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Thread: Using Eurogenes G25 as a PCA

  1. #21
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    Eighteenth plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC19 - This one separates Africans and Polar/Siberian admixture groups within the respective groups, with the Eskimos/Itelman and then Dinka/Ethiopians/Sudanese at the top to the Ju Hoan North and Iberomaurusians at the bottom. There is some separation within the other groups, but these two general types are separated the most. The effect of PC1 pulls the two affected groups to opposite ends of the plot making it wider at the ends, more or less.

    PC1+PC19.png

    My family group has some interesting slight separation on this dimension, almost forming a line top to bottom with the PC1 distorting the line side to side. My father ends up on the lowest end, though about the same as my father in law with my mother pulling the most towards the top. I believe we all are impacted on it by the kinds of minor Asian and African influences we have.

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     JonikW (06-04-2019)

  3. #22
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    Nineteenth plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC19 - Almost all of the basic groups separate top to bottom. The topmost extremes are various European Hunter Gatherers. On the bottom are Iranian Neolithics, some kinds of Siberians (like Yakut, Mari), and some south Asians (like Brahui, Balochi).

    PC1+PC20.png

    My family is spread along this dimension, as well. My father is pulled towards the top and my father in law to the other. This is similar to some of the other later dimensions. I fall between my parents. My wife plots very similarly to my mother on this one.

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     JonikW (06-04-2019)

  5. #23
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    Quote Originally Posted by randwulf View Post
    Nineteenth plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC19 - Almost all of the basic groups separate top to bottom. The topmost extremes are various European Hunter Gatherers. On the bottom are Iranian Neolithics, some kinds of Siberians (like Yakut, Mari), and some south Asians (like Brahui, Balochi).

    PC1+PC20.png

    My family is spread along this dimension, as well. My father is pulled towards the top and my father in law to the other. This is similar to some of the other later dimensions. I fall between my parents. My wife plots very similarly to my mother on this one.
    Note: This one actually should be PC20....I noticed my mistake too late to edit it.

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     JonikW (06-04-2019)

  7. #24
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    Twentieth plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC21 - The top is dominated by European Hunter Gatherers and the most extreme at the bottom are two Ju Hoan North references. There are several groups represented at the bottom above the Ju Hoan North references that are split by PC1 from right to left, including Iberomaurusians, ancient Russian and Mongolian references, and some Siberians/East Asians, such as Tubalar and Shor.

    PC1+PC21.png

    My family splits on this dimension, too. My father and I pull towards the bottom and my wife and father in law towards the top. My mother is in a middle spot in the group. The placement somewhat looks like our northern to southern European tendencies in admixture tests, with me and my father the most "southerly" and my father in law and wife more "northerly" with my mom somewhat split between the two. I am thinking that has the most influence on our placements in this dimension.

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     JonikW (06-04-2019)

  9. #25
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    Twenty first plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC22 - The top are Ket, Yakut, and Selkup references. As outliers on the bottom are the Iberomaurusians and MAR_EN references then dominated by Eskimos, Itelman, Koryak, and Yukagir references. Other north Africans soon join the mix from the bottom and their is a fair spread of East Asians and Amerinds, too.

    PC1+PC22.png

    Some nice differentiation of the family occurs on this dimension after adjusting the eyes for the PC1 left to right differentiation, we form something of a line top to bottom with my father in law, wife, me, father, and mother.

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     JonikW (06-04-2019),  timberwolf (05-31-2019)

  11. #26
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    Twenty second plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC23 - The top are ancient Moroccans, Early Neolithic and Iberomaurusians followed by Siberians like the Ket and Selkup. The other extreme has European Hunter-Gatherers and the Mari.

    PC1+PC23.png

    Me, my father, and my mother plot very close to each other on this dimension and my wife and her father are lower in the graph and somewhat close to each other.

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     JonikW (06-04-2019)

  13. #27
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    Twenty third plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC24 - The top are a mix of ancient Steppe-infused references along with Eskimos/Greenlanders/Itelman references and these aren't strongly separated from the pack, just a bit of a peak. The other extreme has European Hunter-Gatherers and there is a fairly strong separation.

    PC1+PC24.png

    My family forms two groups on this dimension. We aren't strongly differentiated. My father, father in law, and wife are slightly over the middle of the majority up/down and my mother and I are pulled slightly below that same middling line one could draw using PC1 left to right.

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     JonikW (06-04-2019)

  15. #28
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    Twenty fourth (and the last!) plot:

    PC1 - SSA (like Biaka) at one extreme and various northern tier Europeans (like Balts, Irish, Russians, etc.) at the other extreme. It is left to right on the plot.
    PC25 - It seems that all the Asian groups separate somewhat on this dimension. The very top are a mix of Eskimo, Greenlander, Mlabri/Malyasian/Thai southeast Asians and then Tripuri/Jamatia south Asians. There are a few Sherpa in there, too. Towards the bottom are a mix of east Asians, especially the Igorot.

    PC1+PC25.png

    On this one, my wife and I plot almost the same with my father in law pulled to the left by PC1 differences, but otherwise about the same level. My father is attracted towards the top and my mother pulled towards the bottom a bit.

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  17. #29
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    I noticed while I was posting (and commented a couple of times), that it appeared that some of the outliers seem to have been purged from the G25 references, making some slight changes to the shapes of some of the dimensions. Another thing I noticed is that Past3 was making the two axes "equal" in the plotting to make the pleasing shape. But, the actual numbers are used by the modeling tools, so I thought of posting the raw plots, since Past3 offers an option to do this. I also thought of posting unscaled and scaled, so the differences can be seen in a visual form. The family continues with the same symbols, I am +, my father is an X, my mother an O, my wife is the diamond, and my father in law the triangle.

    PC1 + PC2 with the newest values:

    PC1+PC2b.png

    unscaled raw:

    PC1+PC2eaus.png

    scaled raw:

    PC1+PC2easc.png
    Last edited by randwulf; 06-06-2019 at 11:35 AM.

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  19. #30
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    PC1 + PC3 updated:

    PC1+PC3b.png

    unscaled raw:

    PC1+PC3eaus.png

    scaled raw:

    PC1+PC3easc.png

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