An Austronesian signature in mainland East Africa?

From the recent Busby et al. bioRxiv preprint “Admixture into and within sub-Saharan Africa” (14):

We infer direct admixture from Eurasian sources in two populations from Kenya, where specifically South Asian populations (GIH, KHV) are the most closely matched surrogates to the minor sources of admixture (Figure 5). Interestingly, the Chonyi (1138CE: 1080-1182CE) and Kauma (1225CE: 1167-1254CE) are located on the so-called Swahili Coast, a region where Medieval trade across the Indian Ocean is historically documented [Allen, 1993].

1000-1500CEThe authors’ GLOBETROTTER analysis (see 79: Figure 4-Source Data 1) best models Chonyi as 8% KHV (1000 Genomes Kinh Vietnamese) + 92% Wasambaa and Kauma as 6% GIH (1000 Genomes Gujarati) + 94% Mzigua. (Wasambaa and Mzigua are both Niger-Congo-speaking Tanzanian populations.)

Is the Chonyi event admixture not with “South Asians” in the Indian subcontinental sense but instead Austronesian seafarers? If so, it would be the first demonstration of precolonial Southeast Asian genetic impacts on Africa beyond Madagascar that I’m aware of. It would be great to rerun these analyses with a broader palette of Eurasian donors and see if there’s a better proxy than KHV.

Busby, G., Band, G., Si Le, Q., Jallow, M., Bougama, E., Mangano, V., Amenga-Etego, L., Emil, A., Apinjoh, T., Ndila, C., Manjurano, A., Nyirongo, V., Doumbo, O., Rockett, K., Kwiatkowski, D., Spencer, C., & The Malaria Genomic Epidemiology Network. (2016). Admixture into and within sub-Saharan Africa. bioRxiv (p. 038406).

Image modified for clarity from Figure 6-figure supplement 1.

Further Reading

Roger Blench’s picture of Austronesian presence in coastal East Africa around 1000 BP (2010:242):

The East African coast was considered important enough for the ‘Waqwaq’ raiders and traders from Sumatra to mount a raid on Qanbalu (an East African island as yet unidentified) in AD 945, according to Buzurg ibn Shahriyar, Book of the Wonders of India (Freeman-Grenville 1981). The Waqwaq seem also to have settled on the Sofala coast in the early tenth century (al-Mas’udi, in Freeman-Grenville 1962, 14). Al-Idrisi, writing in AD 1154 suggests that the coastal Bantu did not develop seagoing vessels for long-distance trade until quite late:

The Zenjs [the people of the East African coast south of Cape Guardafui] have no ships for voyaging … The people of the isles of Ziibag [here Ziibag = Western Indonesia] come to the country of the Zenjs in large and in small ships. They trade with them and export the Zenj merchandise, for they understand each other’s language. (Al-Idrisi, in Ferrand 1907)

As Hornell (1936) observed, the statement that the Indonesians understood the language of Zenj only makes sense if we assume there were Austronesian-speaking settlements on the East African coast, not merely on Madagascar.

Blench, R. (2010). Evidence for the Austronesian Voyages in the Indian Ocean. In Anderson, A., Barrett, J. H., & Boyle, K. V. (Eds.), The Global Origins and Development of Seafaring, 239–248. Cambridge, UK: McDonald Institute for Archaeological Research.