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Thread: What pops should I used to gauge the percentage of West Eurasian in East Africans?

  1. #21
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    Quote Originally Posted by TuaMan View Post
    Pulling these two tests from your file:

    result: UstIshim Mende Mota Chimp : UstIshim Mende Iberia_HG Chimp 0.210780 0.012997 16.218 1036796
    result: UstIshim Mende Kenya_LSA Chimp : UstIshim Mende Iberia_HG Chimp 0.176014 0.015939 11.043 829506

    If I'm interpreting it right, the alpha number means Mota and Kenya_LSA are about 21% and 17% UstIshim like (the rest being Mende-like), and the strongly positive Z scores make these admixtures roughly good enough fits?

    How exactly does the calculation of alpha work in these tests? If I were to run a one off f4 test of your numerator UstIshim Mende Mota Chimp, I think it would be significantly postive (meaning Mota shares more alleles with UstIshim then he does with Mende - at least, I believe I've seen similar results with Dstats), but not to the extent of the Iberia_HG and UstIshim sharing in your denominator. Ergo, the bigger raw stat in the denominator dominates the ratio, and when dividing the numerator the alpha represents the amount of UstIshim like admixture in Mota?
    Would it be possible to run these models with Yoruba instead of Mende?

    Among modern West-African samples, Mende were found to have the highest amount of archaic_HG-like affinities in deep-layer G25 runs.
    I'm curious how much these fstat results would differ with a West-African reference exhibiting more modern-SSA/less archaic.
    .... .. I have spoken."

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  3. #22
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    Quote Originally Posted by Mnemonics View Post
    But it is very important to remember that F4 ratios just like F-stats capture affinities, which can be a result of admixture or simply due to phylogenetic relationships. A prime example of this is Dinka, which shows a sizable affinity to UstIshim relative to Mende, but this is unlikely to be a consequence of post OOA Eurasian admixture as it has slightly less Neanderthal admixture than is in Yoruba.
    What's your interpretation of the below Dstats if Dinka doesn't have post-OOA admixture?

    Chimp.REF Dinka.DG China_Tianyuan Russia_Ust_Ishim.DG -0.0034 -0.602 38044 38302 800554
    Chimp.REF Dinka.DG Indian_GreatAndaman_100BP.SG Russia_Ust_Ishim.DG -0.0234 -4.657 46872 49114 1007370
    Chimp.REF Dinka.DG Japan_Jomon.SG Russia_Ust_Ishim.DG -0.0196 -3.748 37098 38581 796250
    Chimp.REF Dinka.DG Yana_UP.SG Russia_Ust_Ishim.DG -0.0115 -2.513 48433 49565 1020895
    Chimp.REF Dinka.DG Anatolia_Epipaleolithic Russia_Ust_Ishim.DG -0.0207 -4.027 36315 37852 759826
    Chimp.REF Dinka.DG Jordan_PPNB Russia_Ust_Ishim.DG -0.0232 -4.173 16429 17210 338709
    Chimp.REF Dinka.DG Iran_GanjDareh_N Russia_Ust_Ishim.DG -0.0248 -5.707 45401 47705 944076
    Chimp.REF Dinka.DG Russia_Kostenki14.SG Russia_Ust_Ishim.DG -0.0134 -2.598 44179 45377 933815
    Chimp.REF Dinka.DG DevilsCave_N.SG Russia_Ust_Ishim.DG -0.0193 -4.316 48418 50327 1020610

  4. #23
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    Quote Originally Posted by Angoliga View Post
    Would it be possible to run these models with Yoruba instead of Mende?

    Among modern West-African samples, Mende were found to have the highest amount of archaic_HG-like affinities in deep-layer G25 runs.
    I'm curious how much these fstat results would differ with a West-African reference exhibiting more modern-SSA/less archaic.
    Running this with Mende produces results roughly similar to Yoruba, however I deliberately choose Mende for its archaic ancestry, after all Eurasians have Neanderthal ancestry which can increase attraction to Chimp which could skew the results. By using an African population with Archaic ancestry you can limit the effects of Archaic ancestry on the alpha.

