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[QUOTE]Originally posted by the lioness,: [QB] http://www.sciencedirect.com/science/article/pii/S0002929716304487 [QUOTE]Originally posted by xyyman: ---- Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations. Abstract Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples [b]from Chad, the Near East, and southern Europe[/b], as well as [b]whole-genome sequencing from 19 of them[/b], to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of[b] early Eurasian backflow to Africa [/b]in people speaking the unclassified isolate Laal language in[b] southern Chad[/b] and estimate from linkage-disequilibrium decay that this occurred 4,750-7,200 years ago. [b]It brought to Africa a Y chromosome lineage (R1b-V88) [/b]whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that[b] the Chad R1b-V88 Y chromosomes coalesced 5,700-7,300 years ago.[/b] This migration [b]could thus[/b] have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and [b]was thought[/b] to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have [b]20%-30% Eurasian ancestry today[/b]. We observed a decline in heterozygosity in admixed Africans and [b]found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.[/b] [/QB][/QUOTE]^ more: Multiple Eurasian Admixtures in Africa after 6,000 ya We have previously reported massive gene flow ∼3,000 ya from Eurasians to Ethiopian populations.4 Here, we reassess the presence of Eurasian ancestry in Africa by using f3 statistics25 in the form of f3(X; Eurasian, Yoruba), where a negative value with a Z score < −4 indicates that X is a mixture of Africans and Eurasians. We found, as expected, that most Ethiopians are a mixture of Africans and Eurasians.[b] An exception is the Gumuz population, where f3(Gumuz; Eurasian, Yoruba) is always positive. The Gumuz language belongs to the Nilo-Saharan family, which could have isolated the Gumuz from the Afro-Asiatic-speaking Ethiopians. ____________] We tested the Greek, Lebanese, CEU, and CHB (Han Chinese in Beijing, China) split times from the Yoruba and found that all populations split from the Yoruba ∼70,00080,000 ya, implying that the low proportions of African admixture in the Greeks and Lebanese [/b]did not detectably affect the estimates of relative cross-coalescence rate (Figure S6A). We next tested the Toubou, who have ∼30% Eurasian ancestry. The Toubou appeared to split from Eurasians ∼30,00040,000 ya, a time more recent than expected considering the African-Eurasian split 60,00080,000 ya [b] we found in Chad a Eurasian Y chromosome lineage (Y haplogroup R1b-V88) that had penetrated all Chadian populations examined but was absent or rare from the Ethiopians examined [/b](Table S4; Figure S1). From whole Y chromosome sequences (Figure S2), we estimate that the Chadian R1b-V88 chromosomes sampled emerged 5,7007,300 ya (Figure 3B), a time comparable to the Laal speaker admixture dates (4,7507,200 ya) estimated from genome-wide LD-decay patterns. The first event occurred 2,8503,500 ya (Z score = 11), a time close to the date of mixture in East Africans 2,5002,700 ya (Z score = 26). The second mixture event occurred much more recently at 170260 ya (Z score = 5). In southern Chad, we detected mixture events that were more ancient than those in the north. Mixture occurred 3,9004,800 ya (Z score = 10) in the Sara and 4,7507,200 ya (Z score = 5) in the Laal speakers (Figure 3A). These time estimates overlap, and we interpret them as signals from the same admixture event, We found that, in addition to influencing the relative cross-coalescence rate, admixture can also inflate putative signals of positive selection. For example, using the PBS31 to detect recent positive selection that occurred in the Toubou after their divergence from the Yoruba, we found signals of selection on MCM6 (MIM: 601806) rs4988235, a variant associated with the lactase-persistence phenotype. This SNP was previously found to be under strong positive selection in Europeans, where it was probably advantageous to individuals living in pastoralist societies.34 The frequency of this variant in the Toubou is 2%, and it is absent from the sub-Saharan African and other Chadic samples (the Sara and Laal speakers) examined here. Although this SNP appears to be a candidate for selection, we suggest that it has probably drifted neutrally in the Toubou after the Eurasian gene flow: the Toubou have ∼30% Eurasian ancestry from a population similar to the Greeks, who have 13% derived alleles at rs4988235, suggesting an expectation of ∼3.9% of the derived allele simply from admixture. [b] We detected the earliest Eurasian migrations to Africa in the Laal-speaking people, an isolated language group of fewer than 800 speakers who inhabit southern Chad. We estimate that mixture occurred 4,7507,200 ya, thus after the Neolithic transition in the Near East, a period characterized by exponential growth in human population size. Environmental changes during this period (which possibly triggered the Neolithic transition) also facilitated human migrations. The African Humid Period, for example, was a humid phase across North Africa that peaked 6,0009,000 ya37 and biogeographically connected Africa to Eurasia, facilitating human movement across these regions.38 In Chad, we found a Y chromosome lineage (R1b-V88) that we estimate emerged during the same period 5,7007,300 ya (Figure 3B). The closest related Y chromosome groups today are widespread in Eurasia and have been previously associated with human expansions to Europe.39,40 We estimate that the Eurasian R1b lineages initially diverged 7,3009,400 ya, at the time of the Neolithic expansions. However, we found that the African and Eurasian R1b lineages diverged 17,90023,000 ya, suggesting that genetic structure was already established between the groups who expanded to Europe and Africa. R1b-V88 was previously found in Central and West Africa and was associated with a mid-Holocene migration of Afro-asiatic speakers through the central Sahara into the Lake Chad Basin.8 In the populations we examined, we found R1b in the Toubou and Sara, who speak Nilo-Saharan languages, and also in the Laal people, who speak an unclassified language. This suggests that R1b penetrated Africa independently of the Afro-asiatic language spread or passed to other groups through admixture. In addition to the early Eurasian migration to Africa ∼6,000 ya, a second migration ∼3,000 ya affected the Toubou population in northern Chad but had no detectable genetic impact on other Chadian populations. This migration appears to be associated with the previously reported Eurasian backflow into East Africa, given that the source populations and dates of mixture are similar. Occurring at the start of the Iron Age, these migrations could have been facilitated by advances in warfare and transportation technology in the Near East. It is uncertain why the impact of this migration in Chad affected only the Toubou. The Toubou, despite their Islamic faith, do not show the genetic admixture detected in many Near Eastern and North African populations around 1,100 ya,41 suggesting conversion without population mixing at this time. They did, however, receive additional Eurasian ancestry in the past 200 years from a source represented by North African populations such as Tunisians, Mozabite, Algerians, and Sahrawi (Figure 3C). This recent interaction could have been promoted by the nomadic lifestyle of the present-day Toubou and a shared Muslim religion with North Africans. Unsurprisingly, we also detected a likely mixing of Chad populations in the sample from the capital, which could be even more recent. we detected Neanderthal ancestry in admixed Africans and found it to be proportional to their Eurasian ancestry. Similarly, in admixed Near Easterners, we found a decrease in Neanderthal ancestry proportional to the gene flow they have received from Africans [/b] [/QB][/QUOTE]
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