RT Journal Article
T1 New Insights into the Lake Chad Basin Population Structure Revealed by High-Throughput Genotyping of Mitochondrial DNA Coding SNPs
A1 Cerezo Fernández, María
A1 Černý, Viktor
A1 Carracedo Álvarez, Ángel
A1 Salas Ellacuriaga, Antonio
K1 Chad
K1 Phylogeography
K1 Mitochondrial DNA
K1 Arabic people
K1 Phylogenetics
K1 Population genetics
K1 Species diversity
K1 Lakes
AB 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.
PB PLOS
YR 2011
FD 2011
LK http://hdl.handle.net/10347/23026
UL http://hdl.handle.net/10347/23026
LA eng
NO Cerezo M, Černý V, Carracedo Á, Salas A (2011) New Insights into the Lake Chad Basin Population Structure Revealed by High-Throughput Genotyping of Mitochondrial DNA Coding SNPs. PLoS ONE 6(4): e18682. https://doi.org/10.1371/journal.pone.0018682
NO This research received support from Xunta de Galicia (Grupos Emerxentes; 2008/XA122), two grants from the Fundación de Investigación Médica Mutua Madrileña given to AS, and a Grant Agency of the Czech Republic (Grant no. 206/08/1587) given to VC
DS Minerva
RD 5 may 2026