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Thread: Principal component and qpAdm analyses confirm European admixture in Chinchorro DNA

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    Principal component and qpAdm analyses confirm European admixture in Chinchorro DNA

    In the two latest posts on my blog, I have confirmed my 2015 discovery that a Chinchorro DNA sample from Chile dated to 3972–3806 BC contains 30% European admixture:

    Principal component analysis confirms European admixture in Chinchorro DNA

    qpAdm analysis confirms European admixture in Chinchorro DNA

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    Could you provide more details on the qpadm runs?
    - Outgroups
    - Quality of fits

    EDIT: Woops sorry, I've done too much reading today...missed that you did include outgroups. I think it's important that you add some West Eurasians to the outgroups to determine the precise source of ancestry. Pick the ones least likely to have directly contributed but are phylogenically important in distinguishing potential contributing sources. (Kostenki14, Satsurbila, Natufian, Iran_Neolithic, etc.)
    Last edited by Kale; 03-15-2017 at 06:17 AM.

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    You need some ancient West Eurasian outrgroups champ.

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  7. #4
    Quote Originally Posted by Generalissimo View Post
    You need some ancient West Eurasian outrgroups champ.
    It makes no sense to include Caucasoid populations as outgroups when one is trying to determine how much additional Caucasoid admixture there is in Amerindian samples.

  8. #5
    Quote Originally Posted by Kale View Post
    I think it's important that you add some West Eurasians to the outgroups to determine the precise source of ancestry. Pick the ones least likely to have directly contributed but are phylogenically important in distinguishing potential contributing sources. (Kostenki14, Satsurbila, Natufian, Iran_Neolithic, etc.)
    I've done a few analyses with some of the ancient Caucasoid populations included as outgroups. The results weren't significantly different from those obtained with them omitted.

    qpAdm isn't going to be able to discern exactly which Caucasoid population the additional Caucasoid admixture in the Chinchorro sample is from, at least not with the amount of data currently available.

    ADMIXTURE may be able to however. I've done some higher-resolution admixture analyses, and the only samples that have a pattern of Caucasoid components similar to the pattern in the Chinchorro sample are the pre-LGM Europeans. So I currently think that the European admixture in the Chinchorro sample is from western Aurignacians, western Gravettians, or Solutreans.

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    Quote Originally Posted by genetiker View Post
    I've done a few analyses with some of the ancient Caucasoid populations included as outgroups. The results weren't significantly different from those obtained with them omitted.

    qpAdm isn't going to be able to discern exactly which Caucasoid population the additional Caucasoid admixture in the Chinchorro sample is from, at least not with the amount of data currently available.

    ADMIXTURE may be able to however. I've done some higher-resolution admixture analyses, and the only samples that have a pattern of Caucasoid components similar to the pattern in the Chinchorro sample are the pre-LGM Europeans. So I currently think that the European admixture in the Chinchorro sample is from western Aurignacians, western Gravettians, or Solutreans.
    Those guys didn't really have red hair and other phenotype traits that (per your opinion) are evident in South American Indian mummies

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    Considering there is no uniparental overlap, and UP Europeans being further from Native Americans than all hunters; I'll just go out on a limb and say, fat chance.

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  14. #8
    Quote Originally Posted by Padre Organtino View Post
    Those guys didn't really have red hair and other phenotype traits that (per your opinion) are evident in South American Indian mummies
    The Chinchorro mummies have brown and chestnut hair, and it's not clear what their skin color was. Only mummies from later Peruvian and Chilean cultures have red and blond hair and white skin.

  15. #9
    Quote Originally Posted by Chad Rohlfsen View Post
    Considering there is no uniparental overlap, and UP Europeans being further from Native Americans than all hunters; I'll just go out on a limb and say, fat chance.
    None of that has any bearing on what the results for the Chinchorro sample are.

    There aren't any Australoid uniparental markers in South American Indians, and yet no one has any problem with the idea that Australoids were in South America thousands of years ago. It's only the idea that Europeans were in South America thousands of years ago that everyone for some reason regards as heresy.

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    Quote Originally Posted by genetiker View Post
    None of that has any bearing on what the results for the Chinchorro sample are.

    There aren't any Australoid uniparental markers in South American Indians, and yet no one has any problem with the idea that Australoids were in South America thousands of years ago. It's only the idea that Europeans were in South America thousands of years ago that everyone for some reason regards as heresy.
    The reason is that only one of these ideas has statistical backing, and it isn't yours. They threw out any UP connection completely with the comparison of UP Euros and MA-1.

    Edit: I still think it is a confounding issue in there somewhere with the Onge, but I haven't taken time to really look at it. Let's keep to the issue at hand though.
    Last edited by Chad Rohlfsen; 03-16-2017 at 02:30 AM.

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