title: Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.
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.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address: mh25@sanger.ac.uk.
authors.forename: Marc
authors.initials: M
authors.lastname: Haber
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Institute for Maternal and Child Health, IRCCS Burlo Garofolo, University of Trieste, 34137 Trieste, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Mezzavilla
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Anders
authors.initials: A
authors.lastname: Bergström
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Javier
authors.initials: J
authors.lastname: Prado-Martinez
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Pille
authors.initials: P
authors.lastname: Hallast
authors.affiliation: Department of Biochemistry and Molecular Biology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a 19065, Yemen.
authors.forename: Riyadh
authors.initials: R
authors.lastname: Saif-Ali
authors.affiliation: Department of Biochemistry and Molecular Biology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a 19065, Yemen.
authors.forename: Molham
authors.initials: M
authors.lastname: Al-Habori
authors.affiliation: Department of Nutrition and Dietetics, Harokopio University Athens, Athens 17671, Greece.
authors.forename: George
authors.initials: G
authors.lastname: Dedoussis
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Eleftheria
authors.initials: E
authors.lastname: Zeggini
authors.affiliation: National Geographic Society, Washington, DC 20036, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Blue-Smith
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: R Spencer
authors.initials: RS
authors.lastname: Wells
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Lebanese American University, Chouran, Beirut 1102 2801, Lebanon; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
authors.forename: Pierre A
authors.initials: PA
authors.lastname: Zalloua
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address: cts@sanger.ac.uk.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
mesh_terms: D000818:Animals; D001208:Asia / Q000208:ethnology; D002596:Chad; D005002:Ethiopia; D005060:Europe / Q000208:ethnology; D051456:Gene Flow / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics; D006579:Heterozygote; D049690:History, Ancient; D063426:Human Migration / Q000266:history*; D006801:Humans; D015810:Linkage Disequilibrium; D008877:Middle East; D059125:Neanderthals / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011156:Population Density
keywords: admixture; genetic isolate; genetic structure; genome-wide SNPs; human population history; whole-genome sequencing