From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves, via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their genetic ancestries and history of admixture and natural selection remain largely undefined. Here we studied the genome-wide diversity of the African-descent Makranis, residing on the Arabian Sea coast of Pakistan, together with that of four neighboring Pakistani populations, to investigate the genetic legacy, population dynamics and tempo of the Indian Ocean slave trade. We show that the Makranis result from an admixture event between local Baluch tribes and Bantu-speaking populations from eastern/southeastern Africa, which we dated to ~300 years ago during the Omani Empire domination. Levels of inbreeding, measured through cumulative runs of homozygosity, were found to be similar across Pakistani populations, suggesting that the admixed Makranis rapidly adopted the traditional practice of ... (Show More)

From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves, via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their genetic ancestries and history of admixture and natural selection remain largely undefined. Here we studied the genome-wide diversity of the African-descent Makranis, residing on the Arabian Sea coast of Pakistan, together with that of four neighboring Pakistani populations, to investigate the genetic legacy, population dynamics and tempo of the Indian Ocean slave trade. We show that the Makranis result from an admixture event between local Baluch tribes and Bantu-speaking populations from eastern/southeastern Africa, which we dated to ~300 years ago during the Omani Empire domination. Levels of inbreeding, measured through cumulative runs of homozygosity, were found to be similar across Pakistani populations, suggesting that the admixed Makranis rapidly adopted the traditional practice of endogamous marriages. Finally, we searched for signatures of post-admixture selection at several traits evolving under positive selection, including skin color, lactase persistence and resistance to malaria. We demonstrate that the African-specific Duffy-null blood group — believed to confer resistance against Plasmodium vivax infection — was recently introduced to Pakistan through the slave trade and evolved under positive selection in this vivax malaria-endemic region. Collectively, our study reconstructs the genetic and adaptive history of a neglected episode of the African Diaspora, and illustrates the impact of recent admixture on the diffusion of adaptive traits across human populations.

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