Circum-Saharan Prehistory through the Lens of mtDNA Diversity

Abstract

African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions.

Evolutionary Genetics and Admixture in African Populations

“…Genetic analyses generally revealed weak population structure, with most of the variation found within groups rather than between groups ( Čížková et al 2017 ; Nováčková et al 2020 ; Diallo et al 2022 ; Fortes-Lima et al 2022 ). Depending on subsistence strategy, different distributions of uniparental markers have been observed in the Sahel.…”

“…Whereas sedentary farmers are stratified based on geography but not linguistics, the opposite is true for western Fulani pastoralists ( Nováčková et al 2020 ). Furthermore, Y chromosomal haplogroups are genetically more diverse in nomadic pastoralists groups, whereas mtDNA haplogroups are more diverse in sedentary farmers ( Čížková et al 2017 ; Nováčková et al 2020 ; Diallo et al 2022 ). It has been suggested that low levels of sex-biased gene flow with sedentary farmers caused the Fulani to lose mtDNA diversity ( Čížková et al 2017 ).…”

Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt

“…The population history of the Sahel/Savannah belt has been studied thus far mainly through genetic variation of the uniparental markers ( Pereira et al 2010 ; Černý et al 2011 ; Nováčková et al 2020 ; Diallo et al 2022 ), or specific genes, such as LCT , NAT2 , TAS2R16 , or HLA-B ( Podgorná et al 2015 ; Triska et al 2015 ; Sanchez-Mazas et al 2017 ; Vicente et al 2019 ; Priehodová et al 2020 ; Kulichová et al 2021 ). It has been shown that the genetic differentiation among pastoralists and farmers does not represent significant population structure and that intensive gene-flow or shared ancestry might be among the possible reasons for this ( Černý et al 2021 ).…”

“…Interestingly, all sampled local populations of the Fulani pastoralists (collected between Senegal and Chad) have very similar genetic components, and also show genetic affinities with other western African groups. They also have a non-negligible Eurasian contribution (∼20%) that is missing in neighboring western African populations ( Triska et al 2015 ; Vicente et al 2019 ; Nováčková et al 2020 ; Diallo et al 2022 ).…”

A Population Genetic Perspective on Subsistence Systems in the Sahel/Savannah Belt of Africa and the Historical Role of Pastoralism

“…Other differences between the pastoralists and the farmers in the Sahel belt can be demonstrated in the degree of inbreeding. The farmers tend to practice exogamy, while the pastoralists practice endogamy, which manifests itself among other things by a reduction of several genetic diversity measures in the mtDNA genome (such as gene diversity, nucleotide diversity, and the mean number of pairwise differences) of pastoralists analysed so far [ 69 ]. This finding is most evident in the Rashaayda Arab population from eastern Sudan, whose founders emigrated to the Sahel belt just ~150 years ago from Saudi Arabia [ 70 ].…”