Page 3 of 3 FirstFirst 123
Results 21 to 26 of 26

Thread: The Puzzle of West Eurasian and SSA relationship

  1. #21
    Registered Users
    Posts
    1,194
    Sex
    Omitted

    Here's a handful of qpadm outputs testing Taforalt as a mixture of Natufian + Oase1/Ust_Ishim + Mota/MbutiDG/South_Africa_2000BP if anyone's interested.

    Taforalt.zip (just realized 16 + 19 are duplicates)
    Last edited by Kale; 08-27-2018 at 04:58 AM.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, or f3-outgroup nmonte models. Looking for: KEB-IAM-TOR and Baikal_EN in plink/eigenstrat 1240k panel

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

     palamede (08-29-2018),  pgbk87 (03-05-2019)

  3. #22
    Registered Users
    Posts
    1,194
    Sex
    Omitted

    Is it known whether any of the Taforalts (10-14) were related? I'm shocked how much drift they share by F3 outgroup (Taforalt## Taforalt## MbutiDG).

    10-11 = 0.3349
    10-12 = 0.3318
    10-13 = 0.3298
    10-14 = 0.3330
    Pretty much even, doesn't look like 10 is specifically related to any of the others

    11-12 =0.4074
    11-13 = 0.3444
    11-14 = 0.3611
    12-13 = 0.3360
    12-14 = 0.3418
    13-14 = 0.3345

    General pattern is ~0.33-0.34, which is very high, incredibly so if they are supposed to be a mix of two steams of ancestry that are highly divergent from each other (Natufian-like + SSA).
    For comparison...
    AG3-MA1 = 0.3275
    Loschbour-Bichon = 0.3793
    LaBrana1-ElMiron = 0.3292
    Levant_N-Natufian = 0.2785
    Mentese_N-Barcin_N = 0.2939
    Satsurblia-Kotias = 0.3020
    Latvia_HG-Latvia_MN1 = 0.3427
    Last edited by Kale; 08-28-2018 at 06:10 AM.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, or f3-outgroup nmonte models. Looking for: KEB-IAM-TOR and Baikal_EN in plink/eigenstrat 1240k panel

  4. The Following User Says Thank You to Kale For This Useful Post:

     palamede (08-29-2018)

  5. #23
    Registered Users
    Posts
    947
    Sex
    Location
    France
    Ethnicity
    Franchouillard
    Y-DNA
    G2a2b2a1b1a2a1-S2808
    mtDNA
    H2a2a1

    Normandie Wallonia
    Quote Originally Posted by Kale View Post
    Is it known whether any of the Taforalts (10-14) were related? I'm shocked how much drift they share by F3 outgroup (Taforalt## Taforalt## MbutiDG).

    10-11 = 0.3349
    10-12 = 0.3318
    10-13 = 0.3298
    10-14 = 0.3330
    Pretty much even, doesn't look like 10 is specifically related to any of the others

    11-12 =0.4074
    11-13 = 0.3444
    11-14 = 0.3611
    12-13 = 0.3360
    12-14 = 0.3418
    13-14 = 0.3345

    General pattern is ~0.33-0.34, which is very high, incredibly so if they are supposed to be a mix of two steams of ancestry that are highly divergent from each other (Natufian-like + SSA).
    For comparison...
    AG3-MA1 = 0.3275
    Loschbour-Bichon = 0.3793
    LaBrana1-ElMiron = 0.3292
    Levant_N-Natufian = 0.2785
    Mentese_N-Barcin_N = 0.2939
    Satsurblia-Kotias = 0.3020
    Latvia_HG-Latvia_MN1 = 0.3427
    We can compare with with the table done by Eurogenes F3 (Test, X Mbuti) , for instance for Latvian , Han Chinese and Papuan :

