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Thread: 4500-year-old Ethiopian - Y-DNA E1b1, mtDNA L3, and considerable Eurasian admixture

  1. #101
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    Quote Originally Posted by Chad Rohlfsen View Post
    Well, it's about 1.8% with LBK, and we have some Africans still in the negatives, so it can't be far off. I'm going to try and get the fixed genome and run these stats myself.
    Some Nilotics who look more "Eurasian" on PCA's than Yorubas and Pygmies have no Eurasian in the model regardless of whether Mota or Yoruba was used to estimate it. Maybe it's just that Mota is closer to OOA than even those? Checking for East Eurasian ancestry also would likely do to test these ideas, closer to OOA should bring Africans closer to all Eurasians.

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  3. #102
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    The one we have is no good. There's no use in trying to run any stats with it. Yoruba do have some West Eurasian. I'm sure it will be re-run by others, and this will be cleared up.

  4. #103
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    Quote Originally Posted by Awale View Post
    Yeah, this is something myself and Lank have been talking about in respect to "East Africans" for well over a year now... That a closer relationship between EAs and Eurasians seemingly exists. It is indeed possible... But again; their "new results" seem about as funky as their old ones but this time for Eastern Africans.

    I'd like to see this run on North Africans & West Eurasians because Somalis cluster very much right in-between Egyptians/Tunisians/Moroccans and Anuaks & Tigrinyas sit right between Europeans like Sardinians and Anuaks so either Sardinians are ~10% post-OoA "African" admixed (ignoring what Basal Eurasian may or may not be here...) and Egyptians are in fact ~30% "African" instead of their usual ~20% or Anuaks are pretty West Eurasian or generally Eurasian admixed and this is somehow being masked. <- All outcomes I find pretty unlikely.
    Here are Mota's results using the puntDNAL k15, puntDNAL k8 African only and Ethiohelix K10 African only.

    puntDNAL k15

    Population
    S_Indian -
    Mediterranean -
    Siberian -
    Wht_Nile_River 25.40
    Amerindian 0.93
    S_African 13.74
    E_Asian -
    Caucasian -
    NE_European -
    Omo_River 52.68
    W_African 4.35
    Horn_Of_Africa 2.79
    Oceanian 0.11
    Beringian -
    SW_Asian -

    puntDNAL k8

    Population
    Nilo_Saharan 29.06
    Ubangian_Congo 7.36
    W_Benue_Congo 0.38
    Eastern_HG 7.53
    E_Benue_Congo 12.69
    Omotic 24.69
    Southern_HG 14.06
    Western_Semitic 4.25

    Ethiohelix K10 African only

    Population
    Nilo-Saharan 20.46
    East-Africa2 5.26
    Mbuti-Pygmy 6.57
    East_Africa1 7.57
    Khoi-San 13.02
    West_Africa 4.05
    Hadza 7.19
    Biaka-Pygmy 3.56
    North-Africa -
    Omotic 32.31

    Mota is most likely 3% Eurasian and 97 Percent African, 73% East African, 8% Central African, 13% South African and the rest 5% West African.

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  6. #104
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    Quote Originally Posted by gihanga.rwanda View Post
    Very interesting, I will go hunch and bet that these humans will share ancestry with the divergent San-like ancestry found in the Hadze, Sandawe, Omotics, and Mota. These were the likely indigenous inhabitants of East Africa south of the Ethiopian highlands.
    I am going to bet they will be the best proxy for the ALEA ancestry in Cushites and Ethio-Semites (Ancestral Lowland East African). It will be much more interesting if I am right

  7. #105
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    Quote Originally Posted by Awale View Post

    For the record, what Kurd told me is that he seems "broadly Eurasian" admixed not "West Eurasian" admixed in particular which lends credence to what Shaikorth suggested.
    There are a couple of problems with Mota's genome.

    In the Erratum to Gallego Llorente et al. 2015 : "leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota"

    What this means is that positions which are homozygotes for the minor allele (MAF=100%) , and positions which are homozygotes for the major allele (MAF=0%) were not included in the sequence!! The positions homozygotes for the major allele, may not affect the analysis much, but the positons homozygotes for the minor allele, most certainly will affect the analysis. In fact, whoever wrote the erratum is being a little generous by saying that Neanderthal and Denisovan analysis was not affected. I believe it actually was, but because we are dealing with values less than 1% it may not affect things as much. So this is 1st problem.

