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Reconstructing Prehistoric African Population Structure, Skoglund et al. - http://www.cell.com/cell/fulltext/S0092-8674(17)31008-5
Levantine Ancestry (I'm guessing Natufian) found in an African individual from 1000BC. If the latter hypothesis given here is correct perhaps it is a signal of shared ancestry from the first Afro-Asiatic Speakers?
"Western-Eurasian-related ancestry is pervasive in eastern Africa today (Pagani et al., 2012, Tishkoff et al., 2009), and the timing of this admixture has been estimated to be ∼3,000 BP on average (Pickrell et al., 2014). We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia. These results could be explained by migration into Africa from descendants of pre-pottery Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East. We fit the remaining approximately two-thirds of Tanzania_Luxmanda_3100BP as most closely related to the Ethiopia_4500BP (p = 0.029) or, allowing for three-way mixture, also from a source closely related to the Dinka (p = 0.18; the Levantine-related ancestry in this case was 39% ± 1%) (Table S4)."
Also Somalians are best modeled with Iran Neo ancestry, seems CHG like ancestry didnt just creep into Southern Europe and the Steppes... it eventually made it's way south to Africa as well
"While these findings show that a Levant-Neolithic-related population made a critical contribution to the ancestry of present-day eastern Africans (Lazaridis et al., 2016), present-day Cushitic speakers such as the Somali cannot be fit simply as having Tanzania_Luxmanda_3100BP ancestry. The best fitting model for the Somali includes Tanzania_Luxmanda_3100BP ancestry, Dinka-related ancestry, and 16% ± 3% Iranian-Neolithic-related ancestry (p = 0.015). This suggests that ancestry related to the Iranian Neolithic appeared in eastern Africa after earlier gene flow related to Levant Neolithic populations, a scenario that is made more plausible by the genetic evidence of admixture of Iranian-Neolithic-related ancestry throughout the Levant by the time of the Bronze Age (Lazaridis et al., 2016) and in ancient Egypt by the Iron Age (Schuenemann et al., 2017)."
Also some significant discoveries about the ancient genetic make up of Africa. San related ancestry used to be found in much larger percentages all over prehistoric east africa. A South to North East cline of African ancestry used to exist mirroring the modern day South to North West cline of African Ancestry, but Bantu Migrations seems to have mostly replaced these people.
"We find that ancestry closely related to the ancient southern Africans was present much farther north and east in the past than is apparent today. This ancient southern African ancestry comprises up to 91% of the ancestry of Khoe-San groups today (Table S5), and also 31% ± 3% of the ancestry of Tanzania_Zanzibar_1400BP, 60% ± 6% of the ancestry of Malawi_Fingira_6100BP, and 65% ± 3% of the ancestry of Malawi_Fingira_2500BP (Figure 2A). Notably, the Khoe-San-related ancestry in ancient individuals from Malawi and Tanzania is symmetrically related to the two previously identified lineages present in the San (Z < 2; Figure S2), estimated to have diverged at least 20,000 years ago (Mallick et al., 2016, Pickrell et al., 2012, Schlebusch et al., 2012), implying that this was an ancient divergent branch of this group that lived in eastern Africa at least until 1,400 BP. However, it was not present in all eastern Africans, as we do not detect it in the ∼400-year-old individual from coastal Kenya nor in the present-day Hadza"
"Both unsupervised clustering (Figure 1B) and formal ancestry estimation (Figure 2B) suggest that individuals from the Hadza group in Tanzania can be modeled as deriving all their ancestry from a lineage related deeply to ancient eastern Africans such as the Ethiopia_4500BP individual (Figure 3A; Table S5). However, this lineage appears to have contributed little ancestry to present-day Bantu speakers in eastern Africa, who instead trace their ancestry to a lineage related to present-day western Africans, with additional components related to the Nilotic-speaking Dinka and to the Tanzania_Luxmanda_3100BP pastoralist (see below; Figure 2). The Sandawe, another population that like the Hadza uses click consonants in their spoken language, are modeled as having ancestry similar to the Hadza but also admixture related to that of neighboring populations (Figure 3A; Table S5) consistent with previous findings (Henn et al., 2011, Tishkoff et al., 2009). Population replacement by incoming food producers appears to have been nearly complete in Malawi, where we detect little if any ancestry from the ancient individuals who lived ∼8,100–2,500 BP. Instead, present-day Malawian individuals are consistent with deriving all their ancestry from the Bantu expansion of ultimate western African origin (Figure 3)."