    Villabruna_cluster 0.3012,0.2417, 0.2305
    Bichon 0.3004, 0.2420, 0.2313
    Villabruna9030 0.3000 , 0.2381, 0.2265
    Anatolian-N 0.2810, 0.2303, 0.2188
    Kotias 0.2796, 0.2326, 0.2191
    ElMiron0907 0.2782, 0.2399, 0.2295
    AG3 0.2780, 0.2465, 0.2347
    ElMiron_cluster 0.2765, 0.2389, 0.2285
    Mal'ta cluster 0.2733, 0.2472, 0.2351
    Mal'ta 0.2723, 0.2472, 0.2348
    Satsurblia_cluster 0.2689, 0.2319, 0.2197
    Satsurblia 0.2673, 0.2304, 0.2209
    Vestonice_cluster 0.2648, 0.2362, 0.2277
    Vestonice16 0.2635, 0.2352, 0.2267
    GoyetQ116-1 0.2601, 0.2413, 0.2322
    Kostenki14 0.2571, 0.2352, 0.2288
    Ust-Ishim 0.2271, 0.2389, 0.2354
    Oase1 0.2132, 0.2249, 0.2210

    Do you know the values of f3(x,y, Mbuti) between parents, children, brother/sisters, cousins at different levels ?

  6. #24
    Registered Users
    Posts
    1,194
    Sex
    Omitted

    Well here's the breakdown of the Israel_CA samples with F3 ougroup. I1166 and I1169 are father-and-son (not sure which way).
    I1152 and I1169 might be slightly something too, but I1152 and I1166 are not, so I'd guess to say I1166 is the father, though it's a minor effect between I1152 and I1169 so idk.

    Generally the Israel_CA individuals share 0.275-0.285 with each other, so minimal internal drift over their source populations.
    Israel_CA - Levant_N = 0.2797
    Israel_CA - Barcin_N = 0.2814
    Israel_CA - Hajji_Firuz_CA = 0.2677
    If they shared 0 drift beyond admixture, at proportions of 49/28/23 we'd expect Israel_CA individuals to share with each other something roughly clustering around an average of 0.2774 (I think that's how it works?)

     

    /home/user/AdmixTools-master/bin/datasets/qp3Pop: parameter file: 3poppar
    ### THE INPUT PARAMETERS
    ##PARAMETER NAME: VALUE
    genotypename: dataset15a.geno
    snpname: dataset15a.snp
    indivname: dataset15a.ind
    popfilename: 3poplist
    inbreed: YES
    ## qp3Pop version: 400
    nplist: 21
    number of blocks for block jackknife: 713
    snps: 1151159
    Source 1 Source 2 Target f_3 std. err Z SNPs
    result: I0644 I1168 MbutiDG 0.277495 0.004066 68.242 204376
    result: I0644 I1152 MbutiDG 0.276278 0.004126 66.956 216546
    result: I0644 I1178 MbutiDG 0.275852 0.004117 67.009 253369
    result: I0644 I1160 MbutiDG 0.278206 0.004297 64.737 218402
    result: I0644 I1166 MbutiDG 0.280215 0.004174 67.140 198619
    result: I0644 I1169 MbutiDG 0.275975 0.003962 69.656 318961
    result: I1168 I1152 MbutiDG 0.282327 0.004020 70.236 223863
    result: I1168 I1178 MbutiDG 0.284700 0.004108 69.298 260032
    result: I1168 I1160 MbutiDG 0.284304 0.004158 68.371 228096
    result: I1168 I1166 MbutiDG 0.281698 0.004100 68.711 209638
    result: I1168 I1169 MbutiDG 0.278913 0.003827 72.881 300663
    result: I1152 I1178 MbutiDG 0.279219 0.003833 72.841 274985
    result: I1152 I1160 MbutiDG 0.290740 0.004050 71.793 239083
    result: I1152 I1166 MbutiDG 0.283814 0.003977 71.368 218397
    result: I1152 I1169 MbutiDG 0.309847 0.004097 75.625 327344
    result: I1178 I1160 MbutiDG 0.282852 0.003941 71.779 278150
    result: I1178 I1166 MbutiDG 0.285686 0.003906 73.145 253229
    result: I1178 I1169 MbutiDG 0.279830 0.003838 72.907 387699
    result: I1160 I1166 MbutiDG 0.285790 0.004033 70.868 223370
    result: I1160 I1169 MbutiDG 0.279768 0.003910 71.561 323270
    result: I1166 I1169 MbutiDG 0.411169 0.004101 100.252 295106
    ##end of qp3Pop


