Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations

Marc Haber, Massimo Mezzavilla, Anders Bergström, Javier Prado-Martinez, Pille Hallast, Riyadh Saif-Ali, Molham Al-Habori, George Dedoussis, Eleftheria Zeggini, Jason Blue-Smith, R. Spencer Wells, Yali Xue, Pierre A. Zalloua, Chris Tyler-Smith

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

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.

Original languageBritish English
Pages (from-to)1316-1324
Number of pages9
JournalAmerican Journal of Human Genetics
Volume99
Issue number6
DOIs
StatePublished - 1 Dec 2016

Keywords

  • admixture
  • genetic isolate
  • genetic structure
  • genome-wide SNPs
  • human population history
  • whole-genome sequencing

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