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

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-gen...

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Autores principales: Haber, Marc, Mezzavilla, Massimo, Bergström, Anders, Prado-Martinez, Javier, Hallast, Pille, Saif-Ali, Riyadh, Al-Habori, Molham, Dedoussis, George, Zeggini, Eleftheria, Blue-Smith, Jason, Wells, R. Spencer, Xue, Yali, Zalloua, Pierre A., Tyler-Smith, Chris
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142112/
https://www.ncbi.nlm.nih.gov/pubmed/27889059
http://dx.doi.org/10.1016/j.ajhg.2016.10.012
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author Haber, Marc
Mezzavilla, Massimo
Bergström, Anders
Prado-Martinez, Javier
Hallast, Pille
Saif-Ali, Riyadh
Al-Habori, Molham
Dedoussis, George
Zeggini, Eleftheria
Blue-Smith, Jason
Wells, R. Spencer
Xue, Yali
Zalloua, Pierre A.
Tyler-Smith, Chris
author_facet Haber, Marc
Mezzavilla, Massimo
Bergström, Anders
Prado-Martinez, Javier
Hallast, Pille
Saif-Ali, Riyadh
Al-Habori, Molham
Dedoussis, George
Zeggini, Eleftheria
Blue-Smith, Jason
Wells, R. Spencer
Xue, Yali
Zalloua, Pierre A.
Tyler-Smith, Chris
author_sort Haber, Marc
collection PubMed
description 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.
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spelling pubmed-51421122017-06-01 Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations Haber, Marc Mezzavilla, Massimo Bergström, Anders Prado-Martinez, Javier Hallast, Pille Saif-Ali, Riyadh Al-Habori, Molham Dedoussis, George Zeggini, Eleftheria Blue-Smith, Jason Wells, R. Spencer Xue, Yali Zalloua, Pierre A. Tyler-Smith, Chris Am J Hum Genet Article 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. Elsevier 2016-12-01 2016-11-23 /pmc/articles/PMC5142112/ /pubmed/27889059 http://dx.doi.org/10.1016/j.ajhg.2016.10.012 Text en © 2016 The Author(s) http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Haber, Marc
Mezzavilla, Massimo
Bergström, Anders
Prado-Martinez, Javier
Hallast, Pille
Saif-Ali, Riyadh
Al-Habori, Molham
Dedoussis, George
Zeggini, Eleftheria
Blue-Smith, Jason
Wells, R. Spencer
Xue, Yali
Zalloua, Pierre A.
Tyler-Smith, Chris
Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations
title Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations
title_full Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations
title_fullStr Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations
title_full_unstemmed Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations
title_short Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations
title_sort chad genetic diversity reveals an african history marked by multiple holocene eurasian migrations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142112/
https://www.ncbi.nlm.nih.gov/pubmed/27889059
http://dx.doi.org/10.1016/j.ajhg.2016.10.012
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