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Thread: Questions about PCA

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    Questions about PCA

    I have a couple of questions about PCA maps, two specific and the rest more general or theoretical.

    For my first question, I’m confused by the statement that David Reich and others like Iosif Lazaridis have made—that Levantine farmers, Iranian farmers, EHG, and WHG were as different from each other as present-day Europeans and East Asians. But according to this map, two of the populations, WHG and EHG, seem much closer to each other than present-day Europeans and East Asians. (On the map, grayed out dots represent modern individuals, while colored dots represent ancient individuals.)
    1CAE8857-4A4D-4048-A4AA-81F7253EC700.png
    So my first question is, how can that make sense if those two populations are as different from each other as present-day Europeans and East Asians?

    My second question is, why exactly do EEF and WHG place differently on the map above vs the one below?
    70D96659-F20C-4126-88F5-6155BF8E6225.jpeg

    I also have questions concerning PCAs in general. What do the two dimensions, and the numbers on them, mean? What is the methodology behind producing PCA maps?

    Thanks.

  2. #2
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    There is no way that WHG, EHG and EEF plot together with modern populations. Today such populations don't exist (except maybe Sardinians).
    Every PCA is different and depends on populations which it plots.
    Inform yourself on wikipedia or somewhere else about PCA.
     
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    Ancient populations definitely can be plotted alongside modern populations; in fact this is what the first map does.

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    Quote Originally Posted by Fahr View Post
    Ancient populations definitely can be plotted alongside modern populations; in fact this is what the first map does.
    Ancients are not plotted alongside ancient populations but rather projected on to the PCA of human genetic variation at a global level. Because at a global level PC1 and 2 capture the variation between African, East and West Eurasians, ancient west eurasian individuals overlap with the modern west eurasians. The second PCA is only showing the variation specific to West-Eurasian populations not including the other global populations, it helps differentiate the genetic variation between west eurasians: WHG, ANE, Anatolian_N/Levant_N and Iran_N/CHG, seperate at extreme corners of the PCA plot because of independent drift within each population.
     

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  7. #5
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    Quote Originally Posted by Fahr View Post
    I have a couple of questions about PCA maps, two specific and the rest more general or theoretical.

    For my first question, I’m confused by the statement that David Reich and others like Iosif Lazaridis have made—that Levantine farmers, Iranian farmers, EHG, and WHG were as different from each other as present-day Europeans and East Asians. But according to this map, two of the populations, WHG and EHG, seem much closer to each other than present-day Europeans and East Asians. (On the map, grayed out dots represent modern individuals, while colored dots represent ancient individuals.)
    1CAE8857-4A4D-4048-A4AA-81F7253EC700.png
    So my first question is, how can that make sense if those two populations are as different from each other as present-day Europeans and East Asians?

    My second question is, why exactly do EEF and WHG place differently on the map above vs the one below?
    70D96659-F20C-4126-88F5-6155BF8E6225.jpeg

    I also have questions concerning PCAs in general. What do the two dimensions, and the numbers on them, mean? What is the methodology behind producing PCA maps?

    Thanks.
    Did they say EHG and WHG were that distant, as that would be surprising?

    WHG and Basal-rich EEF, yes.
    WHG and ANE, yes to an extent, as both share drift with ENA.
    "the common ancestry of both MA1 and Loschbour with eastern non-Africans (drift non_African-->X)"

    But WHG and EHG are clearly related post LGM.

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    Reich and Lazaridis have indeed said that WHGs and EHGs are as distant as modern Europeans and East Asians.

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