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Thread: The genomic history of the Aegean palatial civilizations.

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    Quote Originally Posted by Philjames100 View Post
    also probably completely wrong.
    I know it's totally unexpected. Although I always believed that ancient Aeagans were swarthy, I'd never ever imagined that they were that dark. That said, where do you get the confidence, that the predictor likely got it wrong? The data is the data. Anyway, it would be even more amusing and puzzling if the Northern Greek Log 4 who is the closest to Scots and Lithuanians would be also predicted as very dark to black.

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    Quote Originally Posted by Philjames100 View Post
    also probably completely wrong.
    doublepost

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    Quote Originally Posted by Stuvanè View Post
    My Dodecad K12B results based on coordinates provided by Jovialis (post #74)

    Distance to: Dodecadk12bStuvanè
    5.70363919 MBA_Helladic_Logkas:Log02
    8.03052925 MBA_Helladic_Logkas:Log04
    27.91290562 EBA_Helladic_Manika:Mik15
    30.70116284 EBA_Cyclade_Koufanisi:Kou03
    31.07440587 EBA_Minoan_Petras:Pta08
    31.79075495 EBA_Cyclade_Koufanisi:Kou01

    2 way mode

    Distance to: Dodecadk12bStuvanè
    4.44805889 65.20% MBA_Helladic_Logkas:Log02 + 34.80% MBA_Helladic_Logkas:Log04
    4.75862217 19.00% EBA_Helladic_Manika:Mik15 + 81.00% MBA_Helladic_Logkas:Log04
    5.28385242 16.40% EBA_Minoan_Petras:Pta08 + 83.60% MBA_Helladic_Logkas:Log04
    5.43205124 15.80% EBA_Cyclade_Koufanisi:Kou01 + 84.20% MBA_Helladic_Logkas:Log04
    6.06659526 14.80% EBA_Cyclade_Koufanisi:Kou03 + 85.20% MBA_Helladic_Logkas:Log04
    27.88157533 9.40% EBA_Cyclade_Koufanisi:Kou03 + 90.60% EBA_Helladic_Manika:Mik15
    30.66569933 22.80% EBA_Minoan_Petras:Pta08 + 77.20% EBA_Cyclade_Koufanisi:Kou03
    There's that east/west Italian thing again. :)


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    Quote Originally Posted by Philjames100 View Post
    Mathiesen always makes a mess of his charts. He did it with WHG ***mentation in the first paper. He had one grouping for European HG and he included in it the SHG samples, so of course it looked as if European HGs had lighter skin. YOU CAN'T DO THAT. You have to have a grouping for WHG and one for SHG, and one for EHG. They were all different.

    I don't know if it's just carelessness and stupidity, which I wouldn't at all doubt given the quality of his analysis, or he's a secret Nordicist. I certainly wouldn't be surprised by the latter either. He's not a straight shooter at all.

    As for this paper, I don't have time to go back and analyze the paper again, but I think he once again mixed samples of different areas and time periods. I don't remember the precise details, but you can't, for example, include LN/EBA on the Pontic Caspian steppe with samples from the far eastern steppe from much later who picked up de***mentation alleles from central European farmers. You also can't include forest steppe mostly EHG people with the obviously admixed steppe people with more than 40% Iran Neo/CHG. Those groups, especially if they went onto the steppe very early, would NOT have SLC45A2.

    You have to be very careful with Mathiesen in general, as with this paper. You have to check the area and date for all his included samples. If it's from later periods or further north they'll have picked up de***mentation snps from Central and northern Europe.

    Just think about it. Do you think it makes sense that people who were 40+ percent Iran Neo or CHG like would have SLC45A2 in high numbers? We have to use our common sense, as well as watch what some of these "experts" very carefully, especially if, like Mathiesen, they're known for "questionable" charts, to be charitable.

    Take a look at the Wilde paper. Those are the Catacomb people if I remember correctly, who are probably, imo, the ones who went to Greece.

