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Thread: The peopling of the last Green Sahara revealed by high-coverage resequencing of trans

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    The peopling of the last Green Sahara revealed by high-coverage resequencing of trans

    https://genomebiology.biomedcentral....059-018-1393-5

    Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

    Results
    In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase.

    Conclusions
    Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.

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    Could these Nilo-Saharans be descendants of Cushtic speakers who elite dominated certain Nilo-Saharan groups? This would make sense considering some of these Nilotic languages found in Sudan contain Cushtic loan words from perhaps groups like the Beja??

    In the same period, we found evidence of a movement along the same Sahelian axis involving the internal lineages of E-M78/V32. This haplogroup probably differentiated in eastern Africa 5.99 kya, and we observed a shift in its geographic distribution towards the central Sahel, where it arrived not later than 5.17 kya. Interestingly, all the central sahelian E-V32 chromosomes belong to the internal clade E-V32/V6873, which is almost exclusively found among the Nilo-Saharans (Mann–Whitney test, p = 0.01). These findings suggest that the Nilo-Saharan spread along the Sahelian belt was probably a complex event, involving different clades and different movements from the lake Chad basin to eastern Africa and back

    The sub-Saharan clades E-V264/V259 and E-V22/V3262 are restricted to central Sahel and eastern Africa (mainly the Horn of Africa), respectively, whereas E-V12/V32 is very frequent in eastern Africa but it also includes a central Sahelian clade, suggesting a Sahelian movement between 5.99 and 5.17 kya

    Target: Mother_scaled
    Distance: 5.4903% / 0.05490334
    50.8 Dinka
    35.8 Levant_Natufian
    9.0 Yemenite_Al_Jawf
    4.0 ETH_4500BP
    0.4 MAR_Taforalt

    Target: Drobbah_scaled
    Distance: 5.1638% / 0.05163817
    44.8 Dinka
    36.0 Levant_Natufian
    11.6 ETH_4500BP
    6.2 Yemenite_Al_Jawf
    1.4 MAR_EN

    Target: Father_scaled
    Distance: 5.5604% / 0.05560439
    48.0 Dinka
    42.0 Levant_Natufian
    8.6 ETH_4500BP
    1.0 MAR_EN
    0.4 Yemenite_Al_Jawf


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    Finally assuming that movement:
    Outside Africa, both A3-M13 and R-V88 harbour sub-lineages geographically restricted to the island of Sardinia and both seem to indicate ancient trans-Mediterranean contacts. The phylogeography of A3-M13 suggests that the direction of the movement was from Africa to Sardinia, while R-V88 topology indicates a Europe-to-Africa migration. Indeed, our data suggest a European origin of R-V88 about 12.3 kya, considering both the presence of two Sardinian R-V88 basal clades (R-M18 and R-V35) and that the V88 marker arose in the R-M343 background, which in turn includes Near-Eastern/European lineages[52]. It is worth noting that the arrival of R-V88 in the Sahara seems to have occurred between 8.67 and 7.85 kya (considering as an upper limit the time estimates of the last node including a European-specific lineage, while the lower limit is the coalescence age of all the African-specific lineages), refining the time frame of the trans-Saharan migration proposed in previous studies [37, 56]. The route of R-V88 toward the lake Chad basin probably passed through northeastern Africa rather than Arabia, considering the absence of R-V88 in the Horn of Africa. Interestingly, both A3-M13 and R-V88 European sub-clades coalesced in ancient times (> 7.62 kya for A3-M13/V2742 and between 12.34 and 8.67 kya for R-V88/M18 and R-V88/V35) (Additional file 2: Figures S2 and S5). So it is possible that both clades were widespread in southern Europe, where they have been replaced by the Y haplogroups brought by the following recurrent migration waves from Asia [57].
    J1 FGC5987 to FGC6175 (188 new SNPs)
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    So the Green Sahara attracted what would become 4 trans-Saharan haplogroups: E-M78 and R-V88 from the North (Northeastern Africa and Eurasia) and A-M13 and E-M2 from the South (modern central Sahel). Then the Sahara dried out completely and became a barrier, which cut out contacts from both side of the desert which means most Sub-Saharan lineages in North Africa and the Mediterranean (here Sardinia in particular) are no recent than the drying of the Green Sahara (>4.5kya) and the same is true for North African/Eurasian lineages in Subsaharan Africa.

    Makes sense based on what was already known.
    Paternal Y-DNA haplogroup: E-M35>E-Z827>L19>M81>M183
    Maternal [grandfather] Y-DNA: E-M35>E-Z827>L19>M81>M183>PF2477>PF2546
    Hidden Content

    Lactase Persistence (LP)
    13910: TT (rs4988235 AA)
    22018: AA (rs182549 TT)

    (my mother's LP: same results)

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    Quote Originally Posted by drobbah View Post
    Could these Nilo-Saharans be descendants of Cushtic speakers who elite dominated certain Nilo-Saharan groups? This would make sense considering some of these Nilotic languages found in Sudan contain Cushtic loan words from perhaps groups like the Beja??
    Nilo-Saharans like the Masalit and Fur who are predominantly V32 (71% and 68% respectively) yet have negligible amount of Afro-Asiatic maternal lineages or autosomal ancestry kinda reminds me of the R-V88 Chadics except these Cushitic men adopted the tongue of the females they mated with

