Shah, Anish M., R. Tamang, et al. (2011). “Indian Siddis: African Descendants with Indian Admixture.” American Journal of Human Genetics 89(1):154-161.
Compared to Tran-Atlantic slave trade, Indian Ocean Slave trade is less known, maybe less understood, but has longer history. Indigenous Africans were captured and traded by other Africans, Arabs, and Europeans. Some of the slaves were sent to Middle East and South Asia. Sub-Saharan African mtDNA haplogroups have been found among the Middle Eastern populations and the frequencies range from 9 to 34%. Sub-Saharan African Y chromosome haplogroups are rare, but are also found among the Middle Eastern Arab populations. Richards et al. (2003) and Quintana-Murci et al. (2004) argue that these sub-Saharan African mtDNA haplogroups were brought to the Middle East and reached South Asian through the Arab slave trade. African females were incorporated into Islamic societies, but African males did not have much chance of reproduction.
In this article, Shah et al. (2011) demonstrate that Siddis, or Habishis, from India, the descendants of slaves from Africa, have genetic characteristics of sub-Saharan Africans. They genotyped 850,000 autosomal SNPs, 32 Y chromosome biallelic markers, and 17 Y chromosome STR and sequenced mtDNA hypervariable region I.
Among Siddis, sub-Saharan genetic contribution estimated based on autosomal SNPs is quite large ranging 62.3-74.4% and they are plotted more closely to HapMap Yorubans than Indians, Europeans, or Asians on the PC plot. Contrary to the previous studies, they found more male sub-Saharan contribution to the Siddis than female contribution. You could expect this from the Indians marriage rule of endogamy, but gene flow between the Siddis and neighboring ethnic groups or communities was unidirectional. They found South Asians and Eurasian genetic
contribution to the Siddis from their neighboring communities, but they did not find Sub-Saharan genetic contribution from the Siddis to neighboring ethnic groups.
Genetic studies to understand slave trade are usually conducted using uniparental markers (mtDNA and Y-chromosome). The molecular genetic and analytical techniques to trace the origin are relatively simple, but the problem is that you are tracing only two lineages (maternal and paternal) out of thousands of possible ancestors for a particular individual. By analyzing autosomal markers, you are getting genetic information of all the ancestors. Recent advancement in molecular genetics allows researchers to genotypes many single nucleotide polymorphisms (SNPs) per individual. Sometime in the future, it will be possible to genotype over 1 million SNPs per individual without huge cost. Down side of this is that it requires more sophisticated statistical and analytical techniques.
References:
Quintana-Murci L, Chaix R, Wells S, Behar DM, Sayar H, Scozzari R, Rengo C, Al-Zaheri N, Semino O, Santachiara-Benerecetti AS, Coppa A, Ayub Q, Mohyuddin A, Tyler-Smith C, Mehdi SQ, Torroni A, and McElreavey K (2004) Where west meets east: the complex mtDNA landscape of southwest and Central Asian corridor. American Journal of Human Genetics 74:827-845.
Richards M, Rengo C, Cruciani F, Gratrix F, Wilson JF, Scozzari R, Macaulay V, and Torroni A (2003) Extensive female-mediated gene flow from Sub-Saharan Africa into Near Eastern Arab Populaitons. American Journal of Human Genetics 72:1058-1064.