West Africans might harbor lineage that split from San as early as 300,000 years ago, the earliest known divergence of modern human lineage still present today.
"we find that ancient southern Africans, who have none of the eastern African admixture that is ubiquitous today, share significantly more alleles with present-day and ancient eastern Africans (including Dinka, Hadza, and Ethiopia_4500BP) than they do with present-day western Africans (Figure 3B; Table S6). Even within present-day western Africans, the genetic differences between Yoruba from Nigeria and the Mende from Sierra Leone are inconsistent with descent from a homogeneous ancestral population isolated from ancient southern Africans. The asymmetry between Yoruba and Mende is also observed with non-Africans but is no stronger than in eastern Africans (the most closely related Africans to the ancestral out-of-Africa population), and thus these signals are not driven by admixture from outside Africa and instead likely reflect demographic events entirely within Africa (Figure 3C; Table S6)."
"The possible basal western African population lineage would represent the earliest known divergence of a modern human lineage that contributed a major proportion of ancestry to present-day humans. Such a lineage must have separated before the divergence of San ancestors, which is estimated to have begun on the order of 200–300 thousand years ago (Scally and Durbin, 2012). Such a model of basal western African ancestry might support the hypothesis that there has been ancient structure in the ancestry of present-day Africans, using a line of evidence independent from previous findings based on long haplotypes with deep divergences from other human haplotypes (Hammer et al., 2011, Lachance et al., 2012, Plagnol and Wall, 2006). One scenario consistent with this result could involve ancestry related to eastern Africans (and the out-of-Africa population) expanding into western Africa and mixing there with more basal lineages. Our genetic data do not support the theory that this putative basal lineage diverged prior to the ancestors of Neanderthals, since the African populations we analyze here are approximately symmetrically related to Neanderthals (Mallick et al., 2016, Prüfer et al., 2014)."
Levantine Ancestry (I'm guessing Natufian) found in an African individual from 1000BC. If the latter hypothesis given here is correct perhaps it is a signal of shared ancestry from the first Afro-Asiatic Speakers?
"Western-Eurasian-related ancestry is pervasive in eastern Africa today (Pagani et al., 2012, Tishkoff et al., 2009), and the timing of this admixture has been estimated to be ∼3,000 BP on average (Pickrell et al., 2014). We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia. These results could be explained by migration into Africa from descendants of pre-pottery Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East. We fit the remaining approximately two-thirds of Tanzania_Luxmanda_3100BP as most closely related to the Ethiopia_4500BP (p = 0.029) or, allowing for three-way mixture, also from a source closely related to the Dinka (p = 0.18; the Levantine-related ancestry in this case was 39% ± 1%) (Table S4)."
Also Somalians are best modeled with Iran Neo ancestry, seems CHG like ancestry didnt just creep into Southern Europe and the Steppes... it eventually made it's way south to Africa as well
"While these findings show that a Levant-Neolithic-related population made a critical contribution to the ancestry of present-day eastern Africans (Lazaridis et al., 2016), present-day Cushitic speakers such as the Somali cannot be fit simply as having Tanzania_Luxmanda_3100BP ancestry. The best fitting model for the Somali includes Tanzania_Luxmanda_3100BP ancestry, Dinka-related ancestry, and 16% ± 3% Iranian-Neolithic-related ancestry (p = 0.015). This suggests that ancestry related to the Iranian Neolithic appeared in eastern Africa after earlier gene flow related to Levant Neolithic populations, a scenario that is made more plausible by the genetic evidence of admixture of Iranian-Neolithic-related ancestry throughout the Levant by the time of the Bronze Age (Lazaridis et al., 2016) and in ancient Egypt by the Iron Age (Schuenemann et al., 2017)."
