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Thread: Using Eurogenes G25 as a PCA

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    Using Eurogenes G25 as a PCA

    Sometimes in all of the modeling, the great scaling wars, etc., it may get lost that Eurogenes G25 is a PCA with 25 dimensions. I know, a simple thought. I found it interesting to explore the dimensions with reference to this picture that is published in the online store for purchasing your PCA coordinates:

    Global_25_graphic.png

    What I've done is to plot me and my family members within the combination of PCA1 with each of the other 24 dimensions (as it seems this picture is doing). The picture has the "key" to the major groupings by dot color within the PCA groupings. I have said before that I feel the combination of the 25 dimensions has relatively subtle information contained about ancestry and that this is an excellent abstraction of one's autosomal DNA. Background for my family:

    Me: Look French because of my majority South German (around 75%) with some Isles and a little North German, actual French, etc. plus around 3% "spice" (see my parents). I am the "+" sign on the plots.
    Dad: All South German sources, but has many Ashkenazi, as well as Russian and Finnish matches on Gedmatch with admixture consistent with that type of heritage in minor form (maybe 5% to 7%???). He is the "X" sign on the plots.
    Mom: Looks French or Belgian from a little over half South German/French Heritage and a little under half Isles plus some North German. Seems to have some mixed South Asian/Amerindian/African ancestry typical of colonial Americans (about 2%???). My mom is the "O" on the plots.
    Wife: Looks French/Belgian/Dutch from a little over half Isles ancestry combined with pretty mixed West German, French, North German continental ancestry. Has a known Jewish g-g-g grandmother on her mother's side and her father seems also to have Jewish ancestry (see below). My lovely wife is the "diamond" on the plots.
    Father in law: Very NW Euro with lots of Welsh, English, Irish, Scottish, North German ancestry. Also has West German and French ancestors. Has two lines of stated Amerindian ancestry (a lot of it is hanging around with African as far as chromosomal location) and rather obvious African segments in his admixture. Also discovered by one-to-one matching in Gedmatch, he has a lot of Jewish matches, I suspect through his North German g-g grandfather. In spite of this, he usually looks English with all of this other mixed stuff "pulling" him a little away. the other stuff seems to be maybe 5%-7%. He is the "triangle" on the plots.

    This panel makes a nice spread on some of the dimensions and some of the minor "pulls" can be seen, too.

    I am using the ".dat" file that David supplies and doing simple X/Y mapping in Past3. I am not planning to map everyone else's on this one, as it is very simple to do, but if you want to post your results, feel free to participate!

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  3. #2
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    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.
    PC2 - Sardinians/Neolithic farmers, etc. at one extreme and East Asians (like Han, Ami, etc.) at the other. From top to bottom, respectively.

    PC1+PC2.png

    Notice my father in law's (the triangle) slight pull away from the pack towards the middle of the "Africa/Asia" legs of the plot, almost splitting the difference. My father (the plus sign) has something similar going on, but is pulled towards Asia more. The rest of us aren't too distinct in this dimension.
    Last edited by randwulf; 05-04-2019 at 01:28 PM.

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    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.
    PC3 - European Hunter/Gatherers at one extreme and Sahul (like Papuans, Australians etc.) at the other. From top to bottom, respectively.

    PC1+PC3.png

    We all are fairly similar in this one, except my father in law (the triangle) wants to pull towards the "north" and the African tugs at him, too, to the left.
    Last edited by randwulf; 05-04-2019 at 01:29 PM.

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    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.
    PC4 - Sahul (like Papuans, Australians etc.) at one extreme and various Levant/SW Asian references at the other. From top to bottom, respectively.

    PC1+PC4.png

    My mom (the "O"), the only one of us that doesn't seem to have a Levant component to her admixture is the anchor point. My wife (the diamond) has the strongest/clearest pull towards the bottom of the graph. She always models pretty easily with some Ashkenazi, whereas the mixtures of the rest of us sometimes get in the way. Interestingly, doing an "evil twin" on Gedmatch shows my wife not inheriting her father's two largest SSA segments, for the most part and she also didn't get several of his Amerindian and Siberian segments. I think it makes her primary non-European admixture a little easier for the modeling tools to pick out.
    Last edited by randwulf; 05-04-2019 at 01:32 PM.