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    Quote Originally Posted by real expert View Post
    I know it's totally unexpected. Although I always believed that ancient Aeagans were swarthy, I'd never ever imagined that they were that dark. That said, where do you get the confidence, that the predictor likely got it wrong? The data is the data. Anyway, it would be even more amusing and puzzling if the Northern Greek Log 4 who is the closest to Scots and Lithuanians would be also predicted as very dark to black.

    I think there may very well be a mistake somewhere where the alleles were not labeled correctly as to whether they are ancestral or derived, or may have been input incorrectly. I think the authors should be contacted.

    However, those categories or labels are from an American company, from an American context, and are meant to aid the FBI and local police as to the appearance of a suspect. If you go back and look at the painting of the elite Mycenaean warrior, to an American police officer that man would be dark. A lot of African Americans, due to a lot of European admixture (20-25%), do not look like people from Nigeria. However, a very tanned "white" American can sometimes approximate the skin tone of some African Americans.

    Now, as I said, I thought some of that was a tan, but maybe not.

    One thing that has to be kept in mind is that the Greeks of the Classical Era were very aware of their own ***mentation in reference to Eastern Europeans and Egyptians, who at the time did not have much SSA, and so might have looked like Saudis. They said they weren't as fair as the Northern and Eastern "Barbarians", nor as dark as the Egyptians, and therefore had the "perfect" skin tone. :)

    Also, I can tell you that I personally know people who have what you might call "olive" Mediterranean skin, i.e. relatively light if "sallow" in winter, and tanning very dark in summer. They usually have two derived alleles for SLC 24A5, and are heterogeneous for the alleles for SLC45A2.

    People just have to get over the idea that Europeans in the ancient past looked like modern Europeans. Selection for "fairness" is still going on, as is selection for LP.

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    Quote Originally Posted by Angela View Post
    Mathiesen always makes a mess of his charts. He did it with WHG ***mentation in the first paper. He had one grouping for European HG and he included in it the SHG samples, so of course it looked as if European HGs had lighter skin. YOU CAN'T DO THAT. You have to have a grouping for WHG and one for SHG, and one for EHG. They were all different.

    I don't know if it's just carelessness and stupidity, which I wouldn't at all doubt given the quality of his analysis, or he's a secret Nordicist. I certainly wouldn't be surprised by the latter either. He's not a straight shooter at all.

    As for this paper, I don't have time to go back and analyze the paper again, but I think he once again mixed samples of different areas and time periods. I don't remember the precise details, but you can't, for example, include LN/EBA on the Pontic Caspian steppe with samples from the far eastern steppe from much later who picked up de***mentation alleles from central European farmers. You also can't include forest steppe mostly EHG people with the obviously admixed steppe people with more than 40% Iran Neo/CHG. Those groups, especially if they went onto the steppe very early, would NOT have SLC45A2.

    You have to be very careful with Mathiesen in general, as with this paper. You have to check the area and date for all his included samples. If it's from later periods or further north they'll have picked up de***mentation snps from Central and northern Europe.

    Just think about it. Do you think it makes sense that people who were 40+ percent Iran Neo or CHG like would have SLC45A2 in high numbers? We have to use our common sense, as well as watch what some of these "experts" very carefully, especially if, like Mathiesen, they're known for "questionable" charts, to be charitable.

    Take a look at the Wilde paper. Those are the Catacomb people if I remember correctly, who are probably, imo, the ones who went to Greece.

    One would think that researchers would try their best to avoid flawed methodology and misleading conclusions. Whatever.
    After analysing this Aegean paper do you think their phenotype prediction is absolutely legit and truth worthy or do you have some reservations?

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    Quote Originally Posted by real expert View Post
    I know it's totally unexpected. Although I always believed that ancient Aeagans were swarthy, I'd never ever imagined that they were that dark. That said, where do you get the confidence, that the predictor likely got it wrong? The data is the data. Anyway, it would be even more amusing and puzzling if the Northern Greek Log 4 who is the closest to Scots and Lithuanians would be also predicted as very dark to black.
    In k12b Log4 cluster with slav macedonians
    If in the paper he cluster with scots that means
    K12b calculator of dienekes is also way of....
    https://www.yfull.com/tree/E-FGC7391/

    https://yfull.com/mtree/H3ap/

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    In k12b Log4 cluster with slav macedonians
    If in the paper he cluster with scots that means
    K12b calculator of dienekes is also way of....
    Log4 doesn’t cluster anywhere near Scotts, she clearly clusters near south Balkan populations (even if, and to some extent definitely because of coincidence)

    F3 stats dont measure overall similarity. Notice how Anatolia bronze age is mostly similar to Sardinians going by their f3 chart, but on any pca bronze age Anatolians will cluster far away from them and closer to populations like Cypriots. Same with the Myceneans, it's just that both populations have Anatolia Neolithic as their predominant component.

