Abstract
Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.
Highlights
African genetic diversity is still incompletely understood, and vast regions in Africa remain genetically undocumented
Eurasian migrations to Africa: what was the extent of these migrations, how have they affected African genetic diversity, and what present-day populations harbor genetic signals from the ancient migrating Eurasians? We have previously reported evidence of gene flow from the Near East to East Africa ~3,000 ya, as well as subsequent selection in Ethiopians on non-African-derived alleles related to light skin pigmentation.[4]
Y chromosome haplogroups were defined to the highest resolution possible with 636 SNPs from the array data that overlapped International Society of Genetic Genealogy (ISOGG) markers
Summary
African genetic diversity is still incompletely understood, and vast regions in Africa remain genetically undocumented. For example, makes up ~5% of Africa’s surface area, and its central location, connecting sub-Saharan Africa with North and East Africa, positions it to play an important role as a crossroad or barrier to human migrations. Chad has been little studied at a wholegenome level, and its position within African genetic diversity is not well known. Important questions about Africa’s ethnic diversity are the relationships among the different groups and the relationships between cultural groups and existing genetic structures. We analyzed four Chadian populations with different ethnicities, languages, and modes of subsistence. Our samples are likely to capture recent genetic signals of migration and mixing and have the potential to show ancestral genomic relationships that are shared among Chadians and other populations.
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