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Thread: Reconciling the claimed West-African ancestry in certain Great Lakes clans

  1. #21
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    Last edited by SWAHILLI_PRINCE16; 07-29-2020 at 10:09 AM.
    23andMe

    96.3% Sub-Saharan African
    96.3% Congolese & Southern East African
    95.9% Southern East African
    0.4% Angolan & Congolese

    3.4% Central & South Asian
    3.4% Central Asian, Northern Indian & Pakistani
    3.4% Central Asian

    0.3% Unassigned

  2. #22
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    Quote Originally Posted by gihanga.rwanda View Post
    Thank you for this useful information! I think you’re right about the age of some of this gene flow . I wonder if the Indian/Pakistani/Persian ancestry is older than a lot of the Peninsular Arab ancestry, which might have been mediated by Oman.

    In the study I linked, the Arabian ancestry in Anjouan is dated to around the time of Oman’s ascendance as a regional power. It’s interesting that the Swahili from other Comorian islands lacked this same admixture. The Comorians are a very interesting group; I wonder if they received historical Malagasy ancestry or were originally Malagasy but later Swahilized? Not surprisingly, Bantu speakers are suspected to have island hoped from the mainland through the Comoros to Madagascar.

    Comorians from Anjouan result from a second admixture event between a Swahili group (Swahili from Mombasa: 74%) and a Middle Eastern group (UAE Dubai Arab: 26%) around 459 YBP (95% CI: 35–673 YBP).
    swahili genetics.PNG

    This chart might be of your interest

    Source >>
    The Persian & Arab admixture is older because of historical trade links, the South Asian is probably more recent. However, I could be wrong I'm basing this on the historical timeline.
    Last edited by SWAHILLI_PRINCE16; 07-29-2020 at 10:24 AM.
    23andMe

    96.3% Sub-Saharan African
    96.3% Congolese & Southern East African
    95.9% Southern East African
    0.4% Angolan & Congolese

    3.4% Central & South Asian
    3.4% Central Asian, Northern Indian & Pakistani
    3.4% Central Asian

    0.3% Unassigned

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  4. #23
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    Genetic drift analysis via Ancestry

    Screenshot_2020-07-28_16-42-36.pngScreenshot_2020-07-28_16-43-33.png

    Increased from a max of 18% (23andme) to 21% (Ancestry). Combined should be interesting cuz some homozygous allele sharing between myself and Yoruba/WA are missing in the Ancestry file. Interestingly, the max range of African ancestry via Ancestrydna is 18%, in keeping with the original 23andme SAPDA analysis. Likelihood=/=reality in my case, where Ancestry give me a likelihood of 8%, but still the range feature is a lot better than 23andme. S/o to them for keeping that feature. Its just grating cuz max likelihood erases my father's tropical ancestry.

    Some distances from the new file. Made a Luo/Yoruba ghost just to see:

    Distance to: yammington
    0.07785235 yorubaluo
    0.08007734 Laka:T_Laka-1.DG
    0.08034544 Cameroon_Bafut:TK-KVBAF045
    0.08060099 Cameroon_Bafut:TK-KVBAF012
    0.08067125 Ngumba:T_Ngumba-1.DG
    0.08069157 Cameroon_Mbo:CAM-MBO-083
    0.08075927 COG_Kindoki_230BP:KIN004
    0.08079301 Laka:T_Laka-2.DG
    0.08093417 Lemande:S_Lemande-2.DG
    0.08103931 Luo:Ayodo_423C
    0.08104092 Bantu_S.W.:KSP203
    0.08104480 Mada:T_Mada-2.DG
    0.08104622 Bantu_S.W.:KSP201
    0.08116489 Kongo:S_Kongo-2
    0.08120948 Tikar_South:T_Tikar_South-2.DG
    0.08122192 Luo:Ayodo_502C
    0.08135625 Cameroon_Aghem:TK-KVWUM020
    0.08135865 Cameroon_Aghem:TK-KVWUM025
    0.08137782 Cameroon_Mbo:CAM-MBO-093
    0.08142248 Kaba:T_Kaba-2.DG
    0.08156010 Kaba:T_Kaba-1.DG
    0.08160025 Cameroon_Aghem:TK-KVWUM028
    0.08170312 Bantu_S.W.:KSP198
    0.08181180 Luo:Ayodo_438C
    0.08197872 Cameroon_Aghem:TK-KVWUM008
    0.08227138 Lemande:S_Lemande-1.DG
    0.08444762 Cameroon_Bafut:TK-KVBAF081
    0.08447728 Cameroon_Mbo:CAM-MBO-040
    0.08454703 Cameroon_Mbo:CAM-PYKL-047
    0.08460437 Cameroon_Aghem:TK-KVWUM005
    0.08463173 Cameroon_Mbo:CAM-MBO-010
    0.08467414 Cameroon_Aghem:TK-KVWUM026
    0.08474586 Cameroon_Aghem:TK-KVWUM011
    0.08476220 Cameroon_Mbo:CMF-BAK-022
    0.08478372 Mende_Sierra_Leone:HG03052
    0.08482458 Cameroon_Aghem:TK-KVWUM007
    0.08492609 Mandenka:HGDP00912
    Last edited by ThaYamamoto; 07-30-2020 at 02:18 AM.

