Genetic study on North Africans
Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa
PLoS One. 2013; 8(11): e80293.
Published online Nov 27, 2013.
"Early genetic studies have identified an Upper Paleolithic component in current northern African populations, and suggested that the Neolithic transition occurred through cultural diffusion [9], [10]. Studies using autosomal markers such as short tandem repeats (STRs), polymorphic Alu insertions, HLA class II polymorphisms, and GM and KM allotypes have shown close genetic affinity of North Africans to Eurasian populations and found evidence of gene flow from sub-Saharan populations [11]–[24]. Recent genome-wide analysis of North Africans found substantial shared ancestry with the Middle East, and to a lesser extent sub-Saharan Africa and Europe (see Figure S1 for a geographical description of the region). An autochthonous Maghrebi ancestry that increases from east to west across northern Africa was also identified. It was suggested that this ancestry likely derive from “back-to-Africa” gene flow more than 12,000 ya [25]. In addition, it has been suggested that recent gene flow between the Middle East and North Africa was probably promoted by shared cultures after the Islamic expansion, increasing genetic similarities between North Africans and Middle Easterners [26]. Interestingly, genome-wide analysis also shows that increased genetic diversity in Southern Europe, which is higher than in other regions of the continent, is a result of recent gene flow from North Africa [27]."
" In contrast to the Middle Eastern influence, studies have reported only limited contribution of sub-Saharan paternal lineages to the North African gene pool [39], [40]. Previous analyzes of mtDNA lineages in North African populations suggest significant Eurasian origins [41]–[43] with lineages dating back to Paleolithic times [41] and with recent gene flow from sub-Saharan Africa linked to slave trade [44]. mtDNA variations showed an East-West cline accompanied by a genetic discontinuity on the Libyan/Egyptian border, suggesting a differential gene flow in the Nile River Valley [45].\"
"The first two components account for 55.35% of the variation and reveal a strong geographical clustering of the populations analyzed (Figure 2A). The first component separates sub-Saharan Africans which have higher frequencies of B-M60 A-M91, E-M2, and E*-M96 haplogroups. The first component also shows clustering of the Europeans characterized by R*-M207 and I-M170 and Middle Easterners which have higher frequencies of E-M78, E-M123, J-M267, and J-M172. The second component separates all North African populations except Egyptians from all other populations and shows that E-M81 plays a major role in this structure. The Tuareg appear to be drawn towards sub-Saharans while Egyptians clustered with Middle Easterners close to Palestinians"
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http://www.ncbi.nlm.nih.gov/pmc/arti...-0080293-g002/
"Genetic affinity between the studied groups was further investigated by calculating pairwise genetic distances (RST) using Y-STR haplotypes. The MDS (Figure 2B) shows a geographical clustering similar to the PCA. The first dimension splits the sub-Saharan Africans from all other populations. The North Africans cluster close to Middle Easterners with Tuareg drawn towards sub-Saharans and Egypt close to Palestinians."
"Results show significant variance among groups when Morocco, Algeria and Tunisia were pooled in one group and Libya, Tuareg, Egypt and the Middle East pooled in the second group. Variance among groups decreases but remains significant when Libyans and Tuareg are added to the first group. Conversely, significant differences between groups are lost when Egyptians are added to the North African group (Table S3). This result is also reflected in the PCA and MDS and shows Egypt's strong affinity to the Middle East rather than to North Africa."
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"PCA on genome-wide SNPs (Figure 4A) shows that North Africans are diverse and closer to Middle Easterners and Europeans than to Sub-Saharan Africans. Egyptians appear the closest to Middle Easterners and Europeans while South Moroccans are drawn towards Sub-Saharans. Tunisian samples (Chenini-Douiret Berbers) form an orthogonal cluster close but distinct from other North Africans which mostly appear in overlapping clusters."
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http://www.ncbi.nlm.nih.gov/pmc/arti...-0080293-g004/
"We constructed trees that infer population relationships using TreeMix [62]. This method estimates both population splits and the possibility of population mixture. First, we build a maximum-likelihood tree setting the position of the root at the Yoruba (Figure 4B). South Moroccans and Saharawi appear close to Yoruba while Egyptians are on a branch leading to Middle Easterners and Basque. Next, we set TreeMix to allow migration edges (m) and test by increasing m sequentially up to m = 20. The initial tree structure remains mostly unchanged when migration edges are added. All North Africans except Tunisians appear admixed from an ancestral population to Yoruba."
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