    There are a few plausible explanations for those F4 ratios for Dinka.

    1. Dinka has ancestry from the African ancestors of Eurasians who lacked Neanderthal admixture. This would mean that Dinka are potentially substantially admixed with Basal Eurasian or ANA-like ancestry.

    2. West Africans have ancestry from a group deeper in the tree. This deep ancestry could be Ghost Modern admixture or ZAF_2000BP like admixture.

    3.Dinka-Like groups could have contributed to OOA populations differentially to West Africans. Meaning that the OOA population was just closer East Africans phylogenetically.

    My personal opinion is that it is probably a mix of 2 or more of these possibilities.

    Dinka works fairly well as a proxy for the Neanderthal diluting ancestry in Basal Eurasian rich populations using qpadm (even with Iberomaurusians in the right pops list), and it seems like West Africans definitely have more Basal ancestry than Dinka. So, I can't say which of these factors is primarily responsible for the stat without more ancient African samples.
    Last edited by Mnemonics; 09-05-2020 at 01:03 AM.

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    Quote Originally Posted by TuaMan View Post
    What's your interpretation of the below Dstats if Dinka doesn't have post-OOA admixture?

    Chimp.REF Dinka.DG China_Tianyuan Russia_Ust_Ishim.DG -0.0034 -0.602 38044 38302 800554
    Chimp.REF Dinka.DG Indian_GreatAndaman_100BP.SG Russia_Ust_Ishim.DG -0.0234 -4.657 46872 49114 1007370
    Chimp.REF Dinka.DG Japan_Jomon.SG Russia_Ust_Ishim.DG -0.0196 -3.748 37098 38581 796250
    Chimp.REF Dinka.DG Yana_UP.SG Russia_Ust_Ishim.DG -0.0115 -2.513 48433 49565 1020895
    Chimp.REF Dinka.DG Anatolia_Epipaleolithic Russia_Ust_Ishim.DG -0.0207 -4.027 36315 37852 759826
    Chimp.REF Dinka.DG Jordan_PPNB Russia_Ust_Ishim.DG -0.0232 -4.173 16429 17210 338709
    Chimp.REF Dinka.DG Iran_GanjDareh_N Russia_Ust_Ishim.DG -0.0248 -5.707 45401 47705 944076
    Chimp.REF Dinka.DG Russia_Kostenki14.SG Russia_Ust_Ishim.DG -0.0134 -2.598 44179 45377 933815
    Chimp.REF Dinka.DG DevilsCave_N.SG Russia_Ust_Ishim.DG -0.0193 -4.316 48418 50327 1020610
    Those D stats are roughly inline with Dinka having about the same amount of Eurasian admixture as Yoruba. Which is significantly less than the additional 13% increased affinity that the F4 Ratios indicate.

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    Somewhat on topic. Here's a PCA generated by making a matrix of F3 outgroup stats (outgroup being Neanderthal).

    PCA.png
    Cline from South_Africa_2000BP.SG > San/JuHoan > Malawi ancients (the 9000BP one is definitely misdated) > Kenya_PastoralN
    Another from a West-Africanish cluster > Dinka > Masai > Kenya_PastoralN > Israel_Peki'in_CA
    Pygmy & ShumLaka cluster
    ...Then Mota out in no-mans land.
    Last edited by Kale; 09-09-2020 at 04:11 AM.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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    Quote Originally Posted by drobbah View Post
    West Eurasian ancestry for Northern East Africans (Horners):