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  6. #24
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    Reminder for self to update when I have time - will edit.

  7. #25
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    As this has become a kinda personal thread I've been working on some 3D PCAs this tha only one I got saved right now:
    Last edited by ThaYamamoto; 09-12-2020 at 02:08 AM. Reason: more angles soon come

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  9. #26
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    Aite so the default angle, a 2D angle and default at 1,2,4. I did get a great vertical by flipping the PCs but it crashed. Seems too intensive for my laptop. All individuals except for those tagged are the Egyptian individuals from the G25 - I didn't want to use high ANA folks for obvious reasons except user Amhas who should be 25-27% tropical African from my calculations.

     






    If anyone wants to recreate it for validity hmu and I'll send tha code.

  10. #27
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    Quote Originally Posted by ThaYamamoto View Post
    Aite so the default angle, a 2D angle and default at 1,2,4. I did get a great vertical by flipping the PCs but it crashed. Seems too intensive for my laptop. All individuals except for those tagged are the Egyptian individuals from the G25 - I didn't want to use high ANA folks for obvious reasons except user Amhas who should be 25-27% tropical African from my calculations.

     






    If anyone wants to recreate it for validity hmu and I'll send tha code.
    There's no way Amhas has 20-27% African ancestry.Looking at the way he plots, he's probably in the 13-18% range depending on the admixture model.

  11. #28
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    Quote Originally Posted by drobbah View Post
    There's no way Amhas has 20-27% African ancestry.Looking at the way he plots, he's probably in the 13-18% range depending on the admixture model.
    How you figure? 47% of Iberomaurusian=ANA=SSA-like particularly on PCAs for the time being, we know this from tha Shum Laka paper. Amhas 11% Yoruba/Dinka, 30% Iberomaurusian.. 15+11=26. If he was 13% he would't plot near the Egyptian-Intermediate profile. Lol.

  12. #29
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    Quote Originally Posted by ThaYamamoto View Post
    How you figure? 47% of Iberomaurusian=ANA=SSA-like particularly on PCAs for the time being, we know this from tha Shum Laka paper. Amhas 11% Yoruba/Dinka, 30% Iberomaurusian.. 15+11=26. If he was 13% he would't plot near the Egyptian-Intermediate profile. Lol.
    2/3 of Taforalt is Natufian-like with only 33% being ANA from what I've read.I seen his results on another thread, he's 30% IBM and 11% SSA which is roughly 20% not 25-27%.

    IBM also plot closer to North Africans than the Eritreans who are around the 60% Natufian/Arabian ancestry mark.I highly doubt Taforalt and Mar_EN are 47% ANA

  13. #30
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    Quote Originally Posted by drobbah View Post
    2/3 of Taforalt is Natufian-like with only 33% being ANA from what I've read.I seen his results on another thread, he's 30% IBM and 11% SSA which is roughly 20% not 25-27%.

    IBM also plot closer to North Africans than the Eritreans who are around the 60% Natufian/Arabian ancestry mark.I highly doubt Taforalt and Mar_EN are 47% ANA
    Ask K33/Kale/Memonics what they think. Amhas and other Maghrebis will plot past any non-ANA harbouring individuals of the same Yoruba/Dinka score. Way past actually.

    edit: the Shum Laka paper actually had Ghost ANA as 54% and the original Taforalt paper at 45. C'mon bro.




    46% Non-african related Taforalt. Lol.
    Last edited by ThaYamamoto; 09-14-2020 at 04:16 AM.

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