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    Fourth 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.
    PC5 - A very interesting dimension. Sahul (like Papuans, Australians etc.) and Southeast Asians (spreading out the East Asian red dots quite a bit) along with European Hunter Gatherers at one extreme and various Polar/Siberian/some Amerindian (also causing quite a spread) references at the other. From top to bottom, respectively. The combination of PC1 with this dimension causes two "branches" to form in the upper part of the graph separating the Sahul/SE Asians from the European Hunter Gatherers.

    PC1+PC5.png

    We bunch pretty tightly on this one with the usual father in law (triangle) and father (plus sign) separating from the pack just a little in appropriate directions for them.
    Last edited by randwulf; 05-04-2019 at 01:52 PM.

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    Fifth 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.
    PC6 - South and Southeast Asians, but not vastly differentiated from much of Eurasia, at one extreme and very distinct differentiation of Sahul references at the other. From top to bottom, respectively. The combination makes for a fairly flat left to right line with a Sahul "leg" to the plot.

    Attachment 30291

    We are pretty tightly bunched on this one with father in law (triangle) and father (plus sign) separating a little and my mom (the "O") providing a "least non-European admixed" anchor point to the rest of us from which to swing (she does this a fair amount in these plots).
    Last edited by randwulf; 05-04-2019 at 11:26 PM.

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    Quote Originally Posted by randwulf View Post
    I am not planning to map everyone else's on this one, as it is very simple to do, but if you want to post your results, feel free to participate!
    Sounds like a good idea and It will be interesting to see other people's results. However due to being the 'Dumber' of 'Dumb and dumber' I won't be sharing mine or my father's ! Would probably have turned out Isles with a splash of Scandinavian/Nordic anyway.
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    Sixth 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.
    PC7 - Archaic African (like San), at one extreme and South Amerinds at the other. From top to bottom, respectively. This second dimension produces a "hill" on the left side of the plot with Africans that separate from the pack and a "valley" on the right side with Amerinds and some Siberians that separate from the pack.

    PC1+PC7.png

    We plot in a fairly straight line on this one based on our various PC1 values and not too much pull between Archaic African and Amerind.

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    Quote Originally Posted by randwulf View Post
    Fifth 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.
    PC6 - South and Southeast Asians, but not vastly differentiated from much of Eurasia, at one extreme and very distinct differentiation of Sahul references at the other. From top to bottom, respectively. The combination makes for a fairly flat left to right line with a Sahul "leg" to the plot.

    Attachment 30291

    We are pretty tightly bunched on this one with father in law (triangle) and father (plus sign) separating a little and my mom (the "O") providing a "least non-European admixed" anchor point to the rest of us from which to swing (she does this a fair amount in these plots).
    I am getting some bizarre results from the attachment. Trying again:

    PC1+PC6.png

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    Seventh 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.
    PC8 - SSA (Yoruba, Esan, Mandenka, etc. types) and mixed, of all things, with Siberians (like Nganassan, Yukagire,etc.) on one extreme and South and Central Amerinds at the other (but the "other extreme" quickly becomes a mix of North and Polar Amerinds along with maybe, more easterly Siberians plus Archaic Africans (like the San, Ju Hoan North, etc.!). From top to bottom, respectively. There isn't a great differentiation at the "top" (things stay pretty flat and driven by PC1), but the South Amerinds and Archaic Africans jump out of the bottom on both ends of the PC1-driven left to right line.

    PC1+PC8.png

    My family is pretty tight in a PC1-driven line, though my mother for once pulls away a little to the bottom from our pack. She does easily model with a little Amerind which she seems to have a bit of and maybe that causes this. Just a guess. I guess someone that was mixed Surui and San would map in the middle of nowhere on this picture!

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