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    Quote Originally Posted by real expert View Post
    One would think that researchers would try their best to avoid flawed methodology and misleading conclusions. Whatever.
    After analysing this Aegean paper do you think their phenotype prediction is absolutely legit and truth worthy or do you have some reservations?
    As I said in post 130 there may be a mistake somewhere in recording whether an allele was ancestral or derived and whether all the data was input into Hirisplex S correctly. The authors should be contacted in as respectful a manner as possible, of course. It just takes one careless mistake.

    So, I'm keeping an open mind.

    However, if it was all done correctly, you can go to page 17 of the site for Hirisplex 6 to see the examples of the skin tones for each of their categories. Dark is not very dark imo, so maybe that's correct, but I have a hard time believing the "very dark" category, even though that's also not that dark in the sample. The table in the supplement has all the values, so I suppose someone could run them; that would tell us at least whether the values were input correctly.

    Btw, this, imo, is a man with an olive Mediterranean skin in winter. It's "white" skin with a greenish undertone. The following pictures are him in summer.



    Various shades of tan:




    This is my husband's complexion, and how deeply he can tan, while I huddle under an umbrella and can still wind up with skin poisoning. The only important thing about skin ***mentation is whether you're adapted to your climate. I seem to be adapted for very northern latitudes or high atop some mountains; I just don't like them. :)

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    Quote Originally Posted by Angela View Post
    There's that east/west Italian thing again. :)
    Angela do you happen to know why K12b places me closer then K13 with the same input data so to speak?

    vs
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    Quote Originally Posted by Angela View Post
    As I said in post 130 there may be a mistake somewhere in recording whether an allele was ancestral or derived and whether all the data was input into Hirisplex S correctly. The authors should be contacted in as respectful a manner as possible, of course. It just takes one careless mistake.

    So, I'm keeping an open mind.

    However, if it was all done correctly, you can go to page 17 of the site for Hirisplex 6 to see the examples of the skin tones for each of their categories. Dark is not very dark imo, so maybe that's correct, but I have a hard time believing the "very dark" category, even though that's also not that dark in the sample. The table in the supplement has all the values, so I suppose someone could run them; that would tell us at least whether the values were input correctly.

    Btw, this, imo, is a man with an olive Mediterranean skin in winter. It's "white" skin with a greenish undertone. The following pictures are him in summer.



    Various shades of tan:




    This is my husband's complexion, and how deeply he can tan, while I huddle under an umbrella and can still wind up with skin poisoning. The only important thing about skin ***mentation is whether you're adapted to your climate. I seem to be adapted for very northern latitudes or high atop some mountains; I just don't like them. :)
    As someone earlier mentioned... It looks like a tanning thing. In the first picture he could pass in GB, in the third in Portugal (judging by the close/background he has been tanning).

    Have noticed this a lot with some instagram friends from Sweden. During the summer they get that golden bronze complexion. Given that today we have sunscreen maybe that helps not get the sunburn red rash.

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    Quote Originally Posted by Angela View Post




    This is my husband's complexion, and how deeply he can tan, while I huddle under an umbrella and can still wind up with skin poisoning. The only important thing about skin ***mentation is whether you're adapted to your climate. I seem to be adapted for very northern latitudes or high atop some mountains; I just don't like them. :)
    The actor in the last picture is likely how the ancient Greeks looked like in terms of complexion. It’s a bit odd, to think that a 5000 years old predynastic Egyptian that was naturally mummified and exposed to the heat and sun, is still visibly, pretty light skinned. Which means BA Greeks were big time darker than the predynastic Egyptians.

