Abstract
BackgroundLocated in the Sudan belt, the Chad Basin forms a remarkable ecosystem, where several unique agricultural and pastoral techniques have been developed. Both from an archaeological and a genetic point of view, this region has been interpreted to be the center of a bidirectional corridor connecting West and East Africa, as well as a meeting point for populations coming from North Africa through the Saharan desert.Methodology/Principal FindingsSamples from twelve ethnic groups from the Chad Basin (n = 542) have been high-throughput genotyped for 230 coding region mitochondrial DNA (mtDNA) Single Nucleotide Polymorphisms (mtSNPs) using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry. This set of mtSNPs allowed for much better phylogenetic resolution than previous studies of this geographic region, enabling new insights into its population history. Notable haplogroup (hg) heterogeneity has been observed in the Chad Basin mirroring the different demographic histories of these ethnic groups. As estimated using a Bayesian framework, nomadic populations showed negative growth which was not always correlated to their estimated effective population sizes. Nomads also showed lower diversity values than sedentary groups.Conclusions/SignificanceCompared to sedentary population, nomads showed signals of stronger genetic drift occurring in their ancestral populations. These populations, however, retained more haplotype diversity in their hypervariable segments I (HVS-I), but not their mtSNPs, suggesting a more ancestral ethnogenesis. Whereas the nomadic population showed a higher Mediterranean influence signaled mainly by sub-lineages of M1, R0, U6, and U5, the other populations showed a more consistent sub-Saharan pattern. Although lifestyle may have an influence on diversity patterns and hg composition, analysis of molecular variance has not identified these differences. The present study indicates that analysis of mtSNPs at high resolution could be a fast and extensive approach for screening variation in population studies where labor-intensive techniques such as entire genome sequencing remain unfeasible.
Highlights
The African Sahel together with a more southerly localized zone of savannah forms a clearly distinguishable biome
The four nomadic populations included in this study have lower diversity values than the sedentary populations (Table 2)
The values of the diversity indices computed for the hypervariable segments I (HVS-I) and the mtSNPs show clear-cut differences, mirroring the fact that haplotype diversity is enriched in the HVS-I segment by the presence of rare variants, whereas the agglomeration of identical sequences into different hgs enriches the nucleotide diversity
Summary
The African Sahel together with a more southerly localized zone of savannah forms a clearly distinguishable biome. The Lake Chad Basin forms a remarkable ecosystem, where several unique agricultural and pastoral techniques have been developed [5]. In the early Holocene, Lake Mega-Chad was formed covering a maximum surface area of 350,000 km2 Such a giant lake, the largest in Africa at the time, with a wealth of food resources undoubtedly attracted long-term human settlements. Located in the Sudan belt, the Chad Basin forms a remarkable ecosystem, where several unique agricultural and pastoral techniques have been developed. Both from an archaeological and a genetic point of view, this region has been interpreted to be the center of a bidirectional corridor connecting West and East Africa, as well as a meeting point for populations coming from North Africa through the Saharan desert
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