    The Tigrays of Ethiopia




    The Amharas of Ethiopia




    The Agaws & Jews of Ethiopia




    The Afars of Ethiopia,Eritrea & Djibouti




    The Oromos of Ethiopia & Kenya




    The Somalis of Somalia/Somaliland,Djibouti,Ethiopia & Kenya




    The Wolayta & Aris of Ethiopia




    Source samples
     
    Levant_PPNB:BAJ001,0.05805,0.164516,-0.029415,-0.133077,0.022158,-0.060519,-0.015276,-0.017538,0.089786,0.02278,0.018512,-0.025178,0.052031,0.004954,0.000136,-0.000133,-0.012386,-0.00152,-0.008422,0.017133,-0.003244,0.005935,0.000616,-0.013134,0
    Levant_PPNB:I0867,0.072847,0.17264,-0.030924,-0.147935,0.034468,-0.068607,-0.016451,-0.011999,0.072606,0.048839,0.010555,-0.013038,0.029583,-0.008257,-0.024837,0.007425,0.020861,-0.008615,-0.004651,0.023886,-0.00025,0.004328,0,-0.005302,-0.006826
    Levant_PPNB:I1704,0.073985,0.159438,-0.034318,-0.128232,0.037238,-0.072512,-0.018801,-0.017307,0.076492,0.033167,0.016401,-0.007343,0.032854,0.013762,-0.02348,0.00358,0.013169,-0.001014,-0.002011,0.017133,0.005989,0.004328,0.010106,-0.003374,0
    Levant_PPNB:I1707,0.067156,0.140143,-0.041483,-0.137276,0.032929,-0.063029,-0.006345,-0.017768,0.069947,0.036812,0.031991,-0.014237,0.032111,0.008945,-0.018594,-0.001326,0.003129,-0.004687,0.003142,0.009254,-0.009858,0.013849,0.000123,0.004579,-0.002275
    Levant_PPNB:I1710,0.092197,0.182795,-0.021873,-0.134046,0.0397,-0.058009,-0.01034,-0.00923,0.061971,0.038452,0.016564,-0.015586,0.032111,-0.006606,-0.042073,0.020949,0.024251,0.009248,-0.01169,0.026638,-0.001622,0.007296,-0.006409,-0.011206,-0.0097
    Levant_PPNC:I1699,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
    Yamnaya_RUS_Samara,0.1255849,0.089028,0.0426986,0. 1153479,-0.0287232,0.0450564,0.0036033,-0.0025642,-0.0559032,-0.0728943,0.0018222,3.32e-05,-0.0026924,-0.0233041,0.0366141,0.0157633,-0.0012316,-0.0017879,-0.0038408,0.0137704,-0.0031749,0.0007557,0.0110649,0.0186102,-0.004537
    Yamnaya_UKR,0.119514,0.0873355,0.0452545,0.1106285 ,-0.028313,0.042531,0.00846,-0.003461,-0.0521535,-0.0707985,0.0002435,0.004421,-0.0043115,-0.0202305,0.0323015,0.0107395,-0.0002605,-0.011529,-0.005531,0.002376,-0.0028075,0.0004325,-0.009367,0.0192795,0.0031135
    Sudanese:SUDANESE1,-0.574807,0.057885,-0.001886,-0.011305,-0.005539,-0.000837,-0.017391,0.018692,0.084468,-0.097679,-0.016888,0.02278,-0.03776,0.000963,0.006515,-0.01538,0.025425,-0.010769,0.020866,-0.022886,-0.001123,0.00136,-0.003081,-0.000964,0.00491
    Sudanese:SUDANESE10,-0.581636,0.053823,0.003771,-0.001615,0.003077,0.001394,-0.011751,0.013846,0.084264,-0.095127,-0.020786,0.020382,-0.037165,-0.003991,0.010586,-0.021877,0.020079,-0.009882,0.021997,-0.015132,0,0.005812,-0.005916,-0.00241,0.001557
    Sudanese:SUDANESE12,-0.575945,0.049761,0.001508,-0.010013,0.000923,-0.00251,-0.014101,0.013384,0.089581,-0.107337,-0.020948,0.020831,-0.044896,0.003165,0.009636,-0.01843,0.02034,-0.008488,0.018855,-0.021635,-0.000624,0.003462,-0.007025,-0.004217,0.002036