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    Quote Originally Posted by real expert View Post
    The actor in the last picture


    All three pictures are the same actor

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    Quote Originally Posted by iluvatar View Post
    Log4 doesn’t cluster anywhere near Scotts, she clearly clusters near south Balkan populations (even if, and to some extent definitely because of coincidence)

    F3 stats dont measure overall similarity. Notice how Anatolia bronze age is mostly similar to Sardinians going by their f3 chart, but on any pca bronze age Anatolians will cluster far away from them and closer to populations like Cypriots. Same with the Myceneans, it's just that both populations have Anatolia Neolithic as their predominant component.
    Every tool has its good points and its bad points. That's why they should all be looked at. Population Genetics is not for linear thinkers.

    PCAs show only two dimensions and a reduced percentage of the total genes. Novembre et al, for example, captured 45% of them. Some capture far fewer.

    https://journals.plos.org/plosgeneti...l.pgen.1002886

    I shouldn't need to point out that landing near one another on a PCA doesn't necessarily mean that the two populations share the same population history.

    As to F3 etc., perhaps a review of some of the statistical tools is in order.

    https://compvar-workshop.readthedocs...tterson%202012

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    Quote Originally Posted by real expert View Post
    The actor in the last picture is likely how the ancient Greeks looked like in terms of complexion. It’s a bit odd, to think that a 5000 years old predynastic Egyptian that was naturally mummified and exposed to the heat and sun, is still visibly, pretty light skinned. Which means BA Greeks were big time darker than the predynastic Egyptians.
    R.E. they're all the same man. My point was that people who look "white" in winter, can get much darker in summer.

    I don't know whether the "Griffin Man" was naturally that dark or it was a tan.

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    Quote Originally Posted by Angela View Post
    R.E. they're all the same man. My point was that people who look "white" in winter, can get much darker in summer.

    I don't know whether the "Griffin Man" was naturally that dark or it was a tan.
    I also don't think your last conclusion was warranted.

    Egyptians knew very well how they looked in comparison to Sudanese people and Semites, much less Greeks.



    If t-rolling is going to start I'm going to stop responding. PLEASE read the paper and all the Supplement. All I'm seeing is a lot of misinformation from other sites etc.

    One simple thing: Only Log 4 is about 50% steppe. He probably just arrived, for goodness' sakes. Log 2 is very different.

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    Quote Originally Posted by Angela View Post
    Log 2 is very different.
    Would love your analysis of Log2.

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    Quote Originally Posted by Angela View Post
    R.E. they're all the same man. My point was that people who look "white" in winter, can get much darker in summer.

    I don't know whether the "Griffin Man" was naturally that dark or it was a tan.
    I can vouch for that. Due to my 10% Sicilian DNA, I tan quite well; as a kid, a March picture of me looked like a fine English boy, while in a September shot, I could have passed for Hispanic. Even today I have a semipermanent 'farmer tan'.

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    Quote Originally Posted by Angela View Post
    I also don't think your last conclusion was warranted.

    Egyptians knew very well how they looked in comparison to Sudanese people and Semites, much less Greeks.



    If t-rolling is going to start I'm going to stop responding. PLEASE read the paper and all the Supplement. All I'm seeing is a lot of misinformation from other sites etc.

    One simple thing: Only Log 4 is about 50% steppe. He probably just arrived, for goodness' sakes. Log 2 is very different.

    Angela, you got wrong what my point was, probably due to the fact, that you reply to several people. Firstly, I know that you showed me the same guy, Raoul Bova who was shown on this forum several times. I took his tanned complexion to make clear that "dark" in Greek context means such a skin tone and not SSA dark. Plus, I wanted to point out, if the prediction for the two samples is accurate and not flawed, that would mean that these tested Aegeans were darker than this predynastic Egyptian who was clearly not dark brown till black but moderately light skinned. So it‘s beyond me why you think I‘m tr*lling and accuse me of not being interested on your take on this study. If that wasn't the case I wouldn't ask and discuss with you. Again, I was referring to the prediction which we all find surprising because nobody expected very dark to black ancient Greeks as this study proposes. However, we know from history and Greek sources that Ancient Greeks considered Egyptians darker than them. Besides, I talked about the steppe admixed sample since her phenotype was predicted.