    Given all this Taforalt 11 and 12 are probably like second degree relatives.
    Last edited by Kale; 08-29-2018 at 03:44 PM.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, or f3-outgroup nmonte models. Looking for: KEB-IAM-TOR and Baikal_EN in plink/eigenstrat 1240k panel

  7. The Following 2 Users Say Thank You to Kale For This Useful Post:

     Eihwaz (09-04-2018),  palamede (08-29-2018)

  8. #25
    Registered Users
    Posts
    274
    Y-DNA
    I-Y16419
    mtDNA
    T2e1

    There was a ghost population contributing to Africa and West Eurasia, I always felt this was right

    https://www.biorxiv.org/content/bior...23079.full.pdf
    161 Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirms that the Taforalt population was mixed11
    162 , but instead of specifying gene flow from the
    163 ancestors of Natufians into the ancestors of Taforalt as originally reported, we infer gene flow
    164 in the reverse direction (into Natufians). The Neolithic population from Morocco, closely related to Taforalt17
    165 is also consistent with being descended from the source of this gene flow,
    166 and appears to have no admixture from the Levantine Neolithic (Supplementary Information
    167 section 3). If our model is correct, Epipaleolithic Natufians trace part of their ancestry to
    168 North Africa, consistent with morphological and archaeological studies that indicate a spread of morphological features22
    169 and artifacts from North Africa into the Near East. Such a
    170 scenario would also explain the presence of Y-chromosome haplogroup E in the Natufians and Levantine farmers6
    171 , a common link between the Levant and Africa. Moreover, our model
    172 predicts that West Africans (represented by Yoruba) had 12.5±1.1% ancestry from a Taforalt
    173 related group rather than Taforalt having ancestry from an unknown Sub-Saharan African source11

    174 ; this may have mediated the limited Neanderthal admixture present in WestAfricans23
    175 . An advantage of our model is that it allows for a local North African component
    176 in the ancestry of Taforalt, rather than deriving them exclusively from Levantine and Sub
    177 Saharan sources.

  9. The Following 2 Users Say Thank You to IronHorse For This Useful Post:

     Mohammed Zayani (10-13-2018),  Onur Dincer (09-25-2018)

  10. #26
    Registered Users
    Posts
    274
    Y-DNA
    I-Y16419
    mtDNA
    T2e1

    When you apply f3 admixture tests on Europeans taking modern references only, then Sardinian and Native American give the most negative signals, similarly, when its applied to Levantine, Arabian, and some East Med populations (all with major ancestry from Southwest Asian component) the most negative signals are Sardinian and diverse African groups: (Lazaridis et al 2014)


    Test ref1 ref2 Z
    Ashkenazi Jew Basque Dinka -3.784
    BedouinA Sardinian Wambo -39.459
    Cypriot Sardinian Taa_West -4.743
    BedouinB Sardinian Mbuti 17.9
    Iraqi_Jew Sardinian Naro 1.3
    Druze Sardinian Mbuti -1.374
    Jordanian Sardinian Mbuti -23.716
    Jordanian Stuttgart Esan -14.338
    Lebanese Sardinian Wambo -15.997
    Libyan_Jew Sardinian Mende -3.834
    Maltese Basque Esan -10.767
    Moroccan_Jew Sardinian Mandenka -8.68
    Palestinian Sardinian Tswana -28.067
    Palestinian Stuttgart Esan -13.215
    Saudi Sardinian Kgalagadi -1.427
    Saudi Stuttgart Kgalagadi -3.555
    Sicilian Basque Esan -11.966
    Syrian Sardinian Mbuti -15.47
    Syrian Stuttgart Esan -8.712
    Tunisian_Jew Sardinian Mende -1.519
    Tunisian_Jew Stuttgart Gambian -2.025
    Turkish_Jew Basque Damara -11.407
    Yemenite_Jew Sardinian Tswana 0.799
    Yemenite_Jew Stuttgart Esan -2.36

