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Thread: Is this North Caucasian and North Sea in K36 "real"?

  1. #1
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    Is this North Caucasian and North Sea in K36 "real"?

    Modern Native Ecuadorian (kit A521022, uploaded by Marwin from Quito):

    Population
    Amerindian 86.04
    Arabian 0.15
    Armenian 0
    Basque 0
    Central_African 0
    Central_Euro 0.41
    East_African 0
    East_Asian 0.83
    East_Balkan 0
    East_Central_Asian 0
    East_Central_Euro 0
    East_Med 0
    Eastern_Euro 0
    Fennoscandian 0.41
    French 0
    Iberian 0.48
    Indo-Chinese 0
    Italian 0
    Malayan 0
    Near_Eastern 0
    North_African 0
    North_Atlantic 0
    North_Caucasian 1.82
    North_Sea 1.91

    Northeast_African 0
    Oceanian 0.42
    Omotic 0
    Pygmy 0
    Siberian 6.35
    South_Asian 0.57
    South_Central_Asian 0
    South_Chinese 0.55
    Volga-Ural 0
    West_African 0.07
    West_Caucasian 0
    West_Med 0

    This modern Native Ecuadorian (he is at least ~94% Native in K36) scores 1.82% North_Caucasian and 1.92% North Sea. This is very interesting because two of 7 Pre-Columbian Chachapoya samples - NA47 and NA50 - also score North Caucasian and North Sea. But they are poor quality samples. And 5 other ancient Chachapoya samples (NA39, NA40, NA41, NA42, NA43) do not score these two admixtures.

    Chachapoya samples:

    http://www.y-str.org/p/ancient-dna.html

    I uploaded these Chachapoya samples on GEDmatch (I added no-calls to increase file sizes, but Admixture results are exactly the same with no-calls as without them):

    With no-calls:

    Z429545 NA39 ancient Peru ~1250 AD
    Z206602 NA40 ancient Peru ~1250 AD
    Z425019 NA41 ancient Peru ~1250 AD
    Z581272 NA42 ancient Peru ~1250 AD
    Z686312 NA43 ancient Peru ~1250 AD
    Z933319 NA47 ancient Peru ~1250 AD
    Z636374 NA50 ancient Peru ~1250 AD
    Z661857 Peru Ancient (all 7 Merged)

    Without no-calls:

    Z656658 NA40 ancient Peru 1000-1500 AD
    Z713184 NA42 Chachapoya 1000-1500 AD
    Z582576 Ancient Peru (Merged)

    NA50 scores 26.44% North Caucasian and 13.18% Pygmy (as well as 60.38% Amerindian) and NA47 scores 11.21% North Sea and 7.49% South Asian (as well as 81.30% Amerindian).

    Do you think this is due to very poor quality of these samples? But in such case, why does a modern Native Ecuadorian who tested with 23andMe also score these admixtures?

    Average for 5 ancient Chachapoyas (without NA47 and NA50):

    Population
    88.7066666667 Amerindian
    0 Arabian
    0 Armenian
    0 Basque
    0.195 Central_African
    0 Central_Euro
    0.9433333333 East_African
    0 East_Asian
    0 East_Balkan
    0 East_Central_Asian
    0 East_Central_Euro
    0 East_Med
    0.495 Eastern_Euro
    0 Fennoscandian
    0 French
    0 Iberian
    3.585 Indo-Chinese
    0 Italian
    0 Malayan
    0 Near_Eastern
    0 North_African
    0 North_Atlantic
    0 North_Caucasian
    0 North_Sea

    0 Northeast_African
    0.0266666667 Oceanian
    0 Omotic
    0.475 Pygmy
    4.075 Siberian
    0.2216666667 South_Asian
    0 South_Central_Asian
    0 South_Chinese
    0.6233333333 Volga-Ural
    0.6466666667 West_African
    0 West_Caucasian
    0 West_Med

    Average for all 7 ancient Chachapoyas (including NA47 and NA50):

    Population
    84.24 Amerindian
    0 Arabian
    0 Armenian
    0 Basque
    0.14625 Central_African
    0 Central_Euro
    0.7075 East_African
    0 East_Asian
    0 East_Balkan
    0 East_Central_Asian
    0 East_Central_Euro
    0 East_Med
    0.37125 Eastern_Euro
    0 Fennoscandian
    0 French
    0 Iberian
    2.68875 Indo-Chinese
    0 Italian
    0 Malayan
    0 Near_Eastern
    0 North_African
    0 North_Atlantic
    3.305 North_Caucasian
    1.40125 North_Sea

    0 Northeast_African
    0.02 Oceanian
    0 Omotic
    2.00375 Pygmy
    3.05625 Siberian
    1.1025 South_Asian
    0 South_Central_Asian
    0 South_Chinese
    0.4675 Volga-Ural
    0.485 West_African
    0 West_Caucasian
    0 West_Med
    Last edited by Tomenable; 05-08-2017 at 06:50 PM.

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     Angoliga (05-08-2017),  lukaszM (05-08-2017),  parasar (05-08-2017)

  3. #2
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    No it's rather Euro admix in Ecuadorian, it's obvious. I don't mind poor qualitiy ancient samples. This is the reason why author of y-str.org didn't upload them. We could check those poor quality ancients for curiosity but building some historical conception with their results in gedmatch?

    You know what Polako thinks about Genetiker analysis?

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    Quote Originally Posted by lukaszM View Post
    No it's rather Euro admix in Ecuadorian, it's obvious.
    This Ecuadorian has 5.03% Euro-like admix:

    North_Sea 1.91
    North_Caucasian 1.82

    Iberian 0.48
    Central_Euro 0.41
    Fennoscandian 0.41

    And if we extrapolate this to 100%, we get:

    North_Sea 37.97
    North_Caucasian 36.18

    Iberian 9.54
    Central_Euro 8.15
    Fennoscandian 8.15

    This doesn't look like Iberian admixture at all.

    Did recombination distort these proportions?

    ===========================

    He also has some South_Asian and Arabian.

    This could be from European ancestry too.
    Last edited by Tomenable; 05-08-2017 at 07:57 PM.

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    Quote Originally Posted by lukaszM View Post
    This is the reason why author of y-str.org didn't upload them.
    Five of them are actually not so bad.

    But NA50 and NA47 are of exceptionally bad quality (lowest coverage / SNP count of all Chachapoya samples). Check my thread "List of ancient samples on GEDmatch", people uploaded such samples too.

    Quote Originally Posted by lukaszM View Post
    You know what Polako thinks about Genetiker analysis?
    I know.
    Last edited by Tomenable; 05-08-2017 at 07:58 PM.

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     TheDragon (06-29-2019)

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    Quote Originally Posted by Tomenable View Post
    This Ecuadorian has 5.03% Euro-like admix:

    North_Sea 1.91
    North_Caucasian 1.82

    Iberian 0.48
    Central_Euro 0.41
    Fennoscandian 0.41

    And if we extrapolate this to 100%, we get:

    North_Sea 37.97
    North_Caucasian 36.18

    Iberian 9.54
    Central_Euro 8.15
    Fennoscandian 8.15

    This doesn't look like Iberian admixture at all.

    Did recombination distort these proportions?

    ===========================

    He also has some South_Asian and Arabian.

    This could be from European ancestry too.
    But I saw it in other mixed person with very low exotic admix. In such cases frequencies are not reflection of ancestral proportions but they are random. Among Phillipino kits for example I found many times higher Basque and West-Med than Iberian.

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     Tomenable (05-08-2017)

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