    Sudanese:SUDANESE14,-0.578221,0.055854,0.003017,-0.007752,-0.008925,0.004741,-0.014571,0.023307,0.070765,-0.08802,-0.019974,0.019782,-0.041774,-0.004542,0.006243,-0.010872,0.022426,-0.013556,0.018352,-0.017008,-0.001996,0.004575,-0.001972,-0.000602,0.007185
    Sudanese:SUDANESE15,-0.580498,0.05687,0.001131,-0.001292,-0.001846,-0.003068,-0.00893,0.013384,0.074856,-0.093669,-0.019811,0.026077,-0.038206,0.005367,0.013708,-0.015911,0.011213,-0.012415,0.017095,-0.021885,-0.004866,0.003462,-0.00456,-0.00012,0.006945
    Sudanese:SUDANESE18,-0.583913,0.053823,0.003394,-0.003876,-0.001231,-0.00753,-0.015746,0.014307,0.076696,-0.096038,-0.020299,0.02293,-0.046382,-0.000275,0.007465,-0.012331,0.018384,-0.014189,0.017975,-0.015507,0.00025,0.005688,-0.004067,-0.004579,0.003353
    Sudanese:SUDANESE2,-0.57936,0.057885,0.006788,-0.009367,-0.003077,-0.00251,-0.022326,0.02723,0.06013,-0.077086,-0.012991,0.020232,-0.025272,0.001101,0.010043,-0.018297,0.014473,-0.011275,0.023003,-0.014007,0.000499,0.004575,-0.001972,-0.009037,0.00934
    Sudanese:SUDANESE3,-0.604401,0.054839,0.015462,0.010013,-0.00277,0.003068,-0.005405,0.011538,0.021066,-0.035172,-0.004547,0.013488,-0.014717,-0.000275,0.005972,-0.010077,0.011995,-0.003041,0.005656,-0.012881,-0.000125,0.008285,-0.000986,-0.003494,-0.000599
    Sudanese:SUDANESE4,-0.588465,0.053823,-0.000377,-0.002907,-0.003693,-0.001673,-0.00423,0.008077,0.072401,-0.088385,-0.024196,0.029674,-0.03999,0.001376,0.00665,-0.018032,0.02034,-0.013049,0.021871,-0.017008,-0.001373,-0.001731,-0.001109,-0.004097,0.003952
    Sudanese:SUDANESE5,-0.57253,0.054839,0.007165,-0.008075,-0.004308,-0.005857,-0.013161,0.014538,0.089172,-0.104421,-0.02241,0.025927,-0.042517,-0.001514,0.009772,-0.011138,0.02021,-0.013809,0.024134,-0.024262,-0.000374,0.010263,-0.004683,-0.003735,0.005987
    Sudanese:SUDANESE6,-0.575945,0.050776,0.004148,-0.007752,-0.002154,-0.004183,-0.015511,0.010846,0.087536,-0.105515,-0.018188,0.029973,-0.042517,-0.003716,0.007465,-0.017502,0.017732,-0.016089,0.024008,-0.022761,0.000499,0.002349,-0.002095,-0.005302,0.005269
    Sudanese:SUDANESE7,-0.571392,0.046714,-0.007165,-0.007429,-0.005232,-0.002789,-0.00799,0.018922,0.0904,-0.108977,-0.018512,0.020831,-0.047125,0.000688,0.013165,-0.023734,0.021644,-0.012035,0.026145,-0.023261,-0.000998,0.004822,-0.000986,-0.001687,0.003712
    Sudanese:SUDANESE8,-0.586189,0.060932,0.009428,0.00646,-0.003385,-0.002789,0.00423,0.004846,0.056653,-0.078179,-0.02582,0.018284,-0.033746,-0.00234,0.001086,-0.016043,0.011604,-0.013302,0.021369,-0.014507,0.00287,0.005564,-0.00456,-0.006025,-0.001676
    Sudanese:SUDANESE9,-0.587327,0.053823,0.007165,0.000646,-0.001231,0.001952,0.0094,-0.003231,0.059312,-0.072712,-0.019649,0.02218,-0.027651,-0.003441,0.00095,-0.008088,0.018254,-0.009882,0.013324,-0.016758,-0.002371,0.003586,-0.005669,-0.00241,0
