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Thread: Ancient DNA from North Africa (this time with formal stats)

  1. #541
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    Quote Originally Posted by gihanga.rwanda
    According to the model described in Lazaridis et al. 2018, ANA is significantly closer, phylogenetically, to Mota than it is to Crown Eurasians
    Yes, but Mota itself is going to share deep ancestry with the OOA branch... The Chabu of the Ethiopian highlands have the most Mota-like ancestry and it seems to be an important component in Nilotes and Afro-Asiatic speaking East Africans too.

    But the affinity of West Africans, Central Africans, and South Africans to Mota seems considerably lower. When the Shum Laka (Ancestral Central Africans, for lack of a better word) genome data is released, I can guarantee you that ANA will not be closer to Shum Laka than to Basal or Crown Eurasians.
    Last edited by K33; 04-10-2019 at 10:20 PM.

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  3. #542
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    Quote Originally Posted by K33 View Post
    Yes, but Mota itself is going to share deep ancestry with the OOA branch... The Chabu of the Ethiopian highlands have the most Mota-like ancestry and it seems to be an important component in Nilotes and Afro-Asiatic speaking East Africans too.

    But the affinity of West Africans, Central Africans, and South Africans to Mota seems considerably lower. When the Shum Laka (Ancestral Central Africans, for lack of a better word) genome data is released, I can guarantee you that ANA will not be closer to Shum Laka than to Basal or Crown Eurasians.
    I don’t necessarily disagree with anything you’re saying in this post. What you’re describing is ancient population substructure in Africa (Crown Eurasians are nested within African genetic diversity). As I noted earlier, I suspect that most modern SSA populations are complex mixes of less and more basal ancestral populations autochthonous to the continent; ANA and Ancestral East Africans (AEA) (e.g. Mota) on one end, and Ancestral Central and Southern Africans on the other. There’s enough evidence out there to suggest that West Africans derive their ancestry from both ends of that clade.

    The Reich lab put out a study a year or two ago that theorized that West Africans were a 2/1 mix between a Mota-like population and a very basal human population. I wouldn’t be surprised if the Shum Laka population turns out to be that basal human population that was alluded to in that study.

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    Since Generalissimo now has the Moroccan Neolithic samples in G25, I thought I'd run them, considering the whacky results obtained from the bootleg versions.

    Morocco EN IAM5: 98.8% Taforalt, 1.2% Levant N - distance 2.7958%
    Morocco EN IAM7: 94.2% Taforalt, 5.8% Peleponnese N - distance 4.2139%

    Morocco LN KEB4: 30% Peleponnese N, 25% Morocco EN, 24% Iberia SW MLN, 19% Levant N, 2.2% Dinka - distance 3.6831%

    Pretty poor fits, but look reasonable, with no uninvited time-travelling steppe BBs.

    Iberia C CA Afr: 35% Iberia SW EN, 28% Levant N, 25% Morocco EN, 12% Dinka - distance 2.4818%

    Morocco LN is quite a different mix from Iberia C CA Afr, and both are different from what you'd expect the ancestors of modern Maghrebis to look like.

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  7. #544
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    The Algerian Berber samples from Timimoun are interesting, as this region was an important trade route, especially for slaves. It's no wonder then that most of the people there are predominantly sub-Saharan or at least highly-mixed with SSAs. It's also possible that Songhai gene flow affected this area, as the local Berber dialect (Gourara) has arguably been influenced by Songhai. Looking at Chad's recent African admixture run, I noticed that the Nilo-Saharan component reaches respectable frequencies in many of the most Tropical African samples in Timimoun:

    West African Component
    Algeria_BER BerZN113 - 69.23%
    Algeria_BER BerZN146 - 73.53%
    Algeria_BER BerZN151 - 68.55%
    Algeria_BER BerZN182 - 71.03%

    Nilo-Saharan Component
    Algeria_BER BerZN113 - 5.70%
    Algeria_BER BerZN146 - 7.43%
    Algeria_BER BerZN151 - 6.67%
    Algeria_BER BerZN182 - 9.19%

    Could this minor NS component be the result of Songhai gene flow? Maybe this was just mediated by West Africans, but they don't seem to have that much of the NS component (except the Hausa, who have a lot).
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  9. #545
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    Also threw together some G25 Africa-oriented PCAs with all those sexy new North Africa samples:

     

    ^ Zoom-in on Africa, with all Global 25 samples running in PCA.

     

    ^ Africa-only PCA, with PC2 on the bottom for better visualization. West Eurasians cluster at top, a ton of intermediate populations connect North Africa to Tropical Africans at the bottom left. San and pygmies at bottom right.

     

    ^ Africa-only PCA, but focusing on Tropical Africans and West Eurasians. Omitted San, pygmies, and the like. West Africans form a cluster at top left, Nilo-Saharans at bottom left, and West Eurasian North Africans at far right.
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    Guanche_Canary_Islands:gun011 was used as a pre-Arab Berber proxy and pretty much resembles modern North Africans anyways. Germany_Medieval_O is a female outlier born 300-500 AD probably of Greek or Southern Balkan extraction. A little surprised by the extent of drift towards Greece and Anatolia by the Algerians, North Moroccans and one of the Tunisian Berber tribes. Berber_Tunisia_Chen also doesn't appear to need any additional Yoruba or Dinka in the model.