    This cannot be simply attributed to the Arab Slave trade, many have signals from Mbuti and Khoe San related groups (Cypriot, Saudi) while others have extremely low (<1) levels of Sub Saharan ancestry (Ashkenazi Jew, Turkish Jew) and yet show significant evidence of admixture, some show admixture from multiple clusters of Africans (Palestinian, Syrian, Jordanian) like Esan and Mbuti.

    This is not the pattern you'd expect if its related to the Slave trade, it shouldn't display this diversity of Africans.

    African clusters are related, San and Mbuti Fst is lower to West and East Africans, compared to Eurasians.

    from Harappa Project
    C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15
    S Indian Baloch Caucasian NE Euro SE Asian Siberian NE Asian Papuan American Beringian Mediterranean SW Asian San E African Pygmy
    C2 Baloch 0.08
    C3 Caucasian 0.077 0.046
    C4 NE Euro 0.082 0.051 0.036
    C5 SE Asian 0.084 0.112 0.115 0.116
    C6 Siberian 0.093 0.112 0.116 0.112 0.07
    C7 NE Asian 0.081 0.11 0.113 0.113 0.034 0.052
    C8 Papuan 0.145 0.171 0.173 0.175 0.164 0.175 0.161
    C9 American 0.128 0.136 0.143 0.134 0.12 0.11 0.107 0.21
    C10 Beringian 0.116 0.129 0.136 0.129 0.099 0.078 0.081 0.196 0.105
    C11 Mediterranean 0.095 0.066 0.034 0.047 0.129 0.129 0.127 0.185 0.157 0.149
    C12 SW Asian 0.091 0.064 0.044 0.06 0.126 0.129 0.124 0.181 0.156 0.148 0.053
    C13 San 0.203 0.204 0.198 0.208 0.228 0.234 0.227 0.271 0.262 0.253 0.21 0.198
    C14 E African 0.122 0.122 0.114 0.127 0.15 0.156 0.149 0.198 0.185 0.176 0.125 0.116 0.113
    C15 Pygmy 0.188 0.19 0.185 0.194 0.214 0.219 0.212 0.256 0.247 0.238 0.197 0.185 0.095 0.092
    C16 W African 0.142 0.143 0.139 0.149 0.168 0.174 0.167 0.213 0.203 0.194 0.15 0.137 0.1 0.036 0.076


    others: https://drive.google.com/file/d/0B9q...NqcEJDOEU/view , http://2.bp.blogspot.com/-I5hLjqqo6c.../s1600/Fst.png

    Ancient North Africans, the first carriers of haplogroup E, in a similar fashion to Ancient North Eurasians, contributed ancestry to all Africans, and to Eurasians with Southwest Asian admixture.
    Corruption of the soul is a fate that befalls the weak

  11. The Following 2 Users Say Thank You to IronHorse For This Useful Post:

     Onur Dincer (03-07-2019),  Targum (03-05-2019)

Page 3 of 3 FirstFirst 123

Similar Threads

  1. Is Haplogroup R2 West Eurasian?
    By coolguy in forum R2-M479
    Replies: 48
    Last Post: 12-12-2018, 10:36 PM
  2. How much ancient West Eurasian ancestry do Amerindians have?
    By Tsakhur in forum Autosomal (auDNA)
    Replies: 4
    Last Post: 09-18-2017, 12:06 PM
  3. ANE - West Eurasian?
    By parastais in forum Autosomal (auDNA)
    Replies: 0
    Last Post: 10-22-2015, 03:21 PM
  4. Replies: 52
    Last Post: 02-18-2015, 10:14 AM
  5. Replies: 2
    Last Post: 04-18-2013, 12:30 AM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •