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Genetic Analysis Traces Ancestry of Descendants of Indian Ocean Slaves

NEW YORK (GenomeWeb) – Genetic analysis has traced the ancestors of the Makrani people to both the Baluch of Pakistan and Bantu-speaking populations in Africa.

The Makranis have been thought to be the descendants of African slaves brought to Pakistan during the Indian Ocean slave trade, which took place from the 8th century to the 19th century.

An Institut Pasteur-led team of researchers genotyped 118 individuals belonging to five Pakistani populations, including the Makrani. As they reported today in the American Journal of Human Genetics, the researchers found that the Makrani population appears to be the result of a single admixture event that took place between a Pakistani population and a sub-Saharan African population about 300 years ago. They also discovered that the African-specific Duffy-null blood group appears to be under positive selection in Pakistani populations, providing evidence of adaptive admixture among humans.

"This study reconstructs the recent genetic and adaptive history of the descendants of African slaves carried by the Indian Ocean trade, a major yet neglected episode of the African Diaspora," Pasteur's Etienne Patin and his colleagues wrote in their paper.

Patin and his colleagues genotyped 118 people belonging to five Pakistani populations using the Illumina Omni2.5 array. After excluding individuals with cryptic relatedness, their cohort included 24 African-descent Makranis from near Karachi or the Makran coast, 22 Baluch from the Makran coast, 22 Baluch and 18 Brahui from Baluchistan, and 16 Parsi from Karachi.

After filtering, the researchers had some 2.2 million SNPs for analysis, and they merged that with a dataset of 1,316 people from the HapMap3 International Consortium and the African Genome Variation Project.

With the software tool ADMIXTURE, the researchers teased out the ancestry of the Makranis to be 25.5 percent sub-Saharan African and 74.5 percent Pakistani. They also noted varying levels of African ancestry among the other Pakistani populations.

In particular, the researchers traced the Makranis' African ancestry to Bantu-speaking populations from eastern or southeastern Africa. They received similar results when they folded in an additional 1,111 people from 63 global populations.

With the SHAPEIT2 and GLOBETROTTER tools, the researchers found that the admixture linkage disequilibrium decay seen in their cohort could be best explained by a single admixture event that occurred about 300 years ago between a Pakistani population and a sub-Saharan African population. They noted that the best-matching parental populations are likely the Baluch of Pakistan and a Bantu-speaking population from eastern or southeastern Africa.

"[O]ur analyses do not support a scenario of admixture mostly occurring in the 8th century, as suggested by oral traditions, and suggest instead that the genetic legacy of African slaves in present-day Pakistanis is of more recent origin," Patin and his colleagues wrote in their paper.

By examining runs of homozygosity, the researchers gauged how related individuals within the Makrani population were to one another. Based on their analysis, they found the Makranis had similar levels of runs of homozygosity as other Pakistani populations, suggesting that the Makranis likely adopted the local Pakistani practice of endogamy.

Patin and his colleagues also examined whether traits introduced by the African slaves might have conferred a selective advantage in South Asia. In particular, they inspected whether variants associated with skin pigmentation, lactose tolerance, or malaria resistance were more common than would be expected among the various Pakistani populations they analyzed.

One variant in the DARC gene exhibited consistent signals of post-admixture selection, the researchers reported. This variant confers the Duffy-null blood group, which is linked to resistance to Plasmodium vivax malaria. The variant is present in nearly half the Makranis, the researchers reported, and is present in about a quarter of the Makrani Baluch, despite their 7 percent African ancestry. This suggested to the researchers that the Duffy-negative blood group has been under post-admixture selection in a region where 80 percent of those with malaria are infected with P. vivax.