Genetic Impacts of Neolithic Settlement on Indigenous Foragers in Sulawesi

Leonard Taufik1*, Raymond Tobler2, Bastien Llamas2, Gludhug A. Purnomo2, Shyamsundar Ravishankar2, Xavier Roca-Rada2, Roberta Davidson2, Herawati Sudoyo3, Adam Brumm4, Hasanuddin5, Budianto Hakim5, Erlin Novita Idje Djami5, Zubair Mas’ud5, M. Irfan Mahmud5, Bernadeta A.K.W5, Suryatman6, A. M. Saiful6, Isbahuddin7, Vladimir Levchenko8, Shwaron Kumar8, and Fiona Doessel8

South Sulawesi was once inhabited by a now-extinct hunter-gatherer group known as the Toalean. Lithic artefacts confirm Toalean presence in the area between 8 and 1.5 thousand years ago (kya). A previous archaeogenomic study revealed that a 7,200-year-old Toalean individual possessed a distinct genetic ancestry, partly tied to the first Out of Africa human migration that eventually reached Sahul. Nevertheless, little is known about their population structure over time. Additionally, genetic studies of contemporary populations have shown that the Toalean genetic signal was mostly obscured or replaced by the later Austronesian migration from Taiwan around 4 kya. To better understand past Toalean-Austronesian interactions and overall human history in Wallacea, we generated and analysed archaeogenomic data from 11 ancient individuals from two Toalean-associated sites in South Sulawesi – Leang Sumpang Karoro and Balang Metti. We provide the first snapshot of genetic diversity in South Sulawesi between 5.1 and 2.5 kya. Our results support genetic continuity of the Toalean hunter-gatherer population between 7.2 and 5.1 kya, prior to the arrival of Austronesians. Additionally, we provide the earliest genetic evidence of admixture between the Toalean people and Austronesians, dating back at least 2.5 thousand years. The new archaeogenetic results align well with archaeological evidence. Crucially, they also reveal complex and dynamic biological interactions between local foragers and Austronesian migrants in Wallacea.