originally Posted by Philjames100 View Post
    Attachment doesn't work.

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    1 members found this post helpful.

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    1 members found this post helpful.
    The three BA samples carried SLC24A5 and SLC45A2 typical among modern Europeans today. However, these individuals also carried OCA2, which is common among East Asians, and ASIP, which is associated with darker skin color in African Americans. This may be why the study's authors reached the following conclusion.

    Using genotype data, we predicted that Pta08, Kou01, and Log02 most likely had brown eyes, dark brown to black hair, and dark skin (Table S1; STAR Methods). These predictions match the visual representations of male individuals from BA wall paintings of Minoan Crete for hair and eye color. The eye and hair color predictions were similar to those from later periods of the Aegean BA (Lazaridis et al., 2017). Although the overall prediction for all three individuals was of dark skin, they also all carried alleles strongly associated with lighter skin color (rs1426654 in the gene SLC24A5, and rs16891982 in SLC45A2) (Mathieson et al., 2015).
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  22. #197
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    Quote Originally Posted by Ailchu View Post
    it would be a lot clearer if we had the genotypes. looked through the supplements but couldn't find them. if they were not homozygous for 45A2 their ***mentation probably was darker than regular modern people from near east.

    A smart person explained to me how and why the authors predicted the dark skin for the 3 samples.


    Looking at the supplements, the studied ones (the EBA Kou01, Pta08 and MBA Log02) are AA on rs1426654 (SLC24A5) but CC and CG (overwhelmingly GG in contemporary Europeans) on rsrs16891982 (SLC45A2). But they checked other alleles that contribute to ***mentation as well, which the HIrisPLex model is based on. Check the Nuclear capture part of the supplement for more information. Either way, I believe that category implies dark-skinned by contemporary pan-European standards, obviously not by global standards.

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    Quote Originally Posted by ThirdTerm View Post
    The three BA samples carried SLC24A5 and SLC45A2 typical among modern Europeans today. However, these individuals also carried OCA2, which is common among East Asians, and ASIP, which is associated with darker skin color in African Americans. This may be why the study's authors reached the following conclusion.
    if i understand it correctly, looking at the table of genotypes only 1 individual was heterozygous with the derived allele of SLC45A2 associated with light skin. the other 2 were homozygous with the ancestral allele.

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    Quote Originally Posted by real expert View Post
    A smart person explained to me how and why the authors predicted the dark skin for the 3 samples.

    i could imagine their skin color might have been similar to what we find in egypt today. if there was still ongoing selection for light skin in greece because of the change in nutrition then it is also likely that there was a similar selection throughout the near east and north africa. so when the ancient greeks compared their skin color to the northern barbarians and the egyptians then probably we should consider that those 2 groups were also darker ***mented than modern ones.

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    1 members found this post helpful.
    Phenotyping the ancient world: The physical appearance and ancestry of very degraded samples from a chalcolithic human remains-“Therefore, the aim of the present work was the molecular study of a very critical sample, a Chalcolithic (3480 ± 30 YBP) individual found in Asturias, Northern Iberia, intending to discover a possible geographical ancestry for these remains, and the inference of a group of feasible EVCs (hair, skin and iris ***mentation).Given that ancient DNA is often highly damaged, two different methodologies were used in order to determine the biogeographical ancestry of the individual: mitochondrial DNA (HVR-I and -II) and Single Nucleotide Polymorphisms typing. Despite the antiquity of the samples, the genetic information recovered proved of great value. We could determine that the individual had a European ancestry, blond hair, light skin color and brown eyes. Such outcome reveals that it is possible to obtain not only biogeographical but also phenotypic information from a very critical sample"

    This sample comes from the Bronze Age in Asturias (northern Spain) and corresponds exactly to the Griffin warrior dating in Greece. As you can see, this gentleman had fair skin, blond hair and brown eyes, however we have a perfectly preserved mummy from the Argar culture (southeastern Spain) that was buried with his son (4-5 years old). Both have black hair with large braids that reached the waist in the case of the man- During the Bronze Age the phenotypes were very varied but light skin was already a fixed feature for all European regions

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