Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

Denis Pierron (), Margit Heiske, Harilanto Razafindrazaka, Veronica Pereda-loth, Jazmin Sanchez, Omar Alva, Amal Arachiche, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Francois-Xavier Ricaut, Jean-Aimé Rakotoarisoa, Chantal Radimilahy, Mark Stoneking and Thierry Letellier
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Denis Pierron: Université de Toulouse
Margit Heiske: Université de Toulouse
Harilanto Razafindrazaka: Université de Toulouse
Veronica Pereda-loth: Université de Toulouse
Jazmin Sanchez: Université de Toulouse
Omar Alva: Université de Toulouse
Amal Arachiche: Université de Toulouse
Anne Boland: Centre National de Génotypage
Robert Olaso: Centre National de Génotypage
Jean-Francois Deleuze: Centre National de Génotypage
Francois-Xavier Ricaut: Université de Toulouse
Jean-Aimé Rakotoarisoa: Université d’Antananarivo
Chantal Radimilahy: Université d’Antananarivo
Mark Stoneking: Max Planck Institute for Evolutionary Anthropology
Thierry Letellier: Université de Toulouse

Nature Communications, 2018, vol. 9, issue 1, 1-9

Abstract: Abstract While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.

Date: 2018
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DOI: 10.1038/s41467-018-03342-5

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