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    I shouldn't need to point out that landing near one another on a PCA doesn't necessarily mean that the two populations share the same population history.
    Obviously, but I never claimed that modern south balkanites are unadmixed descendants of these samples. Clearly later movements were involved as well as absorption of natives, evident in the fact that these samples score very little CHG/IRAN Neo while both Minoans and Cycladic/Helladic EBA do.

    A thing to note is that their pca is way off. Notice how the Mycenaeans sit right next to the Sardinians while they should be shifted way east of that, since apart from their Anatolian Neolithic base they also score significant chg/Iran neo and some Steppe admixture.
    You can confirm this by checking the 2017 Lazaridis paper in which they had done Fst for the Mycenaean and Anatolian Bronze age samples, both of which were closer to other groups compared to Sardinians (and of course would cluster closer to south Italians and Cypriots respectively on any decent pca). Do you really think Mycenaeans are closer to North Italians than to south Italians? Because that’s what that f3 outgroup stat is showing. I am talking here irrespective of whether or not we think these groups are ancestral to one another, just overall similarity.

    By the same token Log4 been closer to Scotts and Lithuanians, is obviously false by any metric. They are basically a 2 way mix of Anatolian Neolithic like populations and steppe populations (around 35/44 Yamnaya) in similar proportions to modern south balkanites but very different to modern Scotts and Lithuanians, both of which cluster with northern Europeans because they have a lot more WHG compared to these samples. I would post a pca and some models but I don’t think I can post pictures.

    This again doesn’t mean that modern people are unadmixed descendants off these samples but in terms of components theese Helladic MBA northern Greeks are more similar to modern populations from that area and less so to northern Europeans. Having said that and leaving that silly model for moderns in the paper aside, it's possible that these samples are a bit more informative for areas north of the Peloponnese for later periods compared to the Mycenaean samples, even though subsequent populations will certainly not be identical to them. For example later Thessalians might be a bit more derived from them but not identical to them.

    My answer was directed to Kingjohn’s question on why these samples are closer to southern Balkan populations on k12b while on the paper they cluster with Scotts. They obviously don’t and and i doubt you disagree with that.
    Last edited by iluvatar; 02-05-21 at 03:30.

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    Quote Originally Posted by iluvatar View Post
    Obviously, but I never claimed that modern south balkanites are unadmixed descendants of these samples. Clearly later movements were involved as well as absorption of natives, evident in the fact that these samples score very little CHG/IRAN Neo while both Minoans and Cycladic/Helladic EBA do.

    A thing to note is that their pca is way off. Notice how the Mycenaeans sit right next to the Sardinians while they should be shifted way east of that, since apart from their Anatolian Neolithic base they also score significant chg/Iran neo and some Steppe admixture.
    You can confirm this by checking the 2017 Lazaridis paper in which they had done Fst for the Mycenaean and Anatolian Bronze age samples, both of which were closer to other groups compared to Sardinians (and of course would cluster closer to south Italians and Cypriots respectively on any decent pca). Do you really think Mycenaeans are closer to North Italians than to south Italians? Because that’s what that f3 outgroup stat is showing. I am talking here irrespective of whether or not we think these groups are ancestral to one another, just overall similarity.

    By the same token Log4 been closer to Scotts and Lithuanians, is obviously false by any metric. They are basically a 2 way mix of Anatolian Neolithic like populations and steppe populations (around 35/44 Yamnaya) in similar proportions to modern south balkanites but very different to modern Scotts and Lithuanians, both of which cluster with northern Europeans because they have a lot more WHG compared to these samples. I would post a pca and some models but I don’t think I can post pictures.

    This again doesn’t mean that modern people are unadmixed descendants off these samples but in terms of components they are more similar to them and less so to northern Europeans. Having said that and leaving that silly model for moderns in the paper aside, its possible that these samples are a bit more informative for areas north of the Peloponnese for later periods compared to the Mycenaeans samples, even though subsequent populations will certainly not be identical to them. For example later Thessalians might be a bit more derived from them but not identical to them.