    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
    Dinkainka1,-0.574807,0.045699,0,-0.007429,-0.00277,0.002231,-0.020211,0.020538,0.086105,-0.09859,-0.016076,0.027575,-0.039395,-0.001239,0.011808,-0.02559,0.01343,-0.013049,0.028911,-0.024262,0.003993,0.001237,0.008011,0.005422,0.009 939
    Dinkainka2,-0.578221,0.053823,-0.003771,-0.008075,-0.010156,-0.003347,-0.014806,0.020768,0.084264,-0.096585,-0.028256,0.025627,-0.036273,-0.003578,0.005836,-0.021745,0.03064,-0.007728,0.021871,-0.025512,-0.001248,0.002968,-0.000493,-0.000843,0.010059
    Dinkainka3,-0.578221,0.051792,0.004148,-0.008398,-0.003077,-0.001952,-0.020681,0.021461,0.076492,-0.095856,-0.01494,0.018583,-0.036719,0.001927,0.014115,-0.022142,0.008736,-0.007221,0.023128,-0.021635,0.005241,0.006183,-0.000493,-0.00482,0.012334
    MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
    MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5e-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
    MAR_Taforalt,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
    KEN_LSA:I8808,-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
    Yoruba:HGDP00944,-0.628304,0.061947,0.021496,0.01615,-0.001539,0.003347,-0.042067,0.049152,-0.050108,0.030616,-0.000974,0.003897,0.023191,-0.006468,0.00475,-0.004773,0.005737,-0.007601,0.00729,-0.002876,0.004991,0.000495,-0.006409,0.002771,-0.005029
    Yoruba:NA18486,-0.627165,0.060932,0.019987,0.01615,0.001539,0.0178 49,-0.043947,0.043152,-0.050722,0.029522,0.006008,0.001199,0.01888,-0.00055,0.011672,-0.012729,0.00665,0.002027,0.008296,-0.007629,0.004617,0.007172,-0.000863,-0.003253,0.004191
    Yoruba:NA18487,-0.627165,0.066009,0.021496,0.015181,0.002462,0.012 55,-0.050292,0.05169,-0.046836,0.031891,0.005359,-0.003447,0.027651,0.00234,0.015472,-0.011005,0.006258,-0.002027,0.005028,0.001751,-0.001622,-0.000124,-0.000986,0.001205,0.002155
    Yoruba:NA18488,-0.63058,0.067025,0.020742,0.01615,0.001846,0.01506 ,-0.047002,0.050998,-0.052563,0.035172,0.004384,0.004946,0.025124,0.001 376,0.013843,-0.007027,0.009909,0.004307,0.007668,-0.002126,-0.000374,0.000742,-0.001972,-0.002048,-0.002994
    Yoruba:NA18489,-0.627165,0.062963,0.021119,0.016796,0.001539,0.012 271,-0.048647,0.044537,-0.044177,0.035536,0.002598,-0.002248,0.019475,0.002202,0.01045,-0.011403,-0.00013,0.002027,0.008296,-0.006503,0.001996,0.003091,-0.00037,-0.005663,0.003832
    Yoruba:NA18498,-0.627165,0.063978,0.026398,0.017765,-0.001231,0.009761,-0.040187,0.049613,-0.043973,0.03991,0.004709,-0.002548,0.023934,0.004817,0.015201,-0.011933,0.00678,-0.000127,0.004274,-0.001876,0.00574,0.007914,-0.001356,0.000361,0.000599
    Yoruba:NA18499,-0.63058,0.057885,0.019987,0.011951,-0.001539,0.016176,-0.046297,0.044075,-0.048472,0.03098,0.003735,-0.001948,0.026016,0,0.016151,-0.011403,0.006128,-0.000253,0.002011,-0.004502,0.001248,0.002226,-0.000493,0.000723,-0.001557
