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

  1. #11
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    Mota's eurasian seems to be entirely undifferentiated, which may indicate that that the Bab el Mendab crossing theory for OOA is still potentially viable. Ken_LSA seems like it has some West Eurasian admixture on top of the older layer of Eurasian.

    Running admixtools is fairly simple, you just need a Linux OS or a virtual machine to get it running. You might need to download some libraries if you want build it from source, but the simplest way to get it running is download it via conda. The Admixtools documentation on Github shows the formats for preparing the parameter files. You can also download the 1240K/HO data from the Reich Labs site.
    I would also recommend downloading Plink to trim your dataset to a more manageable size.

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    Quote Originally Posted by Mnemonics View Post
    Mota's eurasian seems to be entirely undifferentiated, which may indicate that that the Bab el Mendab crossing theory for OOA is still potentially viable. Ken_LSA seems like it has some West Eurasian admixture on top of the older layer of Eurasian.

    Running admixtools is fairly simple, you just need a Linux OS or a virtual machine to get it running. You might need to download some libraries if you want build it from source, but the simplest way to get it running is download it via conda. The Admixtools documentation on Github shows the formats for preparing the parameter files. You can also download the 1240K/HO data from the Reich Labs site.
    I would also recommend downloading Plink to trim your dataset to a more manageable size.
    I see.

    Thank you but I don't even know how to interpret formal stats like qpadm, f3, d-stats. Would be great to learn from someone here.

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    I have been trying to replicate my successful qpadm models for Mota-like populations using G25.

    The Hadza are basically identical to Mota so I can use them as a modern proxy to account for ancient dna damage.

    Models with ZAF_2000BP
    Screenshot (5).png

    Models with Khomani_San

    Screenshot (6).png

    Look at those tight distances. It seems like there was a very ancient back migration that hit East/South-East Africa from after the OOA-bottleneck and post Neanderthal Admixture.

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    Quote Originally Posted by Mnemonics View Post
    It is generally fine to mix Moderns and Ancients when using transversion snps as they are much less likely to be damaged than transition snps.

    I wouldn't be so sure about it if the signal wasn't so robust. African population history is very complex and some African groups (East Africans and West Africans) share a common ancestor with Eurasians to the exclusion of other Africans (Pygmies, and San). However, using F4ratios it is pretty easy to distinguish between common pre-OOA ancestry and Eurasian ancestry.

    Eurasian African X Chimp/San : Eurasian Africa Eurasian2 Chimp/San

    If you use the above F4 ratio, and the Eurasians selected have similar levels of Neanderthal admixture, you can distinguish between African and Eurasian ancestry by changing the African from the most basal African groups to those closest to Eurasians. If the Eurasian affinity stays when you move past the population you are examining (phylogenetically), than it almost always reflected in Neanderthal F4Ratios.

    This also works pretty well for Eurasians too.

    In fact, using this method, it seems like the African affinity found in some Eurasians seems to have come, at least partially, from some very deep population because It is distinguished reasonably well by including African Hunter-Gatherer populations.

    Maybe the original Iberomaurusian paper was right about them having something Hadza-like.
    Would you mind posting some of the log files from these F4-ratios?

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    Quote Originally Posted by TuaMan View Post
    Would you mind posting some of the log files from these F4-ratios?
    I'll get them up as soon as I get home.

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    Somaliland Ethiopia Adal Sultanate Yemen Canada
    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
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    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
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    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
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    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
    Drobbah_scaled
    Target: Drobbah_scaled
    Distance: 4.2508% / 0.04250752
    52.2 Sudanese
    19.6 Proto-Natufian_(simulated)
    13.6 MAR_Taforalt
    11.0 Yemenite_Al_Bayda
    3.6 ETH_4500BP

    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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  13. #17
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    I have wondered if the San/ZAF 2000 signal in Mota, Kenya LSA, Hadza, etc. was actually Ghost Modern ancestry best proxied by ZAF 2000 rather than actual Southern African gene flow, but I'm not sure if or how this can be known. There does seem to have been a cline from Mota to ZAF 2000 anyway (Malawi samples) so it certainly makes sense if it's real Southern African HG ancestry.
    Ελευθερία ή θάνατος.

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  15. #18
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    Here are some of the F4Ratios with a variety of pairs of Eurasians.

    F4ratios.txt

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  17. #19
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    Quote Originally Posted by Mnemonics View Post
    Here are some of the F4Ratios with a variety of pairs of Eurasians.

    F4ratios.txt
    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?

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  19. #20
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    The actual math involved in calculating the alpha is roughly inline with your description, you can get a clearer description of the principles involved from reading this general overview of the use of F Statistics,
    particularly the bit that shows how the alpha is calculated https://www.genetics.org/content/202/4/1485.

    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.

    An F4 ratio can tell you that Mota shares 17-21% more alleles with UstIshim but it cannot directly tell you that that affinity is due to admixture, qpadm works much better for that as rotating population into the left and right lists allows better analysis of the plausibility of admixture through null hypothesis testing. Also, the Z-scores of an F4 test do not describe the fit of a model, but are instead a measure of the significance of the relationship.

    Typically a Z-score greater than 3 or less than -3 indicates that the affinity is real.

    However, the design nature of an F4 ratio test means that you will probably never see a result with a significant percentage without a highly negative or positive Z-Score.

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