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The Entwined African and Asian Genetic Roots of the Medieval Peoples of the Swahili Coast (Brielle et al. 2022)
Abstract
The peoples of the Swahili coast of eastern Africa established a literate urban culture by the second millennium CE. They traded across eastern Africa and the Indian Ocean and were among the first sub-Saharan practitioners of Islam. An open question has been the extent to which these early interactions between Africans and non-Africans were accompanied by genetic admixture. We report genome-wide ancient DNA from 80 individuals in five medieval and early modern (1300-1800 CE) coastal towns, as well as people from an inland town postdating 1650 CE. Over half of the ancestry of most coastal individuals came from African ancestors; these African ancestors were primarily female. A slightly smaller proportion of ancestry was from Asia. This Asian component was approximately eighty to ninety percent from Near Eastern males and ten to twenty percent from Indian females. Peoples of African and Asian origins began to mix by around 1000 CE, a time when archaeological evidence documents changes on the coast that are often interpreted as marking the large-scale adoption of Islam. Before roughly 1500 CE, the Near Eastern ancestry detected in the individuals was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by the Swahili themselves. After this time, the sources of Near Eastern ancestry became increasingly Arabian, consistent with the archaeological and historical evidence of growing interactions between the Swahili coast and parts of southern Arabia. Subsequent interactions of Swahili coast peoples with other Asian and African groups further changed the ancestry of present-day peoples relative to the ancient individuals we sequenced, highlighting how Swahili genetic legacies can be more clearly understood with ancient DNA.
https://www.biorxiv.org/content/10.1101/2022.07.10.499442v1.full
Abstract
The peoples of the Swahili coast of eastern Africa established a literate urban culture by the second millennium CE. They traded across eastern Africa and the Indian Ocean and were among the first sub-Saharan practitioners of Islam. An open question has been the extent to which these early interactions between Africans and non-Africans were accompanied by genetic admixture. We report genome-wide ancient DNA from 80 individuals in five medieval and early modern (1300-1800 CE) coastal towns, as well as people from an inland town postdating 1650 CE. Over half of the ancestry of most coastal individuals came from African ancestors; these African ancestors were primarily female. A slightly smaller proportion of ancestry was from Asia. This Asian component was approximately eighty to ninety percent from Near Eastern males and ten to twenty percent from Indian females. Peoples of African and Asian origins began to mix by around 1000 CE, a time when archaeological evidence documents changes on the coast that are often interpreted as marking the large-scale adoption of Islam. Before roughly 1500 CE, the Near Eastern ancestry detected in the individuals was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by the Swahili themselves. After this time, the sources of Near Eastern ancestry became increasingly Arabian, consistent with the archaeological and historical evidence of growing interactions between the Swahili coast and parts of southern Arabia. Subsequent interactions of Swahili coast peoples with other Asian and African groups further changed the ancestry of present-day peoples relative to the ancient individuals we sequenced, highlighting how Swahili genetic legacies can be more clearly understood with ancient DNA.
We first analyzed mitochondrial haplogroups transmitted entirely by females, restricting to non-first-degree relatives. All but one individual carries an L* haplogroup, which today is almost wholly restricted to sub-Saharan Africans [41–43]. The one individual with a non-L haplogroup is from Mtwapa and carries haplogroup M30d1, which is largely restricted to South Asia [42]. The mtDNA haplogroup distribution of sampled coastal individuals is consistent with female ancestry deriving almost entirely from African or Indian sources, with a higher proportion of African female ancestors. We also expanded our mtDNA analysis to include ancient coastal and island individuals with low coverage or who did not pass quality control on the autosomes but did have sufficient mtDNA coverage. With this larger group of individuals, all but two have L* haplogroup indicative of sub-Saharan Africa. In addition to the M30d1 haplogroup, common in South Asia, we identified a male individual with haplogroup R0+16189, which is common in Saudi Arabia and the Horn of Africa [44].
We also examined male-transmitted Y chromosome sequences, which tell a different story than female-transmitted mitochondrial DNA. Two of three non-first-degree related males from Manda belong to haplogroup J2, while the third belongs to G2; both haplogroups are characteristic of Near Eastern ancestry (plausibly Persian) and are largely absent in sub-Saharan Africa [45–47]. The Kilwa individual also carries a J2 haplogroup. Fourteen of the twenty male Mtwapa individuals belong to J-family haplogroups, and two belong to R1a haplogroups, all of which are typically non-African lineages. The four remaining individuals belong to E1 family haplogroups, characteristic of sub-Saharan Africa. The Y chromosome haplogroup distribution is consistent with the male ancestry of sampled individuals from Mtwapa deriving mostly, but not entirely, from the Near East. The Y chromosome haplogroup distribution in Mtwapa differs qualitatively from that in Manda and Kilwa in that it includes more J1’s than J2’s, but is still consistent with the male ancestry of sampled individuals from Mtwapa deriving mostly, but not entirely, from the Near East.
https://www.biorxiv.org/content/10.1101/2022.07.10.499442v1.full