     
    [1] "distance%=3.5342"

    Berber_Morocco_TIZ

    Guanche_Canary_Islands,91.2
    Yoruba,6
    Dinka,2.8

    [1] "distance%=3.184"

    Saharawi

    Guanche_Canary_Islands,88.2
    Yoruba,4.8
    Dinka,3.6
    Egypt_Late_Period,3.4

    [1] "distance%=1.9923"

    Berber_Morocco_ERR

    Guanche_Canary_Islands,87.6
    Yoruba,7.2
    Egypt_New_Kingdom,2.8
    Dinka,1.2
    Egypt_Late_Period,1.2

    [1] "distance%=1.997"

    Berber_Tunisia_Chen

    Guanche_Canary_Islands,86.8
    Egypt_New_Kingdom,6
    Anatolia_EBA_Isparta,4
    Germany_Medieval_o,3.2

    [1] "distance%=1.8498"

    Mozabite

    Guanche_Canary_Islands,81.8
    Egypt_New_Kingdom,7.2
    Yoruba,5.8
    Germany_Medieval_o,5.2

    [1] "distance%=1.6317"

    Moroccan_North

    Guanche_Canary_Islands,77.4
    Germany_Medieval_o,7
    Mycenaean,6.8
    Egypt_Late_Period,4.8
    Yoruba,2.4
    Iberia_Northeast_Empuries1,1.6

    [1] "distance%=2.2066"

    Moroccan_South

    Guanche_Canary_Islands,76.4
    Yoruba,20
    Dinka,3.6

    [1] "distance%=1.5337"

    Moroccan

    Guanche_Canary_Islands,67.4
    Egypt_Late_Period,19.6
    Yoruba,10.4
    Egypt_New_Kingdom,2.6

    [1] "distance%=1.4543"

    Algerian

    Guanche_Canary_Islands,61.4
    Germany_Medieval_o,10
    Egypt_Late_Period,9.4
    Yoruba,8.6
    Egypt_New_Kingdom,8.4
    Dinka,1.4
    Iberia_Northeast_Empuries1,0.8

    [1] "distance%=1.2773"

    Tunisian

    Guanche_Canary_Islands,55
    Egypt_Late_Period,25.4
    Germany_Medieval_o,8.4
    Yoruba,5.8
    Egypt_New_Kingdom,3.2
    Dinka,2.2

    [1] "distance%=1.3716"

    Berber_Tunisia_Sen

    Guanche_Canary_Islands,54.2
    Egypt_Late_Period,25.4
    Egypt_New_Kingdom,10.6
    Yoruba,5.2
    Germany_Medieval_o,2.4
    Iberia_Northeast_c.6-8CE_ES,1.4
    Dinka,0.8

    [1] "distance%=1.3846"

    Berber_Algeria

    Guanche_Canary_Islands,45.8
    Yoruba,38.6
    Egypt_Late_Period,9.8
    Dinka,5.8

    [1] "distance%=1.9365"

    Spanish_Canarias

    Iberia_Northeast_c.6-8CE_ES,36.4
    Iberia_Northeast_Empuries1,27
    Guanche_Canary_Islands,21.8
    Iberia_Northeast_Empuries2,14.4
    Dinka,0.4

    [1] "distance%=1.6758"

    Moroccan_Jew

    Levant_BA_North,29.8
    Guanche_Canary_Islands,19.4
    Iberia_Northeast_Empuries1,16.4
    Italy_Medieval_Collegno_o1,14.6
    Anatolia_EBA_Isparta,10.8
    Germany_Medieval_o,9

    [1] "distance%=1.2525"

    Libyan_Jew

    Levant_BA_North,38
    Italy_Medieval_Collegno_o1,20.2
    Guanche_Canary_Islands,17.2
    Anatolia_EBA_Isparta,10.2
    Iberia_Northeast_c.6-8CE_ES,9.8
    Germany_Medieval_o,3.4
    Dinka,0.8
    Iberia_Northeast_Empuries1,0.4

    [1] "distance%=1.0397"

    Tunisian_Jew

    Levant_BA_North,29.8
    Italy_Medieval_Collegno_o1,19.8
    Guanche_Canary_Islands,16.8
    Anatolia_EBA_Isparta,11.4
    Iberia_Northeast_c.6-8CE_ES,6.8
    Iberia_Northeast_Empuries2,4.2
    Egypt_Hellenistic,3.8
    Germany_Medieval_o,3.8
    Egypt_New_Kingdom,3.4
    Yoruba,0.2

    [1] "distance%=0.8498"

    Egyptian

    Levant_BA_North,47.2
    Egypt_Late_Period,20.4
    Guanche_Canary_Islands,11.8
    Dinka,9.6
    Egypt_Hellenistic,6.6
    Egypt_New_Kingdom,2.2
    Yoruba,1.4
    Iberia_Northeast_c.6-8CE_ES,0.8

    Last edited by Seabass; 04-15-2019 at 01:49 PM.

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  13. #547
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    New Berber samples from Tiznit in Morocco included in G25 have very high Iberomaurusian ancestry :

    Scaled:
    Last edited by E_M81_I3A; 04-15-2019 at 08:15 PM.
    Basal K7: Basal 43.7, Villabruna 42.7, ANE 7.7, SSA 4.7, EastEurasian 1
    Global 25 Ancient Scaled: Anatolia_N 53.4, EHG 18.6, Iberomaurusian 10.8, Iran_N 8.6, Ethiopia_4500BP 4.8, WHG 3.8
    Global 25 Scaled Closest Individuals (Moderns and Ancients): Iberia_Southeast_c.10-16CE:I7425 3.29%, Iberia_Southeast_c.10-16CE:I8146 3.93%, Lebanon_Medieval_Mixed:SI-41 3.97%

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  15. #548
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    I assume those are probably Shilha, no?
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