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

Abstract

SummaryThe presence of sub‐Saharan L‐type mtDNA sequences in North Africa has traditionally been explained by the recent slave trade. However, gene flow between sub‐Saharan and northern African populations would also have been made possible earlier through the greening of the Sahara resulting from Early Holocene climatic improvement. In this article, we examine human dispersals across the Sahara through the analysis of the sub‐Saharan mtDNA haplogroup L3e5, which is not only commonly found in the Lake Chad Basin (∼17%), but which also attains nonnegligible frequencies (∼10%) in some Northwestern African populations. Age estimates point to its origin ∼10 ka, probably directly in the Lake Chad Basin, where the clade occurs across linguistic boundaries. The virtual absence of this specific haplogroup in Daza from Northern Chad and all West African populations suggests that its migration took place elsewhere, perhaps through Northern Niger. Interestingly, independent confirmation of Early Holocene contacts between North Africa and the Lake Chad Basin have been provided by craniofacial data from Central Niger, supporting our suggestion that the Early Holocene offered a suitable climatic window for genetic exchanges between North and sub‐Saharan Africa. In view of its younger founder age in North Africa, the discontinuous distribution of L3e5 was probably caused by the Middle Holocene re‐expansion of the Sahara desert, disrupting the clade's original continuous spread.

Subsistence strategy was the main factor driving population differentiation in the bidirectional corridor of the African Sahel

“…It has been well established that in the populations of eastern and central Sahel there is a discernible Eurasian genetic component introduced over a long period of time by numerous migration events from different non‐African regions (Galego Llorente et al, ; Haber et al, ; Pickrell et al, ). Successive waves of migration are clearly reflected in both maternal and paternal genetic pools (Bučková et al, ; Černý et al, ; Podgorná et al, ; Shriner & Rotimi, ) and also in autosomal datasets as shown by allele frequency based methods (Triska et al, ; Vicente et al, ).…”

“…PCR amplification was carried out using primers and previously published protocols (Černý et al, ; Černý et al, ). These sequences have previously appeared in several publications (Černý, Čížková, Poloni, Al‐Meeri, & Mulligan, ; Černý et al, ; Černý et al, ; Černý et al, ; Čížková et al, ; Podgorná, Soares, Pereira, & Černý, ; sequences listed in Table S1) but have never been viewed together or compared with a new Y‐STR dataset. In total, we included 535 mtDNA haplotypes.…”

Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations

“…However, the significant presence of Sub‐Saharan lineages (L0, L1, L2, L3, and L4) in the two Tunisian Arab populations (35%) suggests significant admixture with indigenous Berbers, who are known to display Sub‐Saharan contributions since Paleolithic times (Frigi et al, ; Soares et al, ). This includes contributions from the Early Holocene, across the Sahel Belt, during the African Humid Period (Černý et al, ; Hernández et al, ; Podgorná et al, ; Soares et al, ), without excluding a more recent introduction in North Africa through the trans‐Saharan slave routes suggested to be mainly established in the seventh century (Harich et al, ).…”

“…Other studies revealed the arrival of some L sublineages in North Africa across the Sahel Belt during the Early Holocene at the beginning of the African Humid Period (11 000 years ago), particularly L1b and L3e5 which are commonly found in the Lake Chad Basin (Černý, Salas, Hájek, Žaloudková, & Brdička, ; Frigi et al, ; Hernández et al, ; Podgorná, Soares, Pereira, & Černý, ; Soares et al, ). Conversely, U6 and some L sublineages were introduced from northwest Africa into Iberia probably after the Younger Dryas period (Cerezo et al, ; Hernández et al, ; Podgorná et al, ; Secher et al, ; Soares et al, ).…”

Genetic history of the African Sahelian populations

“…64 A further study dealt with internal variation and phylogeography of another mtDNA haplogroup, L3e5, newly reported in the Lake Chad Basin. 65 Because this haplogroup is also present in north-western Africa, the existence of an ancestral population that spread across the Sahara in the early Holocene (ie, approximately 10 000-8000 years ago depending on the method used) was suggested. However, unlike L3f3, the L3e5 haplogroup is observed across linguistic boundaries in the Sahel, and its age estimate is of 10 000 years before present.…”