    My answer was directed to Kingjohn’s question on why these samples are closer to southern Balkan populations on k12b while on the paper they cluster with Scotts. They obviously don’t and and i doubt you disagree with that.
    Do you think people from Central Macedonia would also be good candidates for people derived from such a source? IIRC, they cluster in the same continuum as Thessalians. I could be wrong though.

    Also think your analysis is spot on.

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    Quote Originally Posted by Archetype0ne View Post
    Angela do you happen to know why K12b places me closer then K13 with the same input data so to speak?

    vs


    The answer is simple, because they are two different calculators created by two different persons.

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    1 members found this post helpful.
    Do you think people from Central Macedonia would also be good candidates for people derived from such a source? IIRC, they cluster in the same continuum as Thessalians. I could be wrong though.

    Also think your analysis is spot on.
    Your guess is as good as mine really. 2 samples from the early bronze age are way too few to draw any safe conclusions from unfortunately, and they may not be relevant to later populations but instead represent some relic of a people present in the area at that time e.g. Luwians.

    As for Macedonians and Thessalians, I would expect these pops and perhaps neighboring populations to be broadly similar, but that is mostly based on intuition and some anthropology work of the previous century, that is of course often hit and miss. These issues remain to be solved by more extensive ancient dna sampling from all over the balkans.

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    Quote Originally Posted by real expert View Post
    Angela, you got wrong what my point was, probably due to the fact, that you reply to several people. Firstly, I know that you showed me the same guy, Raoul Bova who was shown on this forum several times. I took his tanned complexion to make clear that "dark" in Greek context means such a skin tone and not SSA dark. Plus, I wanted to point out, if the prediction for the two samples is accurate and not flawed, that would mean that these tested Aegeans were darker than this predynastic Egyptian who was clearly not dark brown till black but moderately light skinned. So it‘s beyond me why you think I‘m tr*lling and accuse me of not being interested on your take on this study. If that wasn't the case I wouldn't ask and discuss with you. Again, I was referring to the prediction which we all find surprising because nobody expected very dark to black ancient Greeks as this study proposes. However, we know from history and Greek sources that Ancient Greeks considered Egyptians darker than them. Besides, I talked about the steppe admixed sample since her phenotype was predicted.
    Let's back track a bit.

    We have a portrait found in the tomb of the elite "Griffin Man" Mycenaean Warrior. We can see he's rather dark; however, there's no way of telling whether that's a tan or his actual complexion, i.e. did he have a Raoul Bova type "winter" complexion. I tend to doubt he was that light given how long ago it was and that selection for skin color has continued, but I really don't know.

    We also have representations of the Egyptians of themselves in relation to "Kushites", whom they depict as black, themselves, whom they depict as dark brown, and people from the Middle East, who look rather olive skinned to me. So, I think it's highly unlikely that Bronze Age Greeks were as dark as Egyptians. One should never take the color of mummies to mean anything at all, even if you're sure of the provenance of the picture. All sorts of totally bogus pictures are floating around on the internet.

    In a way, however, that's a bit irrelevant in this context. The real question is first, whether there was an error in the calculations. Second, what does "dark" or "very dark" mean in terms of Hirisplex 6.

    I referred to it upthread, but didn't provide the link. I apologize. Here it is below. Go to page 17 for the skin samples.

    https://hirisplex.erasmusmc.nl/pdf/h...asmusmc.nl.pdf

    Given that the sample from Crete is SLC24A5 homogeneous, and SLC45A2 heterogeneous, it's difficult for me to believe that this sample was in the darkest category.

    However, in my experience Hirisplex works, so I'm befuddled. :)

  25. #150
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    Quote Originally Posted by real expert View Post
    One would think that researchers would try their best to avoid flawed methodology and misleading conclusions. Whatever.
    After analysing this Aegean paper do you think their phenotype prediction is absolutely legit and truth worthy or do you have some reservations?

    do you know the genotype of the samples? are they homozygous for both alleles?

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