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

  1. #21
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    Quote Originally Posted by NiloSaharan View Post
    "DJB_GabrielZelalem" user added:

     

    Our first participant of Dijboutian ancestry seen here nearly overlapping Somali users:



    Quote Originally Posted by GabrielZelalem View Post
    Yeah I’m mostly Isaaq which is a the main tribe in northwestern Somalia. But I expected to be closer to the Oromo/ Ethiopian as I thought I had what seems now to be non-significant arabian ancestry ?! Thank you for that !!!!
    Interesting result @GabrielZelalem; basically the same as Somalis from North Somalia. However, I think the Ciise / Issa tribe (Somali Dir tribe from Djibouti) may have more Afar-like admixture because they lived in Djibouti for a longer time than the Isaaq (more recently from Somalia) but this may be just speculation on my part.

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  3. #22
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    Quote Originally Posted by GabrielZelalem View Post
    Yeah Iím mostly Isaaq which is a the main tribe in northwestern Somalia. But I expected to be closer to the Oromo/ Ethiopian as I thought I had what seems now to be non-significant arabian ancestry ?! Thank you for that !!!!
    My pleasure, thanks for joining us!



    Here's a crude run of you along other Horners:

    Interestingly, you appear to have the highest affinity to Mota (ETH_4500BP) compared to other Somalis...
     



    You also have the highest distance (worst fit) among all Horners in this sample-set, even when the most optimal neolithic pastoralist "KEN_pastoral_N" and modern Yemeni are added for a better fit:
     

    *Given the proximity of Djibouti to Arabia, your lower affinity to Yemenis is rather surprising compared to Somalis...


    So there seems to be something unique in your ancestry which we currently don't have available.

    Something that stood out: when comparing your results with NetNomad on this second run, both of your affinities are very similar yet your fit seems unproportionately worse.

    We'll ultimately know with more regional ancient samples but maybe there's a variation of SW-Asian ancestry in Somalis that's not being fully captured by Natufian or any of these neolithic pastoral samples -- perhaps you harbour a higher amount of this paleolithic SW-Asian ancestry.
    .... .. I have spoken."

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  5. #23
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    Quote Originally Posted by Espoir View Post
    @NiloSaharan or anyone who might know why,
    I was looking again on this PCA, what makes Kakwa and Aringa cluster close to Nilotes despite them showing significant input from West Africans or Bantu. Is there anything else playing in that I donít know of.
    It's their East-African forager ancestry pulling them the opposite direction of West-Africans:

     


    These indigenous Ugandans can be modeled as a cross of Hadza/San/Mbuti-like ancestry -- with a higher affinity for the latter compared to MWI HGs:








    They seem closer to Dinka because E_HGs (KEN_LSA, Mota..) are in the opposite-direction of W-Africans, so they plot in an intermediate position making them seem closer to proper-Nilotes.

    It's more visually clear on the Tropical-African PCA:
     


    .... .. I have spoken."

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  7. #24
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    Quote Originally Posted by NiloSaharan View Post
    It's their East-African forager ancestry pulling them the opposite direction of West-Africans:

     


    These indigenous Ugandans can be modeled as a cross of Hadza/San/Mbuti-like ancestry -- with a higher affinity for the latter compared to MWI HGs:








    They seem closer to Dinka because E_HGs (KEN_LSA, Mota..) are in the opposite-direction of W-Africans, so they plot in an intermediate position making them seem closer to proper-Nilotes.

    It's more visually clear on the Tropical-African PCA:
     


    It makes more sense now! U guys got very significant HGs ancestry. And did u include any Bantu group? Is all your West Africa fully west african? Or there is Bantu admixture that is hidden it that Igbo( in case u didn’t include any Bantu group)?

  8. #25
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    Quote Originally Posted by NiloSaharan View Post
    My pleasure, thanks for joining us!



    Here's a crude run of you along other Horners:

    Interestingly, you appear to have the highest affinity to Mota (ETH_4500BP) compared to other Somalis...
     



    You also have the highest distance (worst fit) among all Horners in this sample-set, even when the most optimal neolithic pastoralist "KEN_pastoral_N" and modern Yemeni are added for a better fit:
     

    *Given the proximity of Djibouti to Arabia, your lower affinity to Yemenis is rather surprising compared to Somalis...


    So there seems to be something unique in your ancestry which we currently don't have available.

    Something that stood out: when comparing your results with NetNomad on this second run, both of your affinities are very similar yet your fit seems unproportionately worse.