    Yoruba:NA18501,-0.631718,0.059916,0.020742,0.018088,-0.000615,0.016455,-0.037837,0.046383,-0.048063,0.029704,0.004872,0.002398,0.019921,0.003 028,0.013979,-0.020021,0.005737,0.001267,0.005782,-0.004252,0.006239,0.001855,-0.003821,0.001325,-0.000479
    Yoruba:NA18504,-0.636271,0.061947,0.024136,0.017119,-0.001231,0.012271,-0.040187,0.047767,-0.049086,0.032802,0.007307,0.001499,0.019921,0.000 688,0.010043,-0.006364,0.012256,0.00266,0.00729,-0.004752,-0.002121,0.00136,-0.000863,0.001325,-0.00012
    Yoruba:NA18505,-0.636271,0.062963,0.02489,0.016473,0.002154,0.0083 67,-0.043477,0.052152,-0.052972,0.033714,0.008119,0.003297,0.025124,-0.001927,0.011265,-0.007425,0.007823,-0.000507,0.003394,-0.001251,-0.000873,-0.001237,-0.003081,-0.000964,0.002395
    Yoruba:NA18507,-0.628304,0.061947,0.02225,0.021964,0.002154,0.0131 08,-0.048647,0.045921,-0.050722,0.030616,0.004709,0.001649,0.02438,0.0049 54,0.014929,-0.001591,0.010691,0.003167,0.006913,0.001126,-0.002745,0.001978,0.000863,-0.000964,-0.007664
    Levant_Natufian:I1072,0.021626,0.151314,-0.036204,-0.141475,0.034776,-0.082831,-0.032196,-0.010384,0.128032,0.012028,0.037837,-0.024878,0.085629,0.002615,0.007872,-0.008088,-0.020601,-0.008742,-0.026019,0.040269,0.007112,0.003462,0.007025,0.002 289,0.000599
    Yemenite_Al_Bayda:Y070,0.033009,0.144205,-0.060716,-0.109821,-0.008309,-0.044065,-0.015746,-0.011076,0.055017,-0.002369,0.018675,-0.029973,0.048761,0.003441,-0.0019,0.019225,-0.029467,0.007221,0.002891,0.018384,0.013102,0.015 457,-0.014913,-0.004699,-0.006347
    Yemenite_Al_Bayda:Y086,0.036423,0.129988,-0.054682,-0.109175,-0.016926,-0.05522,-0.014336,-0.009461,0.053994,-0.016766,0.001624,-0.020382,0.052031,0.001239,0.013843,0.028639,-0.014081,0.005954,-0.002388,0.012131,0.011105,0.010263,-0.001849,-0.002048,-0.000718
    Yemenite_Al_Bayda:Y089,0.045529,0.144205,-0.063733,-0.099484,-0.012925,-0.04769,-0.014571,-0.003692,0.060335,-0.007836,0.01023,-0.027426,0.048909,0.007432,0.004343,0.022805,-0.010561,0.002787,0.005405,0.019885,0.010482,0.010 881,-0.003204,-0.00012,-0.005868
    Yemenite_Al_Bayda:Y092,0.036423,0.132019,-0.065619,-0.113374,-0.009848,-0.051316,-0.017156,-0.018692,0.056244,0.001276,0.012666,-0.030573,0.048612,0.002202,0.013165,0.021082,-0.026468,0.010769,0.001508,0.021385,0.012603,0.025 472,-0.009983,0.00964,-0.000359
    Yemenite_Al_Bayda:Y097,0.034147,0.141159,-0.061848,-0.105945,-0.006463,-0.05271,-0.011281,-0.009692,0.05604,-0.007472,0.011367,-0.03357,0.051883,0.004542,-0.000407,0.022142,-0.021513,0.012035,0.001508,0.018509,0.00549,0.0202 79,-0.009983,0.005181,-0.005029
    Yemenite_Al_Bayda:Y100,0.046667,0.140143,-0.06939,-0.106591,-0.006463,-0.039881,-0.005875,-0.008307,0.043155,-0.002734,0.011205,-0.030873,0.055302,0.00578,0.009229,0.031291,-0.008736,0.004181,-0.003897,0.017258,0.005865,0.014715,-0.004683,-0.001205,-0.004191
    I found your model interesting I just replaced yoruba for west african simulated

