Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

Abstract

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 +/- 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.

Genetic Stratigraphy of Key Demographic Events in Arabia

“…It seems likely that some JT lineages, especially T ones, were introduced into Northeast Africa before the Neolithic, following Late Glacial population expansions in the Near East/Arabia. Then, locally they could have been involved in population expansions in the Neolithic period, leading to signs of autochthonous founder effects, such as the one detected in the El-Hayez oasis (400 km southwest of Cairo) for sub-haplogroup T1a2a [52]. …”

Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel

“…For example, the conservation of the high frequency and remarkable internal variability of T1 haplotypes within the distant and relatively isolated Egyptian oasis of el-Hayez led to an estimation of local expansion at around 5138 ± 3633 YBP. 37 There are no indications yet of the ages of local expansions in the more central and western regions of North Africa, which could contribute further insights for its absence in the Tuareg population as a whole.…”

The Genetic Impact of the Lake Chad Basin Population in North Africa as Documented by Mitochondrial Diversity and Internal Variation of the L3e5 Haplogroup

“…It has been shown that these non-Lbut nonetheless already African-clades are present in higher frequency mainly in nomadic pastoralists such as the Fulani (U5) or Tuareg (H1, H3, and V) (Ottoni et al, 2009;Pereira et al, 2010a;Černý et al, 2011b), and that the most probable timeframe for their arrival to the south of the Sahara is 3-9 ka (Pereira et al, 2010a). As a result of the subsequent Neolithic development in the east Mediterranean, other mtDNA lineages originally from the Near East, such as J and T, enriched the North African maternal gene pool especially in its eastern parts (Coudray et al, 2009;Kujanová et al, 2009), but did not reach sub-Saharan locations. In Daza, we identified only M1 and U6 (no H1, H3, V, or JT) clades, suggesting rather the pre-Neolithic formation of their maternal gene pool.…”

“…Phylogeographic analysis and whole genome sequencing of L3f3 (Černý et al, 2009) showed not only that this clade is restricted to the LCB geographical region, where it expanded ∼9 ka, but that it prevails in its Chadic speaking peoples. Because L3f3 has deep roots in East Africa, where its mother clade L3f had already emerged ∼50 ka (Soares et al, 2012), we suggested a possible eastern link of this clade, likely related to the linguistically inferred westward migration of Cushitic pastoralists (Blench, 1999;Černý et al, 2009). …”