    We'll ultimately know with more regional ancient samples but maybe there's a variation of SW-Asian ancestry in Somalis that's not being fully captured by Natufian or any of these neolithic pastoral samples -- perhaps you harbour a higher amount of this paleolithic SW-Asian ancestry.

    Interesting ! Very surprised about the results;

    I already noticed on gedmatch that my results were slightly slightly different in very illogical ways compared to my somali matches. On the oracle feature of GEDmatch, I always appear to have the most distant results to the "Somali typical" out of all my somali relatives (not very significant but still), but I score almost the same distance as them to every other ethnicity available on the oracles. Does it make sense ?

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  10. #26
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    Quote Originally Posted by NiloSaharan View Post
    My pleasure, thanks for joining us!



    Here's a crude run of you along other Horners:

    Interestingly, you appear to have the highest affinity to Mota (ETH_4500BP) compared to other Somalis...
     



    You also have the highest distance (worst fit) among all Horners in this sample-set, even when the most optimal neolithic pastoralist "KEN_pastoral_N" and modern Yemeni are added for a better fit:
     

    *Given the proximity of Djibouti to Arabia, your lower affinity to Yemenis is rather surprising compared to Somalis...


    So there seems to be something unique in your ancestry which we currently don't have available.

    Something that stood out: when comparing your results with NetNomad on this second run, both of your affinities are very similar yet your fit seems unproportionately worse.

    We'll ultimately know with more regional ancient samples but maybe there's a variation of SW-Asian ancestry in Somalis that's not being fully captured by Natufian or any of these neolithic pastoral samples -- perhaps you harbour a higher amount of this paleolithic SW-Asian ancestry.


    I think the problem lies not with a variation of SW-Asian ancestry but rather with the African component. I think we can infer that Somalis may have some unique local hunter-gatherer admixture from somewhere that leads to the bad fits when using Dinka and Mota as the African reference populations in Somalis.

    Luckily there is some ancient DNA from Somalia coming soon from the Reich lab so perhaps that may shine some light into whatever the Unique African component is in Somalis that is causing these bad fits.

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  12. #27
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    Quote Originally Posted by Espoir View Post
    It makes more sense now! U guys got very significant HGs ancestry. And did u include any Bantu group? Is all your West Africa fully west african? Or there is Bantu admixture that is hidden it that Igbo( in case u didnít include any Bantu group)?
    Good questions! Some discretion and historical context helps provide the answers:

    Based on comparitive ADMIXTURE results with the Bulala, a closer-proximate to "proto" Central-Sudanic speakers, the Bantu affinity for Aringa and Kakwa would seem around ~<5% -- maybe a little lower for the latter <~2% :

     


    These are comparitive puntDNAL K8 runs of Kakwa and Aringa family members with "proto" Central-Sudanics (CS speakers from central Chad).
    I'm careful suggesting them as "proto" because the Bulala clearly have recent Afro-Asiatic ("Western_Semitic") ancestry which proto-CSs lacked -- IMO they're still the best hypothetical proxy available atm


    *positive and negative delta avgs are highlighted in green and red respectively
    *"E_Benue_Congo" cluster is highest among Bantu populations

    For contrast, I've included the Alur here at the bottom. They're Luo speakers in the extreme southern and western-end of the Ugandan West-Nile region bordering Congo.


    Since linguistic and archaeological data suggests Central-Sudanics assimilated E_HGs and entered the Great-Lakes region before Bantu migrations, it'd be more conservative to stick with unadmixed E_HG West-African pops even though minor Bantu (~<5%) can be expected in these UG CS-related groups.

    Here's a post I replied you with more on the topic, it includes PCAs with Aringa/Kakwa, Darfurians and Bulala, commercial user results, and a crude nMonte run using Bantu

    **I'd be remissed if I didn't mention the Azande as a likely source of minor Bantu for Kakwa, Aringa and adjacent South-Sudanese. They're notorious for aggressive eastward expansion from C.A.R. into the Equatoria-region of South-Sudan, interrupting a continuous line of CS-speakers from Lake-Albert to Lake Chad: the word Azande means the people who possess much land



    I intend to dedicate a thread on the topic in more detail -- I think it's deserved. I'll also elaborate there on the preference for Igbo when dealing with West-Nile CS-related groups.
    .... .. I have spoken."

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  14. #28
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    "SM_Lank" and "SM_sum1" users added:

     

    * Newly added users are only indicated here with red-X here as a visual reference:



    .... .. I have spoken."