    The 2nd problem with Mota is that of uracil residues, a common miscoding lesion in ancient DNA that results from the deamination of cytosine. I did 2 sets of Dstat runs, one with transition and transversion SNPs, the other with transverions only (to mitigate some of the effects of sequencing errors). This I did with the uncorrected Mota genome. With transitions included, Mota appeared less W Eurasian shifted that the other African genomes in the comparison, except when it came to Onge, where he was more Onge shifted. Once I removed transition SNPs ( transitions are more susceptible to sequencing errors in ancient genomes) from the run, he started to appear more W Eurasian.

    Once we get the corrected genome, I will re-do the analysis. It is likely that he will be substantially more W Eurasian shifted than in these runs, especially when I remove transition SNPs.


    L1 L2 R1 OUT D Z
    MbutiPygmy .MOTA LBK Karitiana -0.0005 -0.159
    Yoruba .MOTA LBK Karitiana 0.0002 0.077
    Khomani .MOTA LBK Karitiana 0.007 2.158
    Masai_Kinyawa .MOTA LBK Karitiana 0.0211 6.829
    Somali .MOTA LBK Karitiana 0.0385 12.298
    Ethiopian_Jew .MOTA LBK Karitiana 0.0478 14.49
    TRANSVERSION SNPs ONLY
    L1 L2 R1 OUT D Z
    Yoruba .MOTA LBK Karitiana -0.0061 -1.03
    MbutiPygmy .MOTA LBK Karitiana -0.0032 -0.494
    Khomani .MOTA LBK Karitiana 0.0029 0.443
    Masai_Kinyaw .MOTA LBK Karitiana 0.0125 2.086
    Somali .MOTA LBK Karitiana 0.03 5.016
    Ethiopian_Je .MOTA LBK Karitiana 0.0425 6.915

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  9. #106
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    L1 L2 R1 OUT D Z
    MbutiPygmy .MOTA Druze Karitiana 0.001 0.357
    Yoruba .MOTA Druze Karitiana 0.0036 1.419
    Khomani .MOTA Druze Karitiana 0.0061 2.208
    Masai_Kinyawa .MOTA Druze Karitiana 0.0196 7.464
    Somali .MOTA Druze Karitiana 0.0327 12.378
    Ethiopian_Jew .MOTA Druze Karitiana 0.0418 14.677
    TRANSVERSION SNPs ONLY
    L1 L2 R1 OUT D Z
    Yoruba .MOTA Druze Karitiana -0.0018 -0.362
    MbutiPygmy .MOTA Druze Karitiana -0.0003 -0.047
    Khomani .MOTA Druze Karitiana 0.0037 0.689
    Masai_Kinyaw .MOTA Druze Karitiana 0.0128 2.523
    Somali .MOTA Druze Karitiana 0.0278 5.514
    Ethiopian_Je .MOTA Druze Karitiana 0.0369 7.096

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  11. #107
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    L1 L2 R1 OUT D Z
    MbutiPygmy .MOTA BedouinB Karitiana 0.0016 0.548
    Yoruba .MOTA BedouinB Karitiana 0.0045 1.63
    Khomani .MOTA BedouinB Karitiana 0.0051 1.705
    Masai_Kinyawa .MOTA BedouinB Karitiana 0.0201 7.182
    Somali .MOTA BedouinB Karitiana 0.034 12.141
    Ethiopian_Jew .MOTA BedouinB Karitiana 0.0416 13.87
    TRANSVERSION SNPs ONLY
    L1 L2 R1 OUT D Z
    Yoruba .MOTA BedouinB Karitiana -0.0012 -0.22
    MbutiPygmy .MOTA BedouinB Karitiana -0.001 -0.167
    Khomani .MOTA BedouinB Karitiana 0.0037 0.651
    Masai_Kinyaw .MOTA BedouinB Karitiana 0.0133 2.522
    Somali .MOTA BedouinB Karitiana 0.0293 5.563
    Ethiopian_Je .MOTA BedouinB Karitiana 0.0371 6.733