    Distance: 1.3066% / 0.01306628
    20.0 MAR_LN
    15.5 Yemenite_Al_Bayda
    15.1 MAR_EN
    13.6 Levant_PPNB
    11.8 West_African_(simulated)
    10.3 Yamnaya_UKR
    10.2 Levant_PPNC
    3.5 MAR_Taforalt
    Distance: 1.5749% / 0.01574923
    40.0 MAR_LN
    22.2 Early_Levantine_Farmer
    11.8 West_African_(simulated)
    10.7 Iberomaurusian
    5.4 Caucasus_Hunter-gatherer
    5.2 Steppe_Pastoralist
    4.7 Iran_Neolithic

    Distance: 1.3659% / 0.01365938
    64.2 Berber
    22.2 Southern_Levant
    10.0 WestAfrican_Yoruba
    2.4 Levantine
    0.8 Cushitic
    0.4 Basque_Spanish

  11. #27
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    Quote Originally Posted by Mnemonics View Post
    Running this with Mende produces results roughly similar to Yoruba, however I deliberately choose Mende for its archaic ancestry, after all Eurasians have Neanderthal ancestry which can increase attraction to Chimp which could skew the results. By using an African population with Archaic ancestry you can limit the effects of Archaic ancestry on the alpha.

    There are a few plausible explanations for those F4 ratios for Dinka.

    1. Dinka has ancestry from the African ancestors of Eurasians who lacked Neanderthal admixture. This would mean that Dinka are potentially substantially admixed with Basal Eurasian or ANA-like ancestry.

    2. West Africans have ancestry from a group deeper in the tree. This deep ancestry could be Ghost Modern admixture or ZAF_2000BP like admixture.

    3.Dinka-Like groups could have contributed to OOA populations differentially to West Africans. Meaning that the OOA population was just closer East Africans phylogenetically.

    My personal opinion is that it is probably a mix of 2 or more of these possibilities.

    Dinka works fairly well as a proxy for the Neanderthal diluting ancestry in Basal Eurasian rich populations using qpadm (even with Iberomaurusians in the right pops list), and it seems like West Africans definitely have more Basal ancestry than Dinka. So, I can't say which of these factors is primarily responsible for the stat without more ancient African samples.
    From what I know west Africans have ana admixture, it’s why I tend to avoid using modern west african samples in ancient models. Shum_Laka Seems to be the best sample to use in ancients these samples don’t seem to have ana admixture

    Distance: 0.0005% / 0.00000503
    Target: Yoruba
    87.5 West_African_(simulated)
    12.5 ANA_(simulated)
    Distance: 1.5749% / 0.01574923
    40.0 MAR_LN
    22.2 Early_Levantine_Farmer
    11.8 West_African_(simulated)
    10.7 Iberomaurusian
    5.4 Caucasus_Hunter-gatherer
    5.2 Steppe_Pastoralist
    4.7 Iran_Neolithic

    Distance: 1.3659% / 0.01365938
    64.2 Berber
    22.2 Southern_Levant
    10.0 WestAfrican_Yoruba
    2.4 Levantine
    0.8 Cushitic
    0.4 Basque_Spanish

  12. The Following 2 Users Say Thank You to maroco For This Useful Post:

     DgidguBidgu (11-22-2020),  Mnemonics (11-22-2020)

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