# Thread: The Puzzle of West Eurasian and SSA relationship

1. 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)

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3. 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

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5. Originally Posted by Kale
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. 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?)

### 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.

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8. 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.

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10. 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

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.

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