Paper short abstract:

Indonesians played an important role in the colonization of Madagascar. To test for a genetic link between Malagasy and linguistically related Indonesian populations, we studied them using uniparental markers. Settlement of Madagascar may have been mediated by ancient Indonesian sea nomad movements.

Paper long abstract:

Genetic, cultural, and linguistic characteristics of the Malagasy suggest that people from both Africa and Island Southeast Asia were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an important role; linguistic evidence suggests that the Malagasy language branches from the Southeast Barito language family of southern Borneo, Indonesia, and is closest to the Ma'anyan language that is spoken in the present-day. There is also evidence of word borrowings from a small number of Austronesian languages spoken on other Indonesian islands, including Proto South Sulawesi, Buginese, Macassarese and Old Javanese.

To test for a genetic link between the Malagasy and these linguistically related Indonesian populations, we studied these populations, well-defined from their historical/linguistic contexts, together with new samples from the Ma'anyan and the sea nomad Bajo from Southeast Sulawesi. The sample size of ~2900 individuals represents the largest known Indonesian dataset investigated to date. Analysis was made using uniparental markers: the mitochondrial DNA and Y-chromosome.

Phylogeography analysis of maternal and paternal DNA lineages suggested that the Malagasy was derived from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands. Settlement may have been mediated by ancient sea nomad movements because the linguistically closest population, Ma'anyan, has only subtle genetic connections to the Malagasy, whereas genetic links with other sea nomads are more strongly supported. Our data hint at a more complex scenario for the Indonesian settlement of Madagascar than has previously been recognized.