    Target: Mother_scaled
    Distance: 5.4903% / 0.05490334
    50.8 Dinka
    35.8 Levant_Natufian
    9.0 Yemenite_Al_Jawf
    4.0 ETH_4500BP
    0.4 MAR_Taforalt

    Target: Drobbah_scaled
    Distance: 5.1638% / 0.05163817
    44.8 Dinka
    36.0 Levant_Natufian
    11.6 ETH_4500BP
    6.2 Yemenite_Al_Jawf
    1.4 MAR_EN

    Target: Father_scaled
    Distance: 5.5604% / 0.05560439
    48.0 Dinka
    42.0 Levant_Natufian
    8.6 ETH_4500BP
    1.0 MAR_EN
    0.4 Yemenite_Al_Jawf


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    Quote Originally Posted by RCO View Post
    Finally assuming that movement:
    Unfortunately I have to disagree with the author's conclusions. Other than Sardinia harbouring some ancient neolithic lineages, I doubt it has any relationship to the African branches as no other Sardinian group such as I2-M26 has turned up in Africa to the best of my knowledge. The bigger mystery in my mind, is what group of wanderers were traveling in and around the Mediterranean during the Neolithic period in 5000 BC?

    In terms of the A3-M13, how many Sardinians actually descend from this branch? Is it the same one that has popped up in Britain and the Middle East?
    YDNA: R1b-BY50830 Stepney, London, UK George Wood b. 1782 English <-> Bavarian cluster
    maternal-gf YDNA: ?? Gurr, James ~1740, Smarden, Kent, England.
    maternal-gm YDNA: R1b-P311+ Beech, John Richard b. 1780, Lewes, England
    maternal-ggf YDNA R1b-U106 Thomas, Edward b 1854, Sittingbourne, Kent
    paternal-ggf YDNA: R1b-Z17901. Gould, John Somerset England 1800s.
    paternal-ggf YDNA: R1b-L48. Scott, William Hamilton Ireland(?) 1800s

    other:
    Welch: early 1800s E-M84 Kent, England.

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    Quote Originally Posted by ADW_1981 View Post
    Other than Sardinia harbouring some ancient neolithic lineages, I doubt it has any relationship to the African branches as no other Sardinian group such as I2-M26 has turned up in Africa to the best of my knowledge. The bigger mystery in my mind, is what group of wanderers were traveling in and around the Mediterranean during the Neolithic period in 5000 BC?
    Cardial Ware settlers, probably obsidian traders. I doubt Sardinian I2-M26 is even Neolithic though, seems more likely Copper Age.

    In terms of the A3-M13, how many Sardinians actually descend from this branch? Is it the same one that has popped up in Britain and the Middle East?
    The more famous British one is A1a. A-M13 is pretty widespread but rare, it's only 0.6% in Sardinia.

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    Strange. It seems like they focused on R-V88 (~17.64%) for Southern Egyptians and they didn't include any of the M78 results.(Supplementary Table 4):

    Screenshot_20180212_215527.png
    Last edited by blackflash16; 02-13-2018 at 03:26 AM.

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    Quote Originally Posted by Ignis90 View Post
    So the Green Sahara attracted what would become 4 trans-Saharan haplogroups: E-M78 and R-V88 from the North (Northeastern Africa and Eurasia) and A-M13 and E-M2 from the South (modern central Sahel). Then the Sahara dried out completely and became a barrier, which cut out contacts from both side of the desert which means most Sub-Saharan lineages in North Africa and the Mediterranean (here Sardinia in particular) are no recent than the drying of the Green Sahara (>4.5kya) and the same is true for North African/Eurasian lineages in Subsaharan Africa.

    Makes sense based on what was already known.
    Please note that desertification was a progressive process, and during centuries Central Sahara maintained enough vegetation for pastoralism (in the mountain range). Bos were domisticated as an consequence of desertification, partially from African stock. In the end of the process, aridity became too high, and even pastoralims were not sufficient to maintain human life. Hence probably migrations to Sahel and/or Egypt, and extinction of some groups.

    Quote Originally Posted by ADW_1981 View Post
    Unfortunately I have to disagree with the author's conclusions. Other than Sardinia harbouring some ancient neolithic lineages, I doubt it has any relationship to the African branches as no other Sardinian group such as I2-M26 has turned up in Africa to the best of my knowledge.
    Mind that this is based on modern distribution, not on ancient results, with huge founder effects. This mean we can't exclude the initial presence of I2 in North Africa 7000 years ago.
    But I'm agree, since R1b V88 seems more and more like a WHG specific haplogroup, the more likely scenario is the presence of R1B V88 in North Africa before the Neolithization (by a Natufian-rich population). The huge hydrographic system oriented South/North in Northern Sahara (especially in Libya and Egypt) during the Green Sahara was probably like an highway to Central Sahara for Northern Populations, and pastoralism based on goat is attested.
    The probable route from Europe would be either Spain or Italy.

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    They forgot about E-L19, E-M33 and also A1a, how foolish...

    As for R-V88, I've already said that it most likely entered from Italy and not Iberia. The haplogroup is well established in the eastern portion of North Africa and Central Africa, but it is almost completely lacking in the west. Add this to the fact that Sardinia has basal sub-clades and you get the idea. Natufian-like rich, we can't know, but it is likely that their original autosomal composition (WHG) was diluted as they were moving toward lake Chad to the extent that there is almost no west eurasian autosomal signal in the populations currently heavy in R-V88. It is possible that at one point V88 predominated along the libyan coast where it would have been mixing with ''natufian-like'' North Africans.

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