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Thread: Program to Calculate Genetic Overlap/ Similarity to Asian Populations

  1. #1
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    Lightbulb Program to Calculate Genetic Overlap/ Similarity to Asian Populations


    Have you wandered how much your total admixture overlaps or is similar to other populations. I was, so I put together a program to calculate the member's total overlap with various populations reference zombies.

    Some tend to focus on only 1 admixture component when comparing with other population. For example, a European with 0% S. Asian may assume that he has no similarity with a S. Asian. We tend to forget that we have to add the overlaps from all admixture components to get an idea of similarity, and not just focus on the component that we typically associate with a particular population. My graphs will show that the total overlap between Europeans and S. Asians is about 20 %, and with Iranians/kurds it is around 60%.

    The steps taken to arrive at the results are as follows:

    1- I created reference zombies from the means of the various components for a population. For example the S. Asian zombie's admixture is the mean of the components for Sein, Sapporo, Varun, etc. The Iranian/Kurd zombie's admixture is the mean of the components for myself, DMXX, Jesus, etc.

    2- Each member's components were individually compared with the reference zombie's for overlap

    3- The component overlaps were totalled for each member

    4- The resulting spreadsheet was sorted and graphed.

    Here are the resuts for Eurogenes k9. Moving forward, I intend to incorporate this data into my community plots:


    Observations on SC Asian: Iranian/Kurds had about 70% overlap, and Europeans had about 25%

    [IMG][/IMG]

    Observations on S. Asian: Iranian/Kurds ~60% overlap. Europeans ~20%

    [IMG][/IMG]
    Last edited by Kurd; 02-24-2015 at 02:55 AM.

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  3. #2
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    Admixture Overlap with Iranians/Kurds

    Europeans had about a 25% overlap with Iranian/Kurd reference;

    [IMG][/IMG]

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  5. #3
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    This one shows a steep gradient from Europe to the Middle East and S. Asia. Not much difference between the Middle East and S. Asia. Both regions show only about a 25% overlap with European admixture.

    [IMG][/IMG]

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  7. #4
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    Percent Similarity to Mediterranean

    This graph shows the percent admixture overlap/similarity of the members to the Mediterranean zombie:

    [IMG][/IMG]

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  9. #5
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    Kurd,
    Looks great! Any chance you could throw me on too?

  10. #6
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    Quote Originally Posted by Chad Rohlfsen View Post
    Kurd,
    Looks great! Any chance you could throw me on too?
    You can go ahead and post your data here. I had to do another run of this anyway, since I wanted to add Zeph, Icebreaker, and a couple of others. I was a little short on Turks, and some other Middle Eastern ethnic groups.

    I would also like to take a moment and remind everyone that the accuracy of the zombies to a certain limit increases with greater number of participants. Although I had plenty of European participants, some of the references such as SC Asia, and Mediterranean where based on 2 members.

    This is not a problem when I start plotting calculators that have posted an adequate number of references in their population spreadsheets.

    It would be interesting to see whether the similarity graphs change substantially depending on the calculator used. I don't expect that to happen by much, however, I can take the similarity data from some of those calculators, and do similarity graphs based on averaging all of them.

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  12. #7
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    Turkey
    Population
    South Asian 5.30%
    Caucasus 40.11%
    Southwest Asian 11.36%
    North Amerindian + Arctic 0.42%
    Siberian 6.69%
    Mediterranean 18.75%
    East Asian 2.84%
    West African 0.24%
    North European 14.30%

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    Very interesting stuff.

    What you could do is take a GEDmatch calculator where the population averages are public (e.g. Dodecad K12b) and ask us to submit our results to you in a thread.

    That way, you'll get a lot more sample coverage for your zombies. You could also better define the zombies further at your discretion. There's a lot of fun tinkering around to be had with this idea and I'm certain you'll produce something informative either way!

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  16. #9
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    Updated S. Asian Similarity Graph

    Here is the updated S. Asian Overlap/Similarity graph with Zeph, Icebreaker, Misspissi, Salkin, and Jtom added. I will be uploading the remaining graphs a little later

    [IMG][/IMG]

    EDIT: Revised AdamYZ's data
    Last edited by Kurd; 02-25-2015 at 03:42 AM.

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  18. #10
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    Turkey Ottoman Empire Ottoman Empire 2
    Me
    Population
    South Asian 2.55%
    Caucasus 55.10%
    Southwest Asian 12.06%
    North Amerindian + Arctic -
    Siberian 2.89%
    Mediterranean 18.03%
    East Asian 2.23%
    West African 0.20%
    North European 6.93%

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