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  13. #108
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    L1 L2 R1 OUT D Z
    MbutiPygmy .MOTA Kotias Karitiana -0.0038 -0.885
    Yoruba .MOTA Kotias Karitiana -0.0036 -0.908
    Khomani .MOTA Kotias Karitiana -0.0013 -0.316
    Masai_Kinyawa .MOTA Kotias Karitiana 0.0055 1.364
    Somali .MOTA Kotias Karitiana 0.0144 3.6
    Ethiopian_Jew .MOTA Kotias Karitiana 0.0196 4.704
    TRANSVERSION SNPs ONLY
    L1 L2 R1 OUT D Z
    Yoruba .MOTA Kotias Karitiana -0.0077 -0.978
    Khomani .MOTA Kotias Karitiana -0.0031 -0.379
    MbutiPygmy .MOTA Kotias Karitiana -0.0005 -0.056
    Masai_Kinyaw .MOTA Kotias Karitiana 0.0034 0.438
    Somali .MOTA Kotias Karitiana 0.017 2.219
    Ethiopian_Je .MOTA Kotias Karitiana 0.0261 3.283

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  15. #109
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    L1 L2 R1 OUT D Z
    Somali .MOTA Onge Karitiana -0.0074 -1.847
    Ethiopian_Jew .MOTA Onge Karitiana -0.0073 -1.687
    Masai_Kinyawa .MOTA Onge Karitiana -0.002 -0.476
    Khomani .MOTA Onge Karitiana -0.0013 -0.291
    Yoruba .MOTA Onge Karitiana 0.0027 0.64
    MbutiPygmy .MOTA Onge Karitiana 0.0027 0.582
    TRANSVERSION SNPs ONLY
    L1 L2 R1 OUT D Z
    Ethiopian_Je .MOTA Onge Karitiana -0.0168 -1.737
    Somali .MOTA Onge Karitiana -0.0163 -1.784
    Masai_Kinyaw .MOTA Onge Karitiana -0.006 -0.006
    MbutiPygmy .MOTA Onge Karitiana -0.0003 -0.035
    Yoruba .MOTA Onge Karitiana -0.0002 -0.017
    Khomani .MOTA Onge Karitiana 0.001 0.107

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  17. #110
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    Quote Originally Posted by gihanga.rwanda View Post
    Quote Originally Posted by Chad
    Well, it's about 1.8% with LBK, and we have some Africans still in the negatives, so it can't be far off. I'm going to try and get the fixed genome and run these stats myself.
    Quoting Chad saying that these stats seem normal to him... You've won the argument, my Tutsi broski, I give up. The Sheikh's jokes aside though... I want you to look at something so you'll understand why these stats seem messed up in regards to Horn Africans like Somalis and Habeshas (I'd say Chad is right in that things mostly make sense for various other Africans now):

     


    ^ That's not Mota V LBK there... That's Yoruba V LBK and we have essentially the exact same scores as when Mota is used by a difference of about ~1%. Right off the bat, this tells you we're getting rather asinine results in regards to Horn Africans like Somalis and Tigrinyas' results. We've been compared in this way to the likes of Yorubas or Dinkas or Anuaks + a completely West Eurasian (i.e. Sardinians) or mostly West Eurasian population and we know clearly that these aren't results one should expect either via formal stats or ADMIXTURE:

     


    .
    .



    And of course, Tigrinyas cluster closer to full West Eurasians like LBKs than to Yorubas = the idea they would be ~40% (the usual Somali range which is more consistent with how Somalis place between Yorubas and some Southern Levantines) in this model makes no sense. I can't say there might be something wrong with how they actually ran the analysis itself this time around (would be interested to see what Chad turns up with) but just that something, whatever it might be, is producing what look to be unreliable results for Cushitic and Ethio-Semitic speaking Horn Africans.

    Quote Originally Posted by puntDNALKing View Post
    Mota is most likely 3% Eurasian and 97 Percent African, 73% East African, 8% Central African, 13% South African and the rest 5% West African.
    Thanks for the input, broski. Interestingly, he doesn't actually pull that close to Eurasians in this global PCA from David. In fact, Somalis and the Beta Israel samples pretty much sit between him and Northern Africans and him and Sardinians respectively in this case too but noticeably more south than with the other PCAs which makes sense as he's somewhat north of where Anuaks would sit.

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