Also some significant discoveries about the ancient genetic make up of Africa. San related ancestry used to be found in much larger percentages all over prehistoric east africa. A South to North East cline of African ancestry used to exist mirroring the modern day South to North West cline of African Ancestry, but Bantu Migrations seems to have mostly replaced these people.
"We find that ancestry closely related to the ancient southern Africans was present much farther north and east in the past than is apparent today. This ancient southern African ancestry comprises up to 91% of the ancestry of Khoe-San groups today (Table S5), and also 31% ± 3% of the ancestry of Tanzania_Zanzibar_1400BP, 60% ± 6% of the ancestry of Malawi_Fingira_6100BP, and 65% ± 3% of the ancestry of Malawi_Fingira_2500BP (Figure 2A). Notably, the Khoe-San-related ancestry in ancient individuals from Malawi and Tanzania is symmetrically related to the two previously identified lineages present in the San (Z < 2; Figure S2), estimated to have diverged at least 20,000 years ago (Mallick et al., 2016, Pickrell et al., 2012, Schlebusch et al., 2012), implying that this was an ancient divergent branch of this group that lived in eastern Africa at least until 1,400 BP. However, it was not present in all eastern Africans, as we do not detect it in the ∼400-year-old individual from coastal Kenya nor in the present-day Hadza"
"Both unsupervised clustering (Figure 1B) and formal ancestry estimation (Figure 2B) suggest that individuals from the Hadza group in Tanzania can be modeled as deriving all their ancestry from a lineage related deeply to ancient eastern Africans such as the Ethiopia_4500BP individual (Figure 3A; Table S5). However, this lineage appears to have contributed little ancestry to present-day Bantu speakers in eastern Africa, who instead trace their ancestry to a lineage related to present-day western Africans, with additional components related to the Nilotic-speaking Dinka and to the Tanzania_Luxmanda_3100BP pastoralist (see below; Figure 2). The Sandawe, another population that like the Hadza uses click consonants in their spoken language, are modeled as having ancestry similar to the Hadza but also admixture related to that of neighboring populations (Figure 3A; Table S5) consistent with previous findings (Henn et al., 2011, Tishkoff et al., 2009). Population replacement by incoming food producers appears to have been nearly complete in Malawi, where we detect little if any ancestry from the ancient individuals who lived ∼8,100–2,500 BP. Instead, present-day Malawian individuals are consistent with deriving all their ancestry from the Bantu expansion of ultimate western African origin (Figure 3)."
West Africans might harbor lineage that split from San as early as 300,000 years ago, the earliest known divergence of modern human lineage still present today.
"we find that ancient southern Africans, who have none of the eastern African admixture that is ubiquitous today, share significantly more alleles with present-day and ancient eastern Africans (including Dinka, Hadza, and Ethiopia_4500BP) than they do with present-day western Africans (Figure 3B; Table S6). Even within present-day western Africans, the genetic differences between Yoruba from Nigeria and the Mende from Sierra Leone are inconsistent with descent from a homogeneous ancestral population isolated from ancient southern Africans. The asymmetry between Yoruba and Mende is also observed with non-Africans but is no stronger than in eastern Africans (the most closely related Africans to the ancestral out-of-Africa population), and thus these signals are not driven by admixture from outside Africa and instead likely reflect demographic events entirely within Africa (Figure 3C; Table S6)."
"The possible basal western African population lineage would represent the earliest known divergence of a modern human lineage that contributed a major proportion of ancestry to present-day humans. Such a lineage must have separated before the divergence of San ancestors, which is estimated to have begun on the order of 200–300 thousand years ago (Scally and Durbin, 2012). Such a model of basal western African ancestry might support the hypothesis that there has been ancient structure in the ancestry of present-day Africans, using a line of evidence independent from previous findings based on long haplotypes with deep divergences from other human haplotypes (Hammer et al., 2011, Lachance et al., 2012, Plagnol and Wall, 2006). One scenario consistent with this result could involve ancestry related to eastern Africans (and the out-of-Africa population) expanding into western Africa and mixing there with more basal lineages. Our genetic data do not support the theory that this putative basal lineage diverged prior to the ancestors of Neanderthals, since the African populations we analyze here are approximately symmetrically related to Neanderthals (Mallick et al., 2016, Prüfer et al., 2014)."