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Thread: Using Eurogenes G25 as a PCA

  1. #11
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    Eighth 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.
    PC9 - Iberomaurusians (the few light brown dots at the top sort of center) at one extreme and the single CHG sample (bottom almost right) by itself at the other. From top to bottom, respectively. Other North and East African samples are attracted towards the top and Caucasian, Near East, and Central Asian pull towards the bottom. A lot of the other groups spread out quite a bit on this dimension, interestingly. Also, it causes an arch to form when combined with PC1.

    PC1+PC9.png

    My family also is pulled on the PC9 dimension with my father in law (the triangle) pulled lowest and me (the plus sign) towards the top. I am not quite how to interpret this one with many of the groups stretching along PC9. It seems to be providing some interesting differentiation, though.

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     JonikW (05-07-2019),  Koolmets21 (05-07-2019)

  3. #12
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    Ninth 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.
    PC10 - Iberian Neolithics grading into other low-steppe references at one extreme and East Africans quickly mixed with high-steppe references at the other. From top to bottom, respectively. Mixed with PC1 creates high sides with a valley in the middle and somewhat of a no-man's land between East Africans and North Africans.

    PC1+PC10.png

    This creates some nice differentiation within my family group with me pulled to the Neolithic references at the top and my father in law pulled towards the steppe at the bottom. The rest of the family forms a line top to bottom with relation to this neolithic-steppe line pulled left-right by the PC1. It is an interesting dimension.
    Last edited by randwulf; 05-08-2019 at 12:26 PM.

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  5. #13
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    Tenth 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.
    PC11 - Specifically the Nganassan Siberians at the most extreme at the top merging into other Siberians and, of all things, southeast Asians (like Vietnamese, Malaysians, etc.) causing two legs to form in the upper part and at the other end are other kinds of East Asians, such as Japanese, Koreans, and various Chinese. It also spreads out the South Asians somewhat, as well as Sahul, but doesn't impact the more western Eurasians, Africans, and Amerinds much.

    PC1+PC11.png

    For my family, there is some good differentiation in this dimension, too. It is a bit hard to interpret why, I guess, but my father is pulled to the Siberians the most, which is typical. Other than that, I don't have any other definite observations. We all have some various Asian minor input from different kinds of sources, so it seems this may be helping sort that out in some way.

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  7. #14
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    Eleventh 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.
    PC12 - This one has changed shape since the release that recently removed the Mbuti from the data set. Rather than start over, I will say that the below picture shows the data set as it existed prior to that removal with the Mbuti at the top and the Biaka at the bottom. In the current data set, the East Africans take over the top, but not by very much and the Biaka still exist separated from the pack at the bottom.

    PC1+PC12.png

    This one doesn't cause much differentiation in my family. We do tend to have some minor African from different sources, but not enough to change the PC1 strong pull and we kind of line up according to our PC1 values with just a little up/down off that line.

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  9. #15
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    Twelfth 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.
    PC13 - This is another one that has changed shape since the release that recently removed the Mbuti from the data set. Again, I will say that the below picture shows the data set as it existed prior to that removal with the Mbuti at the top and the Natufian and Biaka at the bottom. In the current data set, CHG takes over the very top (it is high in my picture too, more to the right side of the plot), but not by very much and the Natufian and Biaka still exist at the bottom. It pulls several of the population groups apart in interesting ways. For example, the southwest Asians pull towards the top and the north and east Africans towards the bottom.

    PC1+PC13.png

    This one does cause some interesting differentiation within my family group. The three of us that show the most "Levant" admixture (my wife, father in law, and father) are pulled towards the top away from me (in the middle between my parents) and my mother, who shows very low southwest Asian admixture in most tests.
    Last edited by randwulf; 05-14-2019 at 01:41 PM.

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  11. #16
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    Thirteenth 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.
    PC14 - This dimension primarily separates the Siberians. On the top side are the Yakut and Sakha. On the lower side are the Ket and Selkup. The Amerinds and Europeans that are Siberian-influenced spread along this dimension, too. Other general groups spread a bit, but not as much.

    PC1+PC14.png

    My family seems influenced by the dimension with my mom and I pulling to towards the top and the others the lower direction.
    Last edited by randwulf; 05-16-2019 at 02:07 PM.

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  13. #17
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    Fourteenth 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.
    PC15 - On the upper side are the Iberomaurasians and mostly European and Anatolian Neolithic individuals on the lower side. Many of the other population groups also spread out on this dimension.

    PC1+PC15.png

    This dimension causes some interesting groupings of my family on the plot. My wife and I are very near each other (nice!). My parents plot close to each other. My father in law is pulled towards the top away from the rest. I am not sure why that happens, but it doesn't happen much in the other dimensions, so this must be describing something. My parents both have a lot of South German, my wife and I are French/Belgian looking mixes between Germany and the Isles, and my father in law is majority Isles. So, maybe that causes the groupings (my best guess!).

  14. #18
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    Fifteenth 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.
    PC16 - On the upper side are the European Hunter-Gatherers (Rochedane is the very highest) mixed with various Neolithic Iranians (such as Ganj Dareh references) and lower side has Iberomaurusians, San-type Africans, and some South Asians, such as the Paniya. Many of the other population groups also spread out on this dimension.

    PC1+PC16.png

    My family gets a pretty good divide on this one, too. My wife and I plot close to each other and I am about halfway between my parents (the + between the X and O). My father in law is the lowest on the plot on the 16th PCA.

  15. #19
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    Sixteenth 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.
    PC17 - Another dimension that spreads several of the groups up/down on the graph in interesting ways. At the top, the most extreme includes some archaic African types (Ju Hoan North) and eastern Africans, then joined by (on the other side of the graph because of PC1) neolithic central to eastern Europeans. Also, some kinds of south Asians, such as Paniya, Datog, etc. On the other extreme of this dimension after discounting the single, now-not-included African reference at the bottom, are some Brahmins and Arabs, quickly joined, of all things, by some ancient steppe references. Actually, all of the various population groups do some spreading on this dimension, somewhat like the prior few.

    PC1+PC17.png

    For my family, all of us get some differentiation on this one, but my father and father in law really separate. My father is towards the top of the European group and my father in law towards the bottom. In any overall plotting, they are the two "terminal" plots for our group of five, with my father having the majority south German ancestry and my father in law the majority very northwestern European version of English/Irish/Scottish and the rest of us falling in line between them. Somehow, I believe this dimension is accentuating that difference.

  16. #20
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    Seventeenth 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.
    PC18 - This one separates Africans, with the Ju Hoan North/Archaic Africans at the top to the Iberomaurusians at the bottom. The rest of the population groups don't separate too much and form a somewhat straight line to the right away from the Africans.

    PC1+PC18.png

    My family group mostly forms a "PC1" dominated line on this dimension, though my father pulls a little to the top and my father in law pulls a little to the other direction.

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