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  16. #29
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    Here's an ad-hoc run of Horners requested by some of our users. I've narrowed down a few pre-selected proxies and ran them against neolithic pastoralists:

    (Source samples listed below)


    For observational purposes, I've split and ranked Somali and Ethiopians in descending order of their distance%:
     



    Source samples:
     
    KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
    ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
    TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
    KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
    TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
    KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
    TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
    KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
    KEN_Early_Pastoral_N,-0.234476,0.102061,-0.036015,-0.081073,0.0018465,-0.0430885,-0.004465,-0.0116535,0.121078,-0.0727125,0,-0.0143875,0.008176,0.001376,0.0259225,-0.016839,0.0203395,0.004941,-0.001697,0.001063,-0.000998,0.004575,0.0042525,-0.0001205,0.005269
    CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
    Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
    Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
    Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
    Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
    Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
    Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
    Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
    Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
    Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
    Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289

    • While removing heavy SSA-neolithic samples, it appears I must have accidentally also removed KEN_Pastoral_N_o and KEN_Pastoral_N_Elmenteitan in the previous run
    • That said, user DJB_GabrielZelalem still has the highest distance with the exception of newly added SM_sum1
    • KEN_Pastoral_N, followed by TZN_PN look like clear winners for neolithic pastoral ancestry among Horners




    Quote Originally Posted by sum1 View Post
    I think the problem lies not with a variation of SW-Asian ancestry but rather with the African component. I think we can infer that Somalis may have some unique local hunter-gatherer admixture from somewhere that leads to the bad fits when using Dinka and Mota as the African reference populations in Somalis.
    Judging by Ethiopian samples with the highest distance%, it does look like something lacking in their higher Mota and Dinka affinities is rendering a worse fit.

    However for Somalis, users with extra KEN_Pastoral_N_o and KEN_Pastoral_N_Elmenteitan have the highest distance%. Referring back to the earlier post, these wide splits of pastoral neolithics might be nMonte trying to find missing Paleolithic-like SW-Asian ancestry which modern SW-Asians now lack, in part due to their high Levantine_LN/EBA affinities.

    Ultimately, paleothic samples from both Arabia and in and around Sudan will provide a clearer picture.
    Last edited by Angoliga; 10-14-2019 at 01:50 PM.
    .... .. I have spoken."

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  18. #30
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    Quote Originally Posted by NiloSaharan View Post
    Good questions! Some discretion and historical context helps provide the answers:

    Based on comparitive ADMIXTURE results with the Bulala, a closer-proximate to "proto" Central-Sudanic speakers, the Bantu affinity for Aringa and Kakwa would seem around ~<5% -- maybe a little lower for the latter <~2% :

     


    These are comparitive puntDNAL K8 runs of Kakwa and Aringa family members with "proto" Central-Sudanics (CS speakers from central Chad).
    I'm careful suggesting them as "proto" because the Bulala clearly have recent Afro-Asiatic ("Western_Semitic") ancestry which proto-CSs lacked -- IMO they're still the best hypothetical proxy available atm


    *positive and negative delta avgs are highlighted in green and red respectively
    *"E_Benue_Congo" cluster is highest among Bantu populations

    For contrast, I've included the Alur here at the bottom. They're Luo speakers in the extreme southern and western-end of the Ugandan West-Nile region bordering Congo.


    Since linguistic and archaeological data suggests Central-Sudanics assimilated E_HGs and entered the Great-Lakes region before Bantu migrations, it'd be more conservative to stick with unadmixed E_HG West-African pops even though minor Bantu (~<5%) can be expected in these UG CS-related groups.

    Here's a post I replied you with more on the topic, it includes PCAs with Aringa/Kakwa, Darfurians and Bulala, commercial user results, and a crude nMonte run using Bantu

    **I'd be remissed if I didn't mention the Azande as a likely source of minor Bantu for Kakwa, Aringa and adjacent South-Sudanese. They're notorious for aggressive eastward expansion from C.A.R. into the Equatoria-region of South-Sudan, interrupting a continuous line of CS-speakers from Lake-Albert to Lake Chad: the word Azande means the people who possess much land



    I intend to dedicate a thread on the topic in more detail -- I think it's deserved. I'll also elaborate there on the preference for Igbo when dealing with West-Nile CS-related groups.
    Useful info, thanks!
    Create a thread please. I kept playing with your coords, now u fit better as NiloSaharan source population in the face of Nilotes. Seems relevant to me considering interactions in the region of Uganda.
    EDDE8349-C6BB-4754-B2F4-349A2E28320C.jpeg

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