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Thread: PCA G25_scaled - Africans only (Users & Ancients/Modern Avgs)

  1. #521
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    Quote Originally Posted by Angoliga View Post
    Is that based on your observations using fstats? Please share, I'm curious



    Interesting! I wonder if some of their ancestry is derived from the colonial period (*presumably as British subjects during Railway construction?).
    There's quite a few families in and around removed towns in NW-Uganda; some going back >6 generations from the latter end of the 19th century.

    It can seem shocking at times hearing them speak our local dialects perfectly : )
    Yeah I'd say the majority is from the colonial period for sure! Outside of the coastal areas Mombasa etc that's usually when the South Asians arrived in these remote villages/towns as you know. Ditto on it being shocking, I remember the first time I saw an Indian gentleman in Jinja speaking fluent Lusoga...bear in mind its a trip seeing some of my own family speaking anything other than Swahili/Arabic/Balochi let alone this fella

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  3. #522
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    Quote Originally Posted by Angoliga View Post
    The issue is the excess East-African HG affinity; Sudanese7 shows 6.4% ETH_4500BP, so it can't possibly be more pristinely AEA. The same goes for the Anuak samples. I recall these HG-Affinities getting eaten-up with runs on Central-Sudanic samples.

    *We could tinker with the Dinka individuals vs. the avg though, to cross-check the purest AEA sample.
    Try replacing ETH_4500BP with ZAF_2000BP and UstIshim, if ZAF_2000BP and UstIshim is not present than we are probably seeing ETH_4500BP compensating for the West African in Dinka rather than actual ETH_4500BP admixture.

  4. #523
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    Quote Originally Posted by Mnemonics View Post
    Try replacing ETH_4500BP with ZAF_2000BP and UstIshim, if ZAF_2000BP and UstIshim is not present than we are probably seeing ETH_4500BP compensating for the West African in Dinka rather than actual ETH_4500BP admixture.
    That's not quite how it works with G25 cords, I think you might be thinking more on the lines of methods using ADMIXTURE?

    There's no way of distilling the embedded West-African affinities of these nilotic samples because West-African is already embedded within the available AEA-reference source-samples ("Dinka", "Sudanese", "Anuak").

    Even the purest Nilotic populations have substantial West-Central African ancestry which is level from ~ >20%; that would include the nilotes in these "Sudanese" samples which should've been correctly labeled as South-Sudanese. This deeper layer of West-African ancestry shouldn't be confounded with more recent regional IA Bantu ancestry in-and-around East-Africa. IMHO it's from episodic events no earlier than the dawn of the Neolithic Sub-pluvial/Wet-Holocene phase (touched on here in this thread).

    Swapping ETH_4500BP with ZAF_2000BP and UstIshim would just shift results for East-HG affinities to the other East-HG related sample; KEN_LSA.
    I include both "KEN_LSA" and "ETH_4500BP" source samples in these runs to distinguish East-HG related affinities of the Ethiopian-Highlands vs. the inner Great-Lakes/Rift Valley. One distinction of the two, is the more apparent minor basal SW-Asian affinity in Mota.

    That said, for open discussion, feel free to run results based on your own interpretations/preference of source-samples.

    Let me know if you'd like some references/runs/analogies to illustrate these afmd points, I can do so if warranted for more clarity, it'll just take a little time and I'm a bit lazy atm : )

    This is good discussion.


    Edit: Btw, which specific target sample did you want a run on?




    @drobbah @gihanga.rwanda

    ANA_(simulated) seems like a dud, not sure what to make of it since it's not teasing out paleolithic ANA's embedded SSA affinities in this MAR_EN run:

    Target: MAR_EN
    Distance: 2.9615% / 0.02961463
    59.6 Levant_Natufian
    35.0 ANA_(simulated)
    3.0 Anatolia_Barcin_N
    2.4 GEO_CHG


    Here's the same run using "MAR_Iberomaurusian" instead of "ANA_(simulated)":

    Target: MAR_EN
    Distance: 2.9323% / 0.02932326
    96.8 MAR_Iberomaurusian
    3.2 Anatolia_Barcin_N
    Last edited by Angoliga; 10-23-2020 at 04:31 AM. Reason: Thread reference added for embedded West-African in Proto-AEA pops. Target sample asked
    .... .. I have spoken."

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  6. #524
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    Quote Originally Posted by Angoliga View Post
    That's not quite how it works with G25 cords, I think you might be thinking more on the lines of methods using ADMIXTURE?

    There's no way of distilling the embedded West-African affinities of these nilotic samples because West-African is already embedded within the available AEA-reference source-samples ("Dinka", "Sudanese", "Anuak").

    Even the purest Nilotic populations have substantial West-Central African ancestry which is level from ~ >20%; that would include the nilotes in these "Sudanese" samples which should've been correctly labeled as South-Sudanese. This deeper layer of West-African ancestry shouldn't be confounded with more recent regional IA Bantu ancestry in-and-around East-Africa. IMHO it's from episodic events no earlier than the dawn of the Neolithic Sub-pluvial/Wet-Holocene phase (touched on here in this thread).

    Swapping ETH_4500BP with ZAF_2000BP and UstIshim would just shift results for East-HG affinities to the other East-HG related sample; KEN_LSA.
    I include both "KEN_LSA" and "ETH_4500BP" source samples in these runs to distinguish East-HG related affinities of the Ethiopian-Highlands vs. the inner Great-Lakes/Rift Valley. One distinction of the two, is the more apparent minor basal SW-Asian affinity in Mota.

    That said, for open discussion, feel free to run results based on your own interpretations/preference of source-samples.

    Let me know if you'd like some references/runs/analogies to illustrate these afmd points, I can do so if warranted for more clarity, it'll just take a little time and I'm a bit lazy atm : )

    This is good discussion.


    Edit: Btw, which specific target sample did you want a run on?




    @drobbah @gihanga.rwanda

    ANA_(simulated) seems like a dud, not sure what to make of it since it's not teasing out paleolithic ANA's embedded SSA affinities in this MAR_EN run:

    Target: MAR_EN
    Distance: 2.9615% / 0.02961463
    59.6 Levant_Natufian
    35.0 ANA_(simulated)
    3.0 Anatolia_Barcin_N
    2.4 GEO_CHG


    Here's the same run using "MAR_Iberomaurusian" instead of "ANA_(simulated)":

    Target: MAR_EN
    Distance: 2.9323% / 0.02932326
    96.8 MAR_Iberomaurusian
    3.2 Anatolia_Barcin_N
    Ah I didn't remember that you had Kenya_LSA included. The Eastern HGs are very likely to be primarily AEA admixed with something ZAF_2000BP like which should be apparent if you remove Eastern HG sources I figured you might be able to test if it is legitimately Eastern HG-like by seeing if the algorithm wants ZAF_2000BP admixture into Sudanese7.

    I don't think Sudanese 7 has none of ancient West African affinity it just has less of the deeper layer than most of the other samples.

  7. #525
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    Quote Originally Posted by Angoliga View Post


    @drobbah @gihanga.rwanda

    ANA_(simulated) seems like a dud, not sure what to make of it since it's not teasing out paleolithic ANA's embedded SSA affinities in this MAR_EN run:

    Target: MAR_EN
    Distance: 2.9615% / 0.02961463
    59.6 Levant_Natufian
    35.0 ANA_(simulated)
    3.0 Anatolia_Barcin_N
    2.4 GEO_CHG


    Here's the same run using "MAR_Iberomaurusian" instead of "ANA_(simulated)":

    Target: MAR_EN
    Distance: 2.9323% / 0.02932326
    96.8 MAR_Iberomaurusian
    3.2 Anatolia_Barcin_N
    The ANA coordinate seems pretty good if you use the other simulated coordinates alongside it. The Natufian samples are between 15-20% ANA which is why the ANA is much lower than the runs below:

    Target: MAR_Taforalt
    Distance: 2.1718% / 0.02171846
    50.2 Proto-Natufian_(simulated)
    47.4 ANA_(simulated)
    1.6 Proto-CHG_(simulated)
    0.8 Proto-IranHG_(simulated)

    Target: MAR_EN
    Distance: 2.8548% / 0.02854832
    50.4 Proto-Natufian_(simulated)
    46.0 ANA_(simulated)
    2.0 Proto-CHG_(simulated)
    1.0 Anatolia-related_(simulated)
    0.6 Proto-IranHG_(simulated)

    Target: MAR_LN
    Distance: 3.2538% / 0.03253783
    55.4 Proto-Natufian_(simulated)
    17.4 Anatolia-related_(simulated)
    15.8 ANA_(simulated)
    7.8 WHG
    3.2 Proto-IranHG_(simulated)
    0.4 Sudanese
    Drobbah_scaled
    Target: Drobbah_scaled
    Distance: 1.2698% / 0.01269848 | ADC: 0.25x
    31.0 KEN_Pastoral_N
    26.4 KEN_Pastoral_N_Elmenteitan
    18.4 TZA_PN
    12.0 KEN_HyraxHill_2300BP
    10.6 